diff --git a/tools/semibin/generate_sequence_features.xml b/tools/semibin/generate_sequence_features.xml
index c979190a93d..b8e17c29a3a 100644
--- a/tools/semibin/generate_sequence_features.xml
+++ b/tools/semibin/generate_sequence_features.xml
@@ -10,18 +10,29 @@
     <expand macro="version"/>
     <command detect_errors="exit_code"><![CDATA[
 #import re
-@BAM_FILES@
+#if $input_type_select.input_type == "bam":
+    @BAM_FILES@
+#else:
+    #for $e in $input_type_select.mode.abundance:
+        #set $identifier = re.sub('[^\s\w\-\\.]', '_', str($e.element_identifier))
+        ln -s '$e' '${identifier}.txt' &&
+    #end for
+#end if
 @FASTA_FILES@
 
 SemiBin2
-#if $mode.select == 'single' or $mode.select == 'co'
+#if $input_type_select.mode.select == 'single' or $input_type_select.mode.select == 'co'
     generate_sequence_features_single
 #else
     generate_sequence_features_multi
     --separator '$separator'
 #end if
     --input-fasta 'contigs.fasta'
+#if $input_type_select.input_type == "bam"
     --input-bam *.bam
+#else:
+    -a *.txt
+#end if
     --output 'output'
     --threads \${GALAXY_SLOTS:-1}
     @MIN_LEN@
@@ -30,7 +41,21 @@ SemiBin2
 #end if
     ]]></command>
     <inputs>
-        <expand macro="mode_fasta_bam"/>
+        <conditional name="input_type_select">
+            <param name="input_type" type="select" label="Use BAM or strobealign abundance information?">
+                <option value="bam">BAM file</option>
+                <option value="txt">strobealign-aemb files</option>
+            </param>
+            <when value="bam">
+                <expand macro="mode_fasta_bam"/>
+            </when>
+            <when value="txt">
+                <expand macro="mode_fasta_strobealign"/>
+            </when>
+        </conditional>
+
+
+
         <expand macro="min_len"/>
         <expand macro="ml-threshold"/>
 
@@ -46,10 +71,13 @@ SemiBin2
     </outputs>
     <tests>
         <test expect_num_outputs="4">
-            <conditional name="mode">
-                <param name="select" value="single"/>
-                <param name="input_fasta" ftype="fasta" value="input_single.fasta"/>
-                <param name="input_bam" ftype="bam" value="input_single.bam"/>
+            <conditional name="input_type_select">
+                <param name="input_type" value="bam"/>
+                <conditional name="mode">
+                    <param name="select" value="single"/>
+                    <param name="input_fasta" ftype="fasta" value="input_single.fasta"/>
+                    <param name="input_bam" ftype="bam" value="input_single.bam"/>
+                </conditional>
             </conditional>
             <conditional name="min_len">
                 <param name="method" value="automatic"/>
@@ -139,13 +167,17 @@ SemiBin2
             </output_collection>
         </test>
         <test expect_num_outputs="7">
-            <conditional name="mode">
-                <param name="select" value="multi"/>
-                <conditional name="multi_fasta">
-                    <param name="select" value="concatenated"/>
-                    <param name="input_fasta" ftype="fasta" value="input_multi.fasta.gz"/>
+            <conditional name="input_type_select">
+                <param name="input_type" value="bam"/>
+                <conditional name="mode">
+                    <param name="select" value="multi"/>
+                    <conditional name="multi_fasta">
+                        <param name="select" value="concatenated"/>
+                        <param name="input_fasta" ftype="fasta" value="input_multi.fasta.gz"/>
+                    </conditional>
+                    <param name="input_fasta" ftype="fasta" value="input_single.fasta"/>
+                    <param name="input_bam" ftype="bam" value="input_multi_sorted1.bam,input_multi_sorted2.bam,input_multi_sorted3.bam,input_multi_sorted4.bam,input_multi_sorted5.bam,input_multi_sorted6.bam,input_multi_sorted7.bam,input_multi_sorted8.bam,input_multi_sorted9.bam,input_multi_sorted10.bam"/>
                 </conditional>
-                <param name="input_bam" ftype="bam" value="input_multi_sorted1.bam,input_multi_sorted2.bam,input_multi_sorted3.bam,input_multi_sorted4.bam,input_multi_sorted5.bam,input_multi_sorted6.bam,input_multi_sorted7.bam,input_multi_sorted8.bam,input_multi_sorted9.bam,input_multi_sorted10.bam"/>
             </conditional>
             <conditional name="min_len">
                 <param name="method" value="automatic"/>
@@ -225,6 +257,77 @@ SemiBin2
                 </element>
             </output_collection>
         </test>
+
+        <test expect_num_outputs="5">
+            <conditional name="input_type_select">
+                <param name="input_type" value="txt"/>
+                <conditional name="mode">
+                    <param name="select" value="multi"/>
+                    <conditional name="multi_fasta">
+                        <param name="select" value="concatenated"/>
+                        <param name="input_fasta" ftype="fasta" value="input_multi.fasta.gz"/>
+                    </conditional>
+                    <param name="input_fasta" ftype="fasta" value="input_single.fasta"/>
+                    <param name="abundance" ftype="txt" value="strobealign_1.txt,strobealign_2.txt,strobealign_3.txt,strobealign_4.txt,strobealign_5.txt"/>
+                </conditional>
+            </conditional>
+            <conditional name="min_len">
+                <param name="method" value="automatic"/>
+            </conditional>
+            <param name="ml_threshold" value="4000"/>
+            <param name="extra_output" value="coverage,contigs"/>
+            <output_collection name="multi_data" count="10">
+                <element name="S1" ftype="csv">
+                    <assert_contents>
+                        <has_n_lines n="21"/>
+                        <has_text text="g1k_0"/>
+                    </assert_contents>
+                </element>
+            </output_collection>
+            <output_collection name="multi_data_split" count="10">
+                <element name="S1" ftype="csv">
+                    <assert_contents>
+                        <has_n_lines n="41"/>
+                        <has_text text="g1k_0_1"/>
+                    </assert_contents>
+                </element>
+            </output_collection>
+            <output_collection name="multi_cov_sample" count="10">
+                <element name="S1" ftype="csv">
+                    <assert_contents>
+                        <has_n_lines n="21"/>
+                        <has_text text="g1k_0"/>
+                    </assert_contents>
+                </element>
+            </output_collection>
+            <output_collection name="multi_split_cov_txt" count="10">
+                <element name="S1" ftype="csv">
+                    <assert_contents>
+                        <has_n_lines n="41"/>
+                        <has_text text="g1k_5_1"/>
+                    </assert_contents>
+                </element>
+                <element name="S9" ftype="csv">
+                    <assert_contents>
+                        <has_n_lines n="401"/>
+                        <has_text text="g1k_5_1"/>
+                    </assert_contents>
+                </element>
+            </output_collection>
+            <output_collection name="multi_contigs" count="10">
+                <element name="S1" ftype="fasta">
+                    <assert_contents>
+                        <has_text text=">g1k_0"/>
+                    </assert_contents>
+                </element>
+                <element name="S9" ftype="fasta">
+                    <assert_contents>
+                        <has_text text=">g1k_0"/>
+                    </assert_contents>
+                </element>
+            </output_collection>
+        </test>
+
         <test expect_num_outputs="2">
             <conditional name="mode">
                 <param name="select" value="multi"/>
diff --git a/tools/semibin/macros.xml b/tools/semibin/macros.xml
index 13e34758785..6327e7bd2f3 100644
--- a/tools/semibin/macros.xml
+++ b/tools/semibin/macros.xml
@@ -1,6 +1,6 @@
 <?xml version="1.0"?>
 <macros>
-    <token name="@TOOL_VERSION@">2.0.2</token>
+    <token name="@TOOL_VERSION@">2.1.0</token>
     <token name="@VERSION_SUFFIX@">0</token>
     <token name="@PROFILE@">21.01</token>
     <xml name="biotools">
@@ -48,6 +48,23 @@
             </when>
         </conditional>
     </xml>
+    <xml name="mode_fasta_strobealign">
+        <conditional name="mode">
+            <expand macro="mode_select"/>
+            <when value="single">
+                <expand macro="input-fasta-single"/>
+                <expand macro="input-txt"/>
+            </when>
+            <when value="co">
+                <expand macro="input-fasta-single"/>
+                <expand macro="input-txt"/>
+            </when>
+            <when value="multi">
+                <expand macro="input-fasta-multi"/>
+                <expand macro="input-txt"/>
+            </when>
+        </conditional>
+    </xml>
     <xml name="mode_select">
         <param name="select" type="select" label="Binning mode">
             <option value="single" selected="true">Single sample binning (each sample is assembled and binned independently)</option>
@@ -55,6 +72,12 @@
             <option value="multi">Multi-sample binning (multiple samples are assembled and binned individually, but information from multiple samples is used together)</option>
         </param>
     </xml>
+    <xml name="bam_or_strobealign">
+        <param name="align_select" type="select" label="Use bam or strobealign abundance files?" help="Strobealign abundance files can only be used when samples used in binning above or equal 5">
+            <option value="bam">BAM</option>
+            <option value="txt">Strobealign-aemb file(s)</option>
+        </param>
+    </xml>
     <xml name="input-fasta-single">
         <param argument="--input-fasta" type="data" format="fasta,fasta.gz" label="Contig sequences"/>
     </xml>
@@ -129,16 +152,26 @@ ln -s 'output/concatenated.fa' 'contigs.fasta' &&
     <xml name="input-bam-multi">
         <param argument="--input-bam" type="data" format="bam" multiple="true" label="Read mapping to the contigs" help="One file per sample, sorted BAM files"/>
     </xml>
+    <!-- Strobealign files -->
+    <xml name="input-txt">
+        <param argument="--abundance" type="data" format="txt" label="Read mapping to the contigs" multiple="true" help="Strobealign abundance files"/>
+    </xml>
     <token name="@BAM_FILES@"><![CDATA[
 #if $mode.select == 'single'
-#set $identifier = re.sub('[^\s\w\-\\.]', '_', str($input_bam.element_identifier))
-ln -s '$input_bam' '${identifier}.bam' &&
+#set $identifier = re.sub('[^\s\w\-\\.]', '_', str($mode.input_bam.element_identifier))
+ln -s '$mode.input_bam' '${identifier}.bam' &&
 #else
-    #for $e in $input_bam
+    #for $e in $mode.input_bam
         #set $identifier = re.sub('[^\s\w\-\\.]', '_', str($e.element_identifier))
 ln -s '$e' '${identifier}.bam' &&
     #end for
 #end if
+    ]]></token>
+    <token name="@STROBEALIGN_FILES@"><![CDATA[
+#for $e in $mode.align_select.abundance
+    #set $identifier = re.sub('[^\s\w\-\\.]', '_', str($e.element_identifier))
+    ln -s '$e' '${identifier}.txt' &&
+#end for
     ]]></token>
     <xml name="ref_select">
         <param name="select" type="select" label="Reference database">
@@ -225,7 +258,6 @@ ln -s '$e' '${identifier}.bam' &&
         <param argument="--orf-finder" type="select" label="ORF finder used to estimate the number of bins">
             <option value="fast-naive" selected="true">Fast-Naive</option>
             <option value="prodigal">Prodigal</option>
-            <option value="fraggenescan">Fraggenescan</option>
         </param>
     </xml>
     <xml name="max-node">
@@ -261,58 +293,153 @@ ln -s '$e' '${identifier}.bam' &&
     </xml>
     <xml name="data_output_single">
         <data name="single_data" format="csv" from_work_dir="output/data.csv" label="${tool.name} on ${on_string}: Training data">
-            <filter>mode["select"]=="single" or mode["select"]=="co"</filter>
+            <filter>input_type_select['mode']['select']=="single" or input_type_select['mode']['select']=="co"</filter>
         </data>
         <data name="single_data_split" format="csv" from_work_dir="output/data_split.csv" label="${tool.name} on ${on_string}: Split training data">
-            <filter>mode["select"]=="single" or mode["select"]=="co"</filter>
+            <filter>input_type_select['mode']['select']=="single" or input_type_select['mode']['select']=="co"</filter>
         </data>
     </xml>
-    <xml name="data_output_multi">
+    <xml name="data_output_multi"> 
         <collection name="multi_data" type="list" label="${tool.name} on ${on_string}: Training data per sample">
-            <filter>mode["select"]=="multi"</filter>
+            <filter>input_type_select['mode']['select']=="multi"</filter>
             <discover_datasets pattern="(?P&lt;designation&gt;.*)\/data.csv" format="csv" directory="output/samples/" recurse="true" match_relative_path="true"/>
         </collection>
         <collection name="multi_data_split" type="list" label="${tool.name} on ${on_string}: Split training data per sample">
-            <filter>mode["select"]=="multi"</filter>
+            <filter>input_type_select['mode']['select']=="multi"</filter>
             <discover_datasets pattern="(?P&lt;designation&gt;.*)\/data_split.csv" format="csv" directory="output/samples/" recurse="true" match_relative_path="true"/>
         </collection>
     </xml>
     <xml name="generate_sequence_features_extra_outputs">
         <data name="single_cov" format="csv" from_work_dir="output/*_data_cov.csv" label="${tool.name} on ${on_string}: Coverage">
-            <filter>mode["select"]=="single" and extra_output and "coverage" in extra_output</filter>
+            <filter>input_type_select['mode']['select']=="single" and extra_output and "coverage" in extra_output</filter>
+            <filter>input_type_select['input_type']=="bam"</filter>
         </data>
         <data name="single_split_cov" format="csv" from_work_dir="output/*_data_split_cov.csv" label="${tool.name} on ${on_string}: Coverage (split data)">
-            <filter>mode["select"]=="single" and extra_output and "coverage" in extra_output</filter>
+            <filter>input_type_select['mode']['select']=="single" and extra_output and "coverage" in extra_output</filter>
+            <filter>input_type_select['input_type']=="bam"</filter>
         </data>
         <collection name="co_cov" type="list" label="${tool.name} on ${on_string}: Coverage (co_cov)">
-            <filter>mode["select"]=="co" and extra_output and "coverage" in extra_output</filter>
+            <filter>input_type_select['mode']['select']=="co" and extra_output and "coverage" in extra_output</filter>
+            <filter>input_type_select['input_type']=="bam"</filter>
             <discover_datasets pattern=".*\.bam_(?P&lt;designation&gt;.*)_data_cov\.csv" format="csv" directory="output/" />
         </collection>
         <collection name="co_split_cov" type="list" label="${tool.name} on ${on_string}: Coverage (split data) per sample">
-            <filter>mode["select"]=="co" and extra_output and "coverage" in extra_output</filter>
+            <filter>input_type_select['mode']['select']=="co" and extra_output and "coverage" in extra_output</filter>
+            <filter>input_type_select['input_type']=="bam"</filter>
             <discover_datasets pattern=".*\.bam_(?P&lt;designation&gt;.*)_data_split_cov\.csv" format="csv" directory="output/" />
         </collection>
+        <data name="cov_txt" label="${tool.name} on ${on_string}: Coverage (split data) per sample (aemb)" from_work_dir="output/cov_split.csv" format="csv">
+            <filter>input_type_select['mode']['select']=="single" or input_type_select['mode']['select']=="co" and extra_output and "coverage" in extra_output</filter>
+            <filter>input_type_select['input_type']=="txt"</filter>
+        </data>
+        <data name="co_cov_txt" label="${tool.name} on ${on_string}: Coverage (aemb)" format="csv" from_work_dir="output/cov.csv">
+            <filter>input_type_select['mode']['select']=="single" or input_type_select['mode']['select']=="co" and extra_output and "coverage" in extra_output</filter>
+            <filter>input_type_select['input_type']=="txt"</filter>
+        </data>
+        <collection name="multi_split_cov_txt" type="list" label="${tool.name} on ${on_string}: Coverage (split data) per sample (multi_split_cov) (aemb)">
+            <filter>input_type_select['mode']['select']=="multi" and extra_output and "coverage" in extra_output</filter>
+            <filter>input_type_select['input_type']=="txt"</filter>
+            <discover_datasets pattern="(?P&lt;designation&gt;.*)\/data_split_cov.csv" format="csv" directory="output/samples/" recurse="true" match_relative_path="true"/>
+        </collection>
         <collection name="multi_cov" type="list" label="${tool.name} on ${on_string}: Coverage (multi_cov)">
-            <filter>mode["select"]=="multi" and extra_output and "coverage" in extra_output</filter>
-            <discover_datasets pattern=".*\.bam_(?P&lt;designation&gt;.*)_data_cov.csv" format="csv" directory="output/samples/" />
+            <filter>input_type_select['mode']['select']=="multi" and extra_output and "coverage" in extra_output</filter>
+            <filter>input_type_select['input_type']=="bam"</filter>
+            <discover_datasets pattern=".*\.bam_(?P&lt;designation&gt;.*)_data_cov.csv" format="csv" directory="output/samples/" recurse="true"/>
         </collection>
         <collection name="multi_cov_sample" type="list" label="${tool.name} on ${on_string}: Coverage per sample">
-            <filter>mode["select"]=="multi" and extra_output and "coverage" in extra_output</filter>
+            <filter>input_type_select['mode']['select']=="multi" and extra_output and "coverage" in extra_output</filter>
             <discover_datasets pattern="(?P&lt;designation&gt;.*)\/data_cov.csv" format="csv" directory="output/samples/" recurse="true" match_relative_path="true"/>
         </collection>
         <collection name="multi_split_cov" type="list" label="${tool.name} on ${on_string}: Coverage (split data) per sample (multi_split_cov)">
-            <filter>mode["select"]=="multi" and extra_output and "coverage" in extra_output</filter>
+            <filter>input_type_select['mode']['select']=="multi" and extra_output and "coverage" in extra_output</filter>
+            <filter>input_type_select['input_type']=="bam"</filter>
             <discover_datasets pattern=".*\.bam_(?P&lt;designation&gt;.*)_data_split_cov.csv" format="csv" directory="output/samples/" />
         </collection>
         <collection name="multi_split_cov_sample" type="list" label="${tool.name} on ${on_string}: Coverage (split data) per sample (multi_split_cov_sample)">
-            <filter>mode["select"]=="multi" and extra_output and "coverage" in extra_output</filter>
-            <discover_datasets pattern="(?P&lt;designation&gt;.*)\/data_split_cov.csv" format="csv" directory="output/samples/" recurse="true" match_relative_path="true"/>
+            <filter>input_type_select['mode']['select']=="multi" and extra_output and "coverage" in extra_output</filter>
+            <filter>input_type_select['input_type']=="bam"</filter>
+            <discover_datasets pattern="(?P&lt;designation&gt;.*)\/data_split_cov.csv" format="csv" directory="output/samples/" match_relative_path="true" recurse="true"/>
+        </collection>
+        <collection name="multi_contigs" type="list" label="${tool.name} on ${on_string}: Contigs">
+            <filter>input_type_select['mode']['select']=="multi" and extra_output and "contigs" in extra_output</filter>
+            <discover_datasets pattern="(?P&lt;designation&gt;.*).fa" format="fasta" directory="output/samples/" />
+        </collection>
+    </xml>
+    <xml name="generate_sequence_features_extra_outputs_main">
+    <!-- Single -->
+        <data name="single_cov" format="csv" from_work_dir="output/*_data_cov.csv" label="${tool.name} on ${on_string}: Coverage">
+            <filter>mode['select']=="single" and extra_output and "coverage" in extra_output</filter>
+        </data>
+        <data name="single_split_cov" format="csv" from_work_dir="output/*_data_split_cov.csv" label="${tool.name} on ${on_string}: Coverage (split data)">
+            <filter>mode['select']=="single" and extra_output and "coverage" in extra_output</filter>
+        </data>
+    <!-- Bam co aligned -->
+        <collection name="co_cov_bam" type="list" label="${tool.name} on ${on_string}: Coverage (co_cov)">
+            <filter>mode['select']=="co" and extra_output and "coverage" in extra_output</filter>
+            <filter>mode['align_select']</filter>
+            <filter>mode['align_select']['align_select']=="bam"</filter>
+            <discover_datasets pattern=".*\.bam_(?P&lt;designation&gt;.*)_data_cov\.csv" format="csv" directory="output/" />
+        </collection>
+        <collection name="co_split_cov_bam" type="list" label="${tool.name} on ${on_string}: Coverage (split data) per sample">
+            <filter>mode['select']=="co" and extra_output and "coverage" in extra_output</filter>
+            <filter>mode['align_select']</filter>
+            <filter>mode['align_select']['align_select']=="bam"</filter>
+            <discover_datasets pattern=".*\.bam_(?P&lt;designation&gt;.*)_data_split_cov\.csv" format="csv" directory="output/" />
+        </collection>
+
+    <!-- Bam Multi aligned -->
+        <collection name="multi_cov_bam" type="list" label="${tool.name} on ${on_string}: Coverage (multi_cov)">
+            <filter>mode['select']=="multi" and extra_output and "coverage" in extra_output</filter>
+            <filter>mode['align_select']</filter>
+            <filter>mode['align_select']['align_select']=="bam"</filter>
+            <discover_datasets pattern=".*\.bam_(?P&lt;designation&gt;.*)_data_cov.csv" format="csv" directory="output/samples/" />
+        </collection>
+        <collection name="multi_cov_sample_bam" type="list" label="${tool.name} on ${on_string}: Coverage per sample">
+            <filter>mode['select']=="multi" and extra_output and "coverage" in extra_output</filter>
+            <filter>mode['align_select']</filter>
+            <filter>mode['align_select']['align_select']=="bam"</filter>
+            <discover_datasets pattern="(?P&lt;designation&gt;.*)\/data_cov.csv" format="csv" directory="output/samples/" recurse="true" match_relative_path="true"/>
+        </collection>
+        <collection name="multi_split_cov_bam" type="list" label="${tool.name} on ${on_string}: Coverage (split data) per sample (multi_split_cov)">
+            <filter>mode['select']=="multi" and extra_output and "coverage" in extra_output</filter>
+            <filter>mode['align_select']</filter>
+            <filter>mode['align_select']['align_select']=="bam"</filter>
+            <discover_datasets pattern=".*\.bam_(?P&lt;designation&gt;.*)_data_split_cov.csv" format="csv" directory="output/samples/" />
+        </collection>
+        <collection name="multi_split_cov_sample_bam" type="list" label="${tool.name} on ${on_string}: Coverage (split data) per sample (multi_split_cov_sample)">
+            <filter>mode['select']=="multi" and extra_output and "coverage" in extra_output</filter>
+            <filter>mode['align_select']</filter>
+            <filter>mode['align_select']['align_select']=="bam"</filter>
+            <discover_datasets pattern=".*\.bam_(?P&lt;designation&gt;.*)_data_split_cov.csv" format="csv" directory="output/samples/" />
         </collection>
         <collection name="multi_contigs" type="list" label="${tool.name} on ${on_string}: Contigs">
-            <filter>mode["select"]=="multi" and extra_output and "contigs" in extra_output</filter>
+            <filter>mode['select']=="multi" and extra_output and "contigs" in extra_output</filter>
             <discover_datasets pattern="(?P&lt;designation&gt;.*).fa" format="fasta" directory="output/samples/" />
         </collection>
-        
+        <!-- Txt co aligned -->
+        <data name="co_split_cov_txt" label="${tool.name} on ${on_string}: Coverage (split data) per sample (aemb)" from_work_dir="output/cov_split.csv" format="csv">
+            <filter>mode['select']=="co" and extra_output and "coverage" in extra_output</filter>
+            <filter>mode['align_select']</filter>
+            <filter>mode['align_select']['align_select']=="txt"</filter>
+        </data>
+        <data name="co_cov_txt" label="${tool.name} on ${on_string}: Coverage (aemb)" format="csv" from_work_dir="output/cov.csv">
+            <filter>mode['select']=="co" and extra_output and "coverage" in extra_output</filter>
+            <filter>mode['align_select']</filter>
+            <filter>mode['align_select']['align_select']=="txt"</filter>
+        </data>
+        <!-- Txt multi aligned -->
+        <collection name="multi_cov_txt" type="list" label="${tool.name} on ${on_string}: Coverage per sample (aemb)">
+            <filter>mode['select']=="multi" and extra_output and "coverage" in extra_output</filter>
+            <filter>mode['align_select']</filter>
+            <filter>mode['align_select']['align_select'] =="txt"</filter>
+            <discover_datasets pattern="(?P&lt;designation&gt;.*)\/data_cov.csv" format="csv" directory="output/samples/" recurse="true" match_relative_path="true"/>
+        </collection>
+        <collection name="multi_split_cov_txt" type="list" label="${tool.name} on ${on_string}: Coverage (split data) per sample (multi_split_cov) (aemb)">
+            <filter>mode['select']=="multi" and extra_output and "coverage" in extra_output</filter>
+            <filter>mode['align_select']</filter>
+            <filter>mode['align_select']['align_select']=="txt"</filter>
+            <discover_datasets pattern="(?P&lt;designation&gt;.*)\/data_split_cov.csv" format="csv" directory="output/samples/" recurse="true" match_relative_path="true"/>
+        </collection>
     </xml>
     <xml name="train_output">
         <data name="model" format="h5" from_work_dir="output/model.h5" label="${tool.name} on ${on_string}: Semi-supervised deep learning model" />
@@ -321,31 +448,34 @@ ln -s '$e' '${identifier}.bam' &&
         <data name="cannot" format="txt" from_work_dir="output/cannot/cannot.txt" label="${tool.name} on ${on_string}: Cannot-link constraints" />
     </xml>
     <token name="@HELP_HEADER@"><![CDATA[
+
 What it does
 ============
 
 SemiBin is a Semi-supervised siamese neural network for metagenomic binning
-
-]]></token>
+    ]]></token>
     <token name="@HELP_INPUT_FASTA@"><![CDATA[
 - Contigs in fasta for 1 or several samples from single or co-assembly
-]]></token>
+    ]]></token>
     <token name="@HELP_INPUT_BAM@"><![CDATA[
 - BAM with reads mapping to the contigs
-]]></token>
+    ]]></token>
+    <token name="@HELP_INPUT_STROBEALIGN@"><![CDATA[
+- TXT alignment files that are the output of strobealign-aemb
+    ]]></token>
     <token name="@HELP_CANNOT@"><![CDATA[
 - Cannot-link constraints
-]]></token>
+    ]]></token>
     <token name="@HELP_DATA@"><![CDATA[
 - Training data and split training data for the model
-]]></token>
+    ]]></token>
     <token name="@HELP_MODEL@"><![CDATA[
 - Semi-supervised deep learning model
-]]></token>
+    ]]></token>
     <token name="@HELP_BINS@"><![CDATA[
 - Reconstructed bins after reclustering
 - Reconstructed bins before reclustering
-]]></token>
+    ]]></token>
     <xml name="citations">
         <citations>
             <citation type="doi">10.1038/s41467-022-29843-y</citation>
diff --git a/tools/semibin/semibin.xml b/tools/semibin/semibin.xml
index e3a3f181bbb..ddbbf271f9b 100644
--- a/tools/semibin/semibin.xml
+++ b/tools/semibin/semibin.xml
@@ -10,7 +10,15 @@
     <expand macro="version"/>
     <command detect_errors="exit_code"><![CDATA[
 #import re
-@BAM_FILES@
+#if $mode.select != "single":
+    #if $mode.align_select.align_select == "bam":
+        @BAM_FILES@
+    #else:
+        @STROBEALIGN_FILES@
+    #end if
+#else:
+    @BAM_FILES@
+#end if
 @FASTA_FILES@
 SemiBin2
 #if $mode.select == 'single' or $mode.select == 'co'
@@ -36,7 +44,15 @@ SemiBin2
     #end if
 #end if
     --input-fasta 'contigs.fasta'
-    --input-bam *.bam
+    #if $mode.select == "single":
+        --input-bam *.bam
+    #else:
+        #if $mode.align_select.align_select == "bam":
+            --input-bam *.bam
+        #else:
+            -a *.txt
+        #end if
+    #end if
     --output 'output'
     --cannot-name 'cannot'
     @MIN_LEN@
@@ -66,18 +82,34 @@ ls output
             <expand macro="mode_select"/>
             <when value="single">
                 <expand macro="input-fasta-single"/>
-                <expand macro="input-bam-single"/>
+                    <expand macro="input-bam-single"/>
                 <expand macro="ref-single"/>
                 <expand macro="environment"/>
             </when>
             <when value="co">
                 <expand macro="input-fasta-single"/>
-                <expand macro="input-bam-multi"/>
+                <conditional name="align_select">
+                    <expand macro="bam_or_strobealign"/>
+                    <when value="bam">
+                        <expand macro="input-bam-multi"/>
+                    </when>
+                    <when value="txt">
+                        <expand macro="input-txt"/>
+                    </when>
+                </conditional>
                 <expand macro="ref-single"/>
             </when>
             <when value="multi">
                 <expand macro="input-fasta-multi"/>
-                <expand macro="input-bam-multi"/>
+                <conditional name="align_select">
+                    <expand macro="bam_or_strobealign"/>
+                    <when value="bam">
+                        <expand macro="input-bam-multi"/>
+                    </when>
+                    <when value="txt">
+                        <expand macro="input-txt"/>
+                    </when>
+                </conditional>
                 <expand macro="ref-multi"/>
             </when>
         </conditional>
@@ -105,36 +137,36 @@ ls output
     </inputs>
     <outputs>
         <collection name="output_pre_recluster_bins" type="list" label="${tool.name} on ${on_string}: Reconstructed bins before reclustering">
-            <filter>mode["select"]!="multi" and extra_output and "pre_reclustering_bins" in extra_output</filter>
+            <filter>mode['select']!="multi" and extra_output and "pre_reclustering_bins" in extra_output</filter>
             <discover_datasets pattern="(?P&lt;designation&gt;.*).fa" format="fasta" directory="output/output_prerecluster_bins"/>
         </collection>
         <collection name="output_after_recluster_bins" type="list" label="${tool.name} on ${on_string}: Reconstructed bins after reclustering">
-            <filter>mode["select"]!="multi" and extra_output and "pre_reclustering_bins" in extra_output</filter>
+            <filter>mode['select']!="multi" and extra_output and "pre_reclustering_bins" in extra_output</filter>
             <discover_datasets pattern="(?P&lt;designation&gt;.*).fa" format="fasta" directory="output/output_recluster_bins"/>
         </collection>
         <collection name="output_bins" type="list" label="${tool.name} on ${on_string}: Reconstructed bins">
-            <filter>mode["select"]!="multi" and not "pre_reclustering_bins" in extra_output</filter>
+            <filter>mode['select']!="multi" and not "pre_reclustering_bins" in extra_output</filter>
             <discover_datasets pattern="(?P&lt;designation&gt;.*).fa" format="fasta" directory="output/output_bins"/>
         </collection>
         <collection name="multi_bins" type="list" label="${tool.name} on ${on_string}: Reconstructed bins before reclustering (multi_bins)">
-            <filter>mode["select"]=="multi"</filter>
+            <filter>mode['select']=="multi"</filter>
             <discover_datasets pattern="(?P&lt;designation&gt;.*).fa" format="fasta" directory="output/bins"/>
         </collection>
         <data name="single_data" format="csv" from_work_dir="output/data.csv" label="${tool.name} on ${on_string}: Training data">
-            <filter>(mode["select"]=="single" or mode["select"]=="co") and extra_output and "data" in extra_output</filter>
+            <filter>(mode['select']=="single" or mode['select']=="co") and extra_output and "data" in extra_output</filter>
         </data>
         <data name="single_data_split" format="csv" from_work_dir="output/data_split.csv" label="${tool.name} on ${on_string}: Split training data">
-            <filter>(mode["select"]=="single" or mode["select"]=="co") and extra_output and "data" in extra_output</filter>
+            <filter>(mode['select']=="single" or mode['select']=="co") and extra_output and "data" in extra_output</filter>
         </data>
         <collection name="multi_data" type="list" label="${tool.name} on ${on_string}: Training data per sample">
-            <filter>mode["select"]=="multi" and extra_output and "data" in extra_output</filter>
+            <filter>mode['select']=="multi" and extra_output and "data" in extra_output</filter>
             <discover_datasets pattern="(?P&lt;designation&gt;.*)\/data.csv" format="csv" directory="output/samples/" recurse="true" match_relative_path="true"/>
         </collection>
         <collection name="multi_data_split" type="list" label="${tool.name} on ${on_string}: Split training data per sample">
-            <filter>mode["select"]=="multi" and extra_output and "data" in extra_output</filter>
+            <filter>mode['select']=="multi" and extra_output and "data" in extra_output</filter>
             <discover_datasets pattern="(?P&lt;designation&gt;.*)\/data_split.csv" format="csv" directory="output/samples/" recurse="true" match_relative_path="true"/>
         </collection>
-        <expand macro="generate_sequence_features_extra_outputs"/>
+        <expand macro="generate_sequence_features_extra_outputs_main"/>
     </outputs>
     <tests>
         <test expect_num_outputs="5">
@@ -196,7 +228,10 @@ ls output
             <conditional name="mode">
                 <param name="select" value="co"/>
                 <param name="input_fasta" ftype="fasta" value="input_single.fasta"/>
-                <param name="input_bam" ftype="bam" value="input_coassembly_sorted1.bam,input_coassembly_sorted2.bam,input_coassembly_sorted3.bam,input_coassembly_sorted4.bam,input_coassembly_sorted5.bam"/>
+                <conditional name="align_select">
+                    <param name="align_select" value="bam"/>
+                    <param name="input_bam" ftype="bam" value="input_coassembly_sorted1.bam,input_coassembly_sorted2.bam,input_coassembly_sorted3.bam,input_coassembly_sorted4.bam,input_coassembly_sorted5.bam"/>
+                </conditional>
                 <conditional name="ref">
                     <param name="select" value="taxonomy"/>
                     <param name="taxonomy_annotation_table" value="taxonomy.tsv"/>
@@ -222,7 +257,7 @@ ls output
             </section>
             <param name="extra_output" value="coverage"/>
             <output_collection name="output_bins" count="0"/>
-            <output_collection name="co_cov" count="5">
+            <output_collection name="co_cov_bam" count="5">
                 <element name="0" ftype="csv">
                     <assert_contents>
                         <has_text text="g1k_0"/>
@@ -242,7 +277,7 @@ ls output
                     </assert_contents>
                 </element>
             </output_collection>
-            <output_collection name="co_split_cov" count="5">
+            <output_collection name="co_split_cov_bam" count="5">
                 <element name="0" ftype="csv">
                     <assert_contents>
                         <has_text text="g1k_0_1"/>
@@ -267,7 +302,10 @@ ls output
             <conditional name="mode">
                 <param name="select" value="co"/>
                 <param name="input_fasta" ftype="fasta" value="input_single.fasta"/>
-                <param name="input_bam" ftype="bam" value="input_coassembly_sorted1.bam,input_coassembly_sorted2.bam,input_coassembly_sorted3.bam,input_coassembly_sorted4.bam,input_coassembly_sorted5.bam"/>
+                <conditional name="align_select">
+                    <param name="align_select" value="bam"/>
+                    <param name="input_bam" ftype="bam" value="input_coassembly_sorted1.bam,input_coassembly_sorted2.bam,input_coassembly_sorted3.bam,input_coassembly_sorted4.bam,input_coassembly_sorted5.bam"/>
+                </conditional>
                 <conditional name="ref">
                     <param name="select" value="taxonomy"/>
                     <param name="taxonomy_annotation_table" value="taxonomy.tsv"/>
@@ -277,7 +315,7 @@ ls output
                 <param name="method" value="ratio"/>
                 <param name="ratio" value="0.05"/>
             </conditional>
-            <param name="orf_finder" value="fraggenescan"/>
+            <param name="orf_finder" value="fast-naive"/>
             <param name="random-seed" value="0"/>
             <section name="annot">
                 <param name="ml_threshold" value=""/>
@@ -293,7 +331,7 @@ ls output
             </section>
             <param name="extra_output" value="coverage"/>
             <output_collection name="output_bins" count="0"/>
-            <output_collection name="co_cov" count="5">
+            <output_collection name="co_cov_bam" count="5">
                 <element name="0" ftype="csv">
                     <assert_contents>
                         <has_text text="g1k_0"/>
@@ -313,7 +351,7 @@ ls output
                     </assert_contents>
                 </element>
             </output_collection>
-            <output_collection name="co_split_cov" count="5">
+            <output_collection name="co_split_cov_bam" count="5">
                 <element name="0" ftype="csv">
                     <assert_contents>
                         <has_text text="g1k_0_1"/>
@@ -348,7 +386,7 @@ ls output
                 <param name="method" value="ratio"/>
                 <param name="ratio" value="0.05"/>
             </conditional>
-            <param name="orf_finder" value="fraggenescan"/>
+            <param name="orf_finder" value="fast-naive"/>
             <param name="random-seed" value="0"/>
             <section name="annot">
                 <param name="ml_threshold" value=""/>
@@ -385,7 +423,7 @@ ls output
                 <param name="method" value="ratio"/>
                 <param name="ratio" value="0.05"/>
             </conditional>
-            <param name="orf_finder" value="fraggenescan"/>
+            <param name="orf_finder" value="fast-naive"/>
             <param name="random-seed" value="0"/>
             <section name="annot">
                 <param name="ml_threshold" value=""/>
@@ -432,7 +470,10 @@ ls output
                     <param name="select" value="concatenated"/>
                     <param name="input_fasta" ftype="fasta" value="input_multi.fasta.gz"/>
                 </conditional>
-                <param name="input_bam" ftype="bam" value="input_multi_sorted1.bam,input_multi_sorted2.bam,input_multi_sorted3.bam,input_multi_sorted4.bam,input_multi_sorted5.bam,input_multi_sorted6.bam,input_multi_sorted7.bam,input_multi_sorted8.bam,input_multi_sorted9.bam,input_multi_sorted10.bam"/>
+                <conditional name="align_select">
+                    <param name="align_select" value="bam"/>
+                    <param name="input_bam" ftype="bam" value="input_multi_sorted1.bam,input_multi_sorted2.bam,input_multi_sorted3.bam,input_multi_sorted4.bam,input_multi_sorted5.bam,input_multi_sorted6.bam,input_multi_sorted7.bam,input_multi_sorted8.bam,input_multi_sorted9.bam,input_multi_sorted10.bam"/>
+                </conditional>
                 <conditional name="ref">
                     <param name="select" value="taxonomy"/>
                     <param name="taxonomy_annotation_table" value="taxonomy.tsv,taxonomy_2.tsv,taxonomy_3.tsv,taxonomy_4.tsv,taxonomy_5.tsv,taxonomy_6.tsv,taxonomy_7.tsv,taxonomy_8.tsv,taxonomy_9.tsv,taxonomy_10.tsv"/>
@@ -442,7 +483,7 @@ ls output
                 <param name="method" value="ratio"/>
                 <param name="ratio" value="0.05"/>
             </conditional>
-            <param name="orf_finder" value="fraggenescan"/>
+            <param name="orf_finder" value="fast-naive"/>
             <param name="random_seed" value="0"/>
             <section name="annot">
                 <param name="ml_threshold" value=""/>
@@ -472,29 +513,29 @@ ls output
                     </assert_contents>
                 </element>
             </output_collection>
-            <output_collection name="multi_cov" count="10">
+            <output_collection name="multi_cov_bam" count="10">
                 <element name="8" ftype="csv">
                     <assert_contents>
                         <has_text text="S1:g1k_5,"/>
                     </assert_contents>
                 </element>
             </output_collection>
-            <output_collection name="multi_cov_sample" count="10">
+            <output_collection name="multi_cov_sample_bam" count="10">
                 <element name="S8" ftype="csv">
                     <assert_contents>
                         <has_text text="g1k_3"/>
                     </assert_contents>
                 </element>
             </output_collection>
-            <output_collection name="multi_split_cov" count="10">
+            <output_collection name="multi_split_cov_bam" count="10">
                 <element name="8" ftype="csv">
                     <assert_contents>
                         <has_text text="S1:g1k_5_1,0."/>
                     </assert_contents>
                 </element>
             </output_collection>
-            <output_collection name="multi_split_cov_sample" count="10">
-                <element name="S8" ftype="csv">
+            <output_collection name="multi_split_cov_sample_bam" count="10">
+                <element name="8" ftype="csv">
                     <assert_contents>
                         <has_text text="g1k_3_1"/>
                     </assert_contents>
@@ -508,6 +549,113 @@ ls output
                 </element>
             </output_collection>
         </test>
+        <test expect_num_outputs="6">
+            <conditional name="mode">
+                <param name="select" value="co"/>
+                <param name="input_fasta" ftype="fasta" value="input_multi.fasta.gz"/>
+                <conditional name="align_select">
+                    <param name="align_select" value="txt"/>
+                    <param name="abundance" ftype="txt" value="strobealign_1.txt,strobealign_2.txt,strobealign_3.txt,strobealign_4.txt,strobealign_5.txt"/>
+                </conditional>
+                <conditional name="ref">
+                    <param name="select" value="taxonomy"/>
+                    <param name="taxonomy_annotation_table" value="taxonomy.tsv"/>
+                </conditional>
+            </conditional>
+            <conditional name="min_len">
+                <param name="method" value="ratio"/>
+                <param name="ratio" value="0.05"/>
+            </conditional>
+            <param name="orf_finder" value="fast-naive"/>
+            <param name="random_seed" value="0"/>
+            <section name="annot">
+                <param name="ml_threshold" value=""/>
+            </section>
+            <section name="training">
+                <param name="epoches" value="20"/>
+                <param name="batch_size" value="2048"/>
+            </section>
+            <section name="bin">
+                <param name="max_node" value="0.15"/>
+                <param name="max_edges" value="20"/>
+                <param name="minfasta_kbs" value="20"/>
+            </section>
+            <param name="extra_output" value="data,coverage,contigs,pre_reclustering_bins"/>
+            <output_collection name="output_pre_recluster_bins" count="37"/>
+            <output_collection name="output_after_recluster_bins" count="51"/>
+        </test> 
+        <test expect_num_outputs="6">
+            <conditional name="mode">
+                <param name="select" value="multi"/>
+                <conditional name="multi_fasta">
+                    <param name="select" value="concatenated"/>
+                    <param name="input_fasta" ftype="fasta" value="input_multi.fasta.gz"/>
+                </conditional>
+                <conditional name="align_select">
+                    <param name="align_select" value="txt"/>
+                    <param name="abundance" ftype="txt" value="strobealign_1.txt,strobealign_2.txt,strobealign_3.txt,strobealign_4.txt,strobealign_5.txt"/>
+                </conditional>
+                <conditional name="ref">
+                    <param name="select" value="taxonomy"/>
+                    <param name="taxonomy_annotation_table" value="taxonomy.tsv,taxonomy_2.tsv,taxonomy_3.tsv,taxonomy_4.tsv,taxonomy_5.tsv,taxonomy_6.tsv,taxonomy_7.tsv,taxonomy_8.tsv,taxonomy_9.tsv,taxonomy_10.tsv"/>
+                </conditional>
+            </conditional>
+            <conditional name="min_len">
+                <param name="method" value="ratio"/>
+                <param name="ratio" value="0.05"/>
+            </conditional>
+            <param name="orf_finder" value="fast-naive"/>
+            <param name="random_seed" value="0"/>
+            <section name="annot">
+                <param name="ml_threshold" value=""/>
+            </section>
+            <section name="training">
+                <param name="epoches" value="20"/>
+                <param name="batch_size" value="2048"/>
+            </section>
+            <section name="bin">
+                <param name="max_node" value="0.15"/>
+                <param name="max_edges" value="30"/>
+                <param name="minfasta_kbs" value="30"/>
+            </section>
+            <param name="extra_output" value="data,coverage,contigs"/>
+            <output_collection name="multi_bins" count="10"/>
+            <output_collection name="multi_data" count="10">
+                <element name="S8" ftype="csv">
+                    <assert_contents>
+                        <has_text text="g1k_0,"/>
+                    </assert_contents>
+                </element>
+            </output_collection>
+            <output_collection name="multi_data_split" count="10">
+                <element name="S8" ftype="csv">
+                    <assert_contents>
+                        <has_text text="g1k_0_1,"/>
+                    </assert_contents>
+                </element>
+            </output_collection>
+            <output_collection name="multi_cov_txt" count="10">
+                <element name="S8" ftype="csv">
+                    <assert_contents>
+                        <has_text text="g1k_5,"/>
+                    </assert_contents>
+                </element>
+            </output_collection>
+            <output_collection name="multi_split_cov_txt" count="10">
+                <element name="S8" ftype="csv">
+                    <assert_contents>
+                        <has_text text="g1k_5_1,1."/>
+                    </assert_contents>
+                </element>
+            </output_collection>
+            <output_collection name="multi_contigs" count="10">
+                <element name="S8" ftype="fasta">
+                    <assert_contents>
+                        <has_text text=">g1k_0"/>
+                    </assert_contents>
+                </element>
+            </output_collection>
+        </test>        
     </tests>
     <help><![CDATA[
 @HELP_HEADER@
diff --git a/tools/semibin/test-data/strobealign_1.txt b/tools/semibin/test-data/strobealign_1.txt
new file mode 100644
index 00000000000..ce292fc3490
--- /dev/null
+++ b/tools/semibin/test-data/strobealign_1.txt
@@ -0,0 +1,400 @@
+S1:g1k_0_1	0.000000
+S1:g1k_0_2	0.000000
+S1:g1k_1_1	0.000000
+S1:g1k_1_2	0.000000
+S1:g1k_2_1	0.000000
+S1:g1k_2_2	0.000000
+S1:g1k_3_1	0.000000
+S1:g1k_3_2	0.000000
+S1:g1k_4_1	0.000000
+S1:g1k_4_2	0.000000
+S1:g1k_5_1	0.000000
+S1:g1k_5_2	0.000000
+S1:g1k_6_1	0.000000
+S1:g1k_6_2	0.000000
+S1:g1k_7_1	0.000000
+S1:g1k_7_2	0.000000
+S1:g1k_8_1	0.000000
+S1:g1k_8_2	0.000000
+S1:g1k_9_1	0.000000
+S1:g1k_9_2	0.000000
+S1:g2k_0_1	0.000000
+S1:g2k_0_2	0.000000
+S1:g2k_1_1	0.000000
+S1:g2k_1_2	0.000000
+S1:g2k_2_1	0.000000
+S1:g2k_2_2	0.000000
+S1:g2k_3_1	0.000000
+S1:g2k_3_2	0.000000
+S1:g2k_4_1	0.000000
+S1:g2k_4_2	0.000000
+S1:g2k_5_1	0.000000
+S1:g2k_5_2	0.000000
+S1:g2k_6_1	0.000000
+S1:g2k_6_2	0.000000
+S1:g2k_7_1	0.000000
+S1:g2k_7_2	0.000000
+S1:g2k_8_1	0.000000
+S1:g2k_8_2	0.000000
+S1:g2k_9_1	0.000000
+S1:g2k_9_2	0.000000
+S2:g1k_0_1	0.000000
+S2:g1k_0_2	0.000000
+S2:g1k_1_1	0.000000
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diff --git a/tools/semibin/test-data/strobealign_2.txt b/tools/semibin/test-data/strobealign_2.txt
new file mode 100644
index 00000000000..ce292fc3490
--- /dev/null
+++ b/tools/semibin/test-data/strobealign_2.txt
@@ -0,0 +1,400 @@
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diff --git a/tools/semibin/test-data/strobealign_3.txt b/tools/semibin/test-data/strobealign_3.txt
new file mode 100644
index 00000000000..ce292fc3490
--- /dev/null
+++ b/tools/semibin/test-data/strobealign_3.txt
@@ -0,0 +1,400 @@
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diff --git a/tools/semibin/test-data/strobealign_4.txt b/tools/semibin/test-data/strobealign_4.txt
new file mode 100644
index 00000000000..ce292fc3490
--- /dev/null
+++ b/tools/semibin/test-data/strobealign_4.txt
@@ -0,0 +1,400 @@
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diff --git a/tools/semibin/test-data/strobealign_5.txt b/tools/semibin/test-data/strobealign_5.txt
new file mode 100644
index 00000000000..ce292fc3490
--- /dev/null
+++ b/tools/semibin/test-data/strobealign_5.txt
@@ -0,0 +1,400 @@
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