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Update semibin2 to 2.1.0 #6503

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Update semibin2 to 2.1.0 #6503

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652f648
update semibin2 to 2.1.0
Oct 31, 2024
35dddea
remove deprecated fraggenscan option
Oct 31, 2024
724571d
update
Jan 6, 2025
1d5d850
tests failing
Jan 8, 2025
5d89a9a
text alignment files work
Jan 15, 2025
b587808
add test data
Jan 15, 2025
976856f
fix one test
Jan 15, 2025
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129 changes: 116 additions & 13 deletions tools/semibin/generate_sequence_features.xml
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Original file line number Diff line number Diff line change
Expand Up @@ -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@
Expand All @@ -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"/>

Expand All @@ -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"/>
Expand Down Expand Up @@ -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"/>
Expand Down Expand Up @@ -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"/>
Expand Down
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