hicBuildMatrix SAM inputs changed from repeat to plain params

galaxyproject · Jan 10, 2025 · 3686c38 · 3686c38
1 parent 637a6eb
commit 3686c38
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Showing 4 changed files with 28 additions and 64 deletions.
diff --git a/tools/hicexplorer/hicBuildMatrix.xml b/tools/hicexplorer/hicBuildMatrix.xml
@@ -1,4 +1,4 @@
-<tool id="hicexplorer_hicbuildmatrix" name="@BINARY@" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
+<tool id="hicexplorer_hicbuildmatrix" name="@BINARY@" version="@TOOL_VERSION@+galaxy2" profile="@PROFILE@">
     <description>create a contact matrix</description>
     <macros>
         <token name="@BINARY@">hicBuildMatrix</token>
@@ -10,10 +10,7 @@
         mkdir ./QCfolder &&
         mkdir '$qc.files_path' &&
         @BINARY@
-            --samFiles
-            #for $repeat in $samFiles:
-                '${repeat.samFile}'
-            #end for
+            --samFiles '$samFile1' '$samFile2'
 
             --restrictionCutFile '$restrictionCutFile'
 
@@ -43,7 +40,7 @@
             #if $dbKey:
                 --genomeAssembly '$dbKey'
             #else
-                --genomeAssembly '$samFiles[0].samFile.metadata.dbkey'
+                --genomeAssembly '$samFile1.metadata.dbkey'
             #end if
 
             #if $region:
@@ -79,12 +76,7 @@
 ]]>
     </command>
     <inputs>
-        <!-- can we use multiple=True here with min="2" and max="2" ? -->
-        <repeat max="2" min="2" name="samFiles" title="Sam/Bam files to process (forward/reverse)" help="Please use the special BAM datatype: qname_input_sorted.bam and use for 'bowtie2' the '--reorder' option to create a BAM file.">
-            <param name="samFile" type="data" format="sam,qname_input_sorted.bam">
-            </param>
-        </repeat>
-
+        <expand macro="samFiles" />
         <expand macro="restrictionCutFile" />
         <expand macro="restrictionSequence" />
         <expand macro="danglingSequence" />
@@ -142,12 +134,8 @@
     </outputs>
     <tests>
         <test expect_num_outputs="4">
-            <repeat name="samFiles">
-                <param name="samFile" value="small_test_R1_unsorted.sam" dbkey="hg38" />
-            </repeat>
-            <repeat name="samFiles">
-                <param name="samFile" value="small_test_R2_unsorted.sam" dbkey="hg38" />
-            </repeat>
+            <param name="samFile1" value="small_test_R1_unsorted.sam" dbkey="hg38" />
+            <param name="samFile2" value="small_test_R2_unsorted.sam" dbkey="hg38" />
             <param name="outputFormat" value="h5" />
             <repeat name="binSizes">
                 <param name="binSize" value="5000" />
@@ -165,12 +153,8 @@
             <output name="raw_qc" file="raw_qc_report" compare="diff" lines_diff="2" />
         </test>
         <test expect_num_outputs="4">
-            <repeat name="samFiles">
-                <param name="samFile" value="small_test_R1_unsorted.sam" dbkey="hg38" />
-            </repeat>
-            <repeat name="samFiles">
-                <param name="samFile" value="small_test_R2_unsorted.sam" dbkey="hg38" />
-            </repeat>
+            <param name="samFile1" value="small_test_R1_unsorted.sam" dbkey="hg38" />
+            <param name="samFile2" value="small_test_R2_unsorted.sam" dbkey="hg38" />
             <repeat name="binSizes">
                 <param name="binSize" value="5000" />
             </repeat>

diff --git a/tools/hicexplorer/hicBuildMatrixMicroC.xml b/tools/hicexplorer/hicBuildMatrixMicroC.xml
@@ -1,4 +1,4 @@
-<tool id="hicexplorer_hicbuildmatrixmicroc" name="@BINARY@" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
+<tool id="hicexplorer_hicbuildmatrixmicroc" name="@BINARY@" version="@TOOL_VERSION@+galaxy2" profile="@PROFILE@">
     <description>create a contact matrix</description>
     <macros>
         <token name="@BINARY@">hicBuildMatrixMicroC</token>
@@ -10,10 +10,7 @@
         mkdir ./QCfolder &&
         mkdir '$qc.files_path' &&
         @BINARY@
-            --samFiles
-            #for $repeat in $samFiles:
-                '${repeat.samFile}'
-            #end for
+            --samFiles '$samFile1' '$samFile2'
 
             #if $maxLibraryInsertSize:
                 --maxLibraryInsertSize $maxLibraryInsertSize
@@ -32,7 +29,7 @@
             #if $dbKey:
                 --genomeAssembly '$dbKey'
             #else
-                --genomeAssembly '$samFiles[0].samFile.metadata.dbkey'
+                --genomeAssembly '$samFile1.metadata.dbkey'
             #end if
 
             #if $region:
@@ -67,11 +64,7 @@
 ]]>
     </command>
     <inputs>
-        <!-- can we use multiple=True here with min="2" and max="2" ? -->
-        <repeat max="2" min="2" name="samFiles" title="Sam/Bam files to process (forward/reverse)" help="Please use the special BAM datatype: qname_input_sorted.bam and use for 'bowtie2' the '--reorder' option to create a BAM file.">
-            <param name="samFile" type="data" format="sam,qname_input_sorted.bam">
-            </param>
-        </repeat>
+        <expand macro="samFiles" />
 
         <param argument="--maxLibraryInsertSize" type="integer" optional="true" value="" label="Maximum library insert size defines different cut offs based on the maximum expected library size" help="*This is not the average fragment size* but the higher end of the fragment size distribution (obtained using for example Fragment Analyzer)
                         which usually is between 800 to 1500 bp. If this value if not known use the default of 1000. The insert value is used to decide if two mates
@@ -123,12 +116,8 @@
     </outputs>
     <tests>
         <test expect_num_outputs="4">
-            <repeat name="samFiles">
-                <param name="samFile" value="small_test_R1_unsorted.sam" dbkey="hg38" />
-            </repeat>
-            <repeat name="samFiles">
-                <param name="samFile" value="small_test_R2_unsorted.sam" dbkey="hg38" />
-            </repeat>
+            <param name="samFile1" value="small_test_R1_unsorted.sam" dbkey="hg38" />
+            <param name="samFile2" value="small_test_R2_unsorted.sam" dbkey="hg38" />
             <param name="outputFormat" value="h5" />
             <repeat name="binSizes">
                 <param name="binSize" value="5000" />
@@ -143,12 +132,8 @@
             <output name="raw_qc" file="raw_qc_report_micro-c" compare="diff" lines_diff="2" />
         </test>
         <test expect_num_outputs="4">
-            <repeat name="samFiles">
-                <param name="samFile" value="small_test_R1_unsorted.sam" dbkey="hg38" />
-            </repeat>
-            <repeat name="samFiles">
-                <param name="samFile" value="small_test_R2_unsorted.sam" dbkey="hg38" />
-            </repeat>
+            <param name="samFile1" value="small_test_R1_unsorted.sam" dbkey="hg38" />
+            <param name="samFile2" value="small_test_R2_unsorted.sam" dbkey="hg38" />
             <repeat name="binSizes">
                 <param name="binSize" value="5000" />
             </repeat>
@@ -169,7 +154,7 @@ Creation of the contact matrix
 ===============================
 
 
-**hicBuildMatrixMicroC** generates a contact matrix from Micro-C read pairs, using paired-end Hi-C reads mapped to a reference genome. This process requires two SAM or BAM files: one for the first mate and one for the second mate of the paired-end reads. These files must be unaligned by position (i.e., not sorted). Unlike traditional Hi-C data, where restriction enzyme cut sites determine resolution, Micro-C does not rely on such sites. Instead, the contact matrix is created using a fixed bin size (e.g., 10,000 bp). 
+**hicBuildMatrixMicroC** generates a contact matrix from Micro-C read pairs, using paired-end Hi-C reads mapped to a reference genome. This process requires two SAM or BAM files: one for the first mate and one for the second mate of the paired-end reads. These files must be unaligned by position (i.e., not sorted). Unlike traditional Hi-C data, where restriction enzyme cut sites determine resolution, Micro-C does not rely on such sites. Instead, the contact matrix is created using a fixed bin size (e.g., 10,000 bp).
 
 Additionally, **hicBuildMatrixMicroC** produces a quality control report to evaluate the quality of the Hi-C reads, aiding in determining the success of both the experimental protocol and sequencing process.
 

diff --git a/tools/hicexplorer/hicQuickQC.xml b/tools/hicexplorer/hicQuickQC.xml
@@ -1,4 +1,4 @@
-<tool id="hicexplorer_hicquickqc" name="@BINARY@" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
+<tool id="hicexplorer_hicquickqc" name="@BINARY@" version="@TOOL_VERSION@+galaxy2" profile="@PROFILE@">
     <description>get a first quality estimate of Hi-C data</description>
     <macros>
         <token name="@BINARY@">hicQuickQC</token>
@@ -11,13 +11,10 @@
         mkdir $qc.files_path &&
         @BINARY@
 
-            --samFiles
-            #for $repeat in $samFiles:
-                '${repeat.samFile}'
-            #end for
+            --samFiles '$samFile1' '$samFile2'
 
             --restrictionCutFile '$restrictionCutFile'
-            
+
             #if $restrictionSequence:
                 --restrictionSequence $restrictionSequence
             #end if
@@ -34,10 +31,7 @@
         && mv $qc.files_path/*.log raw_qc
     ]]>    </command>
     <inputs>
-        <!-- can we use multiple="true" with min="2" and max="2" ? -->
-        <repeat max="2" min="2" name="samFiles" title="Sam/Bam files to process (forward/reverse)" help="Please use the special BAM datatype: qname_input_sorted.bam and use for 'bowtie2' the '--reorder' option to create a BAM file.">
-            <param name="samFile" type="data" format="sam,qname_input_sorted.bam" />
-        </repeat>
+        <expand macro="samFiles" />
         <expand macro="restrictionCutFile" />
         <expand macro="restrictionSequence" />
         <expand macro="danglingSequence" />
@@ -49,12 +43,8 @@
     </outputs>
     <tests>
         <test expect_num_outputs="2">
-            <repeat name="samFiles">
-                <param name="samFile" value="small_test_R1_unsorted.sam" />
-            </repeat>
-            <repeat name="samFiles">
-                <param name="samFile" value="small_test_R2_unsorted.sam" />
-            </repeat>
+            <param name="samFile1" value="small_test_R1_unsorted.sam" />
+            <param name="samFile2" value="small_test_R2_unsorted.sam" />
             <param name="restrictionCutFile" value="DpnII_10k.bed" />
             <param name="restrictionSequence" value="GATC" />
             <param name="danglingSequence" value="GATC" />

diff --git a/tools/hicexplorer/macros.xml b/tools/hicexplorer/macros.xml
@@ -47,6 +47,11 @@
         <param argument='--dpi' type='integer' optional='true' min="10" max="1000" label='DPI for image' help='Change the default resolution of the plot.' />
     </xml>
 
+    <xml name="samFiles">
+        <param name="samFile1" type="data" format="sam,qname_input_sorted.bam" label="Forward SAM/BAM file to process" help="Please use the special BAM datatype: qname_input_sorted.bam and use for 'bowtie2' the '--reorder' option to create a BAM file."/>
+        <param name="samFile2" type="data" format="sam,qname_input_sorted.bam" label="Reverse SAM/BAM file to process" help="Please use the special BAM datatype: qname_input_sorted.bam and use for 'bowtie2' the '--reorder' option to create a BAM file."/>
+    </xml>
+
     <xml name="restrictionCutFile">
         <param argument="--restrictionCutFile" type="data" format="bed" optional="false" label="BED file with all restriction cut places" help="Should contaion only mappable restriction sites. If given, the bins are set to match the restriction fragments
                 (i.e. the region between one restriction site and the next)." />