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hicBuildMatrix SAM inputs changed from repeat to plain params #6670

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hicBuildMatrix SAM inputs changed from repeat to plain params #6670

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3686c38
hicBuildMatrix SAM inputs changed from repeat to plain params
pavanvidem Jan 10, 2025
674a639
add unspecified_build validator for samFile1 and samFile2
pavanvidem Jan 14, 2025
51f6ffc
add dbkey in the test
pavanvidem Jan 17, 2025
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32 changes: 8 additions & 24 deletions tools/hicexplorer/hicBuildMatrix.xml
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Original file line number Diff line number Diff line change
@@ -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>
Expand All @@ -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'

Expand Down Expand Up @@ -43,7 +40,7 @@
#if $dbKey:
--genomeAssembly '$dbKey'
#else
--genomeAssembly '$samFiles[0].samFile.metadata.dbkey'
--genomeAssembly '$samFile1.metadata.dbkey'
#end if

#if $region:
Expand Down Expand Up @@ -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" />
Expand Down Expand Up @@ -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" />
Expand All @@ -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>
Expand Down
33 changes: 9 additions & 24 deletions tools/hicexplorer/hicBuildMatrixMicroC.xml
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Original file line number Diff line number Diff line change
@@ -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>
Expand All @@ -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
Expand All @@ -32,7 +29,7 @@
#if $dbKey:
--genomeAssembly '$dbKey'
#else
--genomeAssembly '$samFiles[0].samFile.metadata.dbkey'
--genomeAssembly '$samFile1.metadata.dbkey'
#end if
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We should add a unspecified_build validator to both inputs.


#if $region:
Expand Down Expand Up @@ -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
Expand Down Expand Up @@ -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" />
Expand All @@ -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>
Expand All @@ -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.

Expand Down
22 changes: 6 additions & 16 deletions tools/hicexplorer/hicQuickQC.xml
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Original file line number Diff line number Diff line change
@@ -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>
Expand All @@ -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
Expand All @@ -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" />
Expand All @@ -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" />
Expand Down
5 changes: 5 additions & 0 deletions tools/hicexplorer/macros.xml
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Original file line number Diff line number Diff line change
Expand Up @@ -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."/>
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Probably you want unsorted.bam instead of qname_input_sorted.bam. unsorted.bam will allow any bam file.

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Please do not change this behavior at all. You would need to change the behavior of the according mappers, and test if the unsorted type hicBuildMatrix still works under all unsorted scenarios.

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OK. Was just wondering, because sam has to be assumed unsorted. But I guess this is treated in the command block (if so analogous changes could be done for the other bam types).

<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)." />
Expand Down
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