Mercurial > repos > bgruening > hicexplorer_hicbuildmatrix
diff hicBuildMatrix.xml @ 2:eb0d14cdf8b8 draft
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
| author | bgruening |
|---|---|
| date | Thu, 02 Nov 2017 11:11:01 -0400 |
| parents | 9767c021cd58 |
| children | 2a13bfe5bff2 |
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--- a/hicBuildMatrix.xml Mon Apr 03 07:07:13 2017 -0400 +++ b/hicBuildMatrix.xml Thu Nov 02 11:11:01 2017 -0400 @@ -5,15 +5,12 @@ <import>macros.xml</import> </macros> <expand macro="requirements" > - <requirement type="package" version="1.3.1">samtools</requirement> + <requirement type="package" version="1.6">samtools</requirement> </expand> - <command> -<![CDATA[ + <command detect_errors="exit_code"><![CDATA[ mkdir ./QCfolder && - mkdir $qc.files_path - && - + mkdir $qc.files_path && hicBuildMatrix --samFiles @@ -21,21 +18,16 @@ '${repeat.samFile}' #end for - #if $binSize: - --binSize $binSize - #end if - - #if $restrictionCutFile: - --restrictionCutFile '$restrictionCutFile' + #if $restrictionCutFileBinSize_conditional.restrictionCutFileBinSize_selector == "optionRestrictionCutFile": + --restrictionCutFile '$restrictionCutFileBinSize_conditional.restrictionCutFile' + --minDistance $restrictionCutFileBinSize_conditional.minDistance + --maxDistance $restrictionCutFileBinSize_conditional.maxDistance #end if - #if $minDistance: - --minDistance $minDistance + #if $restrictionCutFileBinSize_conditional.restrictionCutFileBinSize_selector == "optionBinSize": + --binSize $restrictionCutFileBinSize_conditional.binSize #end if - #if $maxDistance: - --maxDistance $maxDistance - #end if #if $restrictionSequence: --restrictionSequence '$restrictionSequence' @@ -48,49 +40,56 @@ --outFileName ./matrix.h5 --outBam ./unsorted.bam - #if $restrictionCutFile: - --restrictionCutFile '$restrictionCutFile' - #end if - - $removeSelfCircles + $keepSelfCircles #if $minMappingQuality and $minMappingQuality is not None: --minMappingQuality $minMappingQuality #end if + #if $danglingSequence: + --danglingSequence '$danglingSequence' + #end if + + --threads @THREADS@ + --QCfolder ./QCfolder && mv ./QCfolder/* $qc.files_path/ && mv $qc.files_path/hicQC.html $qc - && - samtools sort ./unsorted.bam -o sorted.bam - + && samtools sort ./unsorted.bam -o sorted.bam + ]]> </command> <inputs> <repeat max="2" min="2" name="samFiles" title="Sam/Bam files to process"> <param name="samFile" type="data" format="sam,bam"/> </repeat> - - <param argument="--restrictionCutFile" type="data" format="bed" optional="True" - help="BED file with all restriction cut places. Should contain 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)"/> + <conditional name="restrictionCutFileBinSize_conditional"> + <param name="restrictionCutFileBinSize_selector" type="select" label="Choose to use a restriction cut file or a bin size"> + <option value="optionRestrictionCutFile">Restriction cut file</option> + <option value="optionBinSize" selected="True">Bin size</option> + </param> + <when value="optionRestrictionCutFile"> + <param argument="--restrictionCutFile" type="data" format="bed" optional="True" + help="BED file with all restriction cut places. Should contain 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)"/> + <param name="restrictionCutFile" type="data" format="bed" optional="true" 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)." argument="--restrictionCutFile"/> + <param name="minDistance" type="integer" value="" optional="true" label="Minimum distance between restriction sites" + help="Restriction sites that are closer that this distance are merged into one. + This option only applies if --restrictionCutFile is given." argument="--minDistance"/> - <param name="binSize" type="integer" value="" optional="true" label="Bin size in bp" - help="If used, the restriction cut places (if given) are used to only consider reads that are in the vicinity of the resctriction sites. - Otherwise all reads in the interval are considered. " argument="--binSize"/> - - <param name="restrictionCutFile" type="data" format="bed" optional="true" 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)." argument="--restrictionCutFile"/> - - <param name="minDistance" type="integer" value="" optional="true" label="Minimum distance between restriction sites" - help="Restriction sites that are closer that this distance are merged into one. - This option only applies if --restrictionCutFile is given." argument="--minDistance"/> - - <param name="maxDistance" type="integer" value="" optional="true" label="Maximum distance in bp from restriction site to read, to consider a read a valid one" - help="This option only applies if --restrictionCutFile is given." argument="--maxDistance"/> + <param name="maxDistance" type="integer" value="" optional="true" label="Maximum distance in bp from restriction site to read, to consider a read a valid one" + help="This option only applies if --restrictionCutFile is given." argument="--maxDistance"/> + </when> + <when value="optionBinSize"> + <param name="binSize" type="integer" value="" optional="true" label="Bin size in bp" + help="If used, the restriction cut places (if given) are used to only consider reads that are in the vicinity of the resctriction sites. + Otherwise all reads in the interval are considered. " argument="--binSize"/> + </when> + </conditional> <param name="restrictionSequence" type="text" optional="true" label="Sequence of the restriction site" help="This is used to discard reads that end/start with such sequence and that are considered un-ligated fragments or @@ -98,11 +97,19 @@ <expand macro="region" /> - <param argument="--removeSelfCircles" type="boolean" truevalue="--removeSelfCircles" falsevalue="" - label="Save the matrix of values underlying the heatmap" help="If set, outward facing reads, at a distance of less thatn 25kbs are removed." /> + <param argument="--keepSelfCircles" type="boolean" truevalue="--keepSelfCircles" falsevalue="" + label="Keep self circles" help="If set, outward facing reads without any restriction fragment (self circles) are kept. ' + + 'They will be counted and shown in the QC plots." /> <expand macro="minMappingQuality" /> + <param name="danglingSequence" type="text" optional="true" label="The dangling sequence" + help="Dangling end sequence left by the restriction enzyme. For DpnII for example, + the dangling end is the same restriction sequence. This is used + to discard reads that end/start with such sequence + and that are considered un-ligated fragments or + 'dangling-ends'. If not given, such statistics will + not be available." argument="--danglingSequence"/> </inputs> <outputs> <data name="outBam" from_work_dir="sorted.bam" format="bam" label="${tool.name} BAM file on ${on_string}"/> @@ -117,9 +124,12 @@ <repeat name="samFiles"> <param name="samFile" value="small_test_R2_unsorted.bam" ftype="sam"/> </repeat> - <param name="binSize" value="5000"/> - <output name="outBam" file="hicBuildMatrix_result1.bam" ftype="bam"/> - <output name="outFileName" file="hicBuildMatrix_result1.h5" ftype="h5" compare="sim_size"/> + <conditional name="restrictionCutFileBinSize_conditional"> + <param name="restrictionCutFileBinSize_selector" value="optionBinSize"/> + <param name="binSize" value="5000"/> + </conditional> + <output name="outBam" file="small_test_matrix_result_sorted.bam" ftype="bam"/> + <output name="outFileName" file="small_test_matrix.h5" ftype="h5" compare="sim_size" delta="30000"/> </test> </tests> <help><![CDATA[