Mercurial > repos > bgruening > deeptools
diff correctGCBias.xml @ 13:b4c5dd45778a draft
Uploaded
| author | bgruening |
|---|---|
| date | Mon, 16 Dec 2013 04:36:19 -0500 |
| parents | 135f3bae5c56 |
| children | 5ea8782d650c |
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--- a/correctGCBias.xml Sat Dec 14 08:58:41 2013 -0500 +++ b/correctGCBias.xml Mon Dec 16 04:36:19 2013 -0500 @@ -5,91 +5,84 @@ <macros> <import>deepTools_macros.xml</import> </macros> - <command> - #import tempfile - #set $temp_dir = os.path.abspath(tempfile.mkdtemp()) + <command> + #import tempfile + #set $temp_dir = os.path.abspath(tempfile.mkdtemp()) - #set $temp_bam_handle = tempfile.NamedTemporaryFile( dir=$temp_dir ) - #set $temp_bam_path = $temp_bam_handle.name + '.bam' - #silent $temp_bam_handle.close() - #silent os.system("ln -s %s %s" % (str($bamInput), $temp_bam_path)) - #silent os.system("ln -s %s %s.bai" % (str($bamInput.metadata.bam_index), $temp_bam_path)) + #set $temp_bam_handle = tempfile.NamedTemporaryFile( dir=$temp_dir ) + #set $temp_bam_path = $temp_bam_handle.name + '.bam' + #silent $temp_bam_handle.close() + #silent os.system("ln -s %s %s" % (str($bamInput), $temp_bam_path)) + #silent os.system("ln -s %s %s.bai" % (str($bamInput.metadata.bam_index), $temp_bam_path)) - correctGCBias + correctGCBias - @THREADS@ + @THREADS@ - --bamfile '$temp_bam_path' - --GCbiasFrequenciesFile $GCbiasFrequenciesFile + --bamfile '$temp_bam_path' + --GCbiasFrequenciesFile $GCbiasFrequenciesFile - @reference_genome_source@ + @reference_genome_source@ - #if $effectiveGenomeSize.effectiveGenomeSize_opt == "specific": - --effectiveGenomeSize $effectiveGenomeSize.effectiveGenomeSize - #else: - --effectiveGenomeSize $effectiveGenomeSize.effectiveGenomeSize_opt - #end if - + #if $effectiveGenomeSize.effectiveGenomeSize_opt == "specific": + --effectiveGenomeSize $effectiveGenomeSize.effectiveGenomeSize + #else: + --effectiveGenomeSize $effectiveGenomeSize.effectiveGenomeSize_opt + #end if - #if $advancedOpt.showAdvancedOpt == "yes": - #if str($advancedOpt.region.value) != '': - --region '$advancedOpt.region' - #end if - - --binSize '$advancedOpt.binSize' - #end if - - #set newoutFileName="corrected."+str($outFileFormat) - - --correctedFile $newoutFileName; mv $newoutFileName $outFileName + #if $advancedOpt.showAdvancedOpt == "yes": + #if str($advancedOpt.region.value) != '': + --region '$advancedOpt.region' + #end if + --binSize '$advancedOpt.binSize' + #end if - </command> - - <inputs> + #set newoutFileName="corrected."+str($outFileFormat) + --correctedFile $newoutFileName; - <param name="GCbiasFrequenciesFile" type="data" format="tabular" label="Output of computeGCBias" /> - - <param name="bamInput" format="bam" type="data" label="BAM file" help="This should be same file that was used for computeGCbias. The BAM file must be sorted."/> - + mv $newoutFileName $outFileName + </command> + <inputs> + <param name="GCbiasFrequenciesFile" type="data" format="tabular" label="Output of computeGCBias" /> + <param name="bamInput" format="bam" type="data" label="BAM file" help="This should be same file that was used for computeGCbias. The BAM file must be sorted."/> <expand macro="reference_genome_source" /> <expand macro="effectiveGenomeSize" /> - <param name="outFileFormat" type="select" label="File format of the output"> - <option value="bam">bam</option> - <option value="bw">bigwig</option> - <option value="bg">bedgraph</option> - </param> - - <conditional name="advancedOpt"> - <param name="showAdvancedOpt" type="select" label="Show advanced options" > - <option value="no" selected="true">no</option> - <option value="yes">yes</option> - </param> - <when value="no" /> - <when value="yes"> - <param name="region" type="text" value="" - label="Region of the genome to limit the operation to" - help="This is useful when testing parameters to reduce the computing time. The format is chr:start:end, for example "chr10" or "chr10:456700:891000"" /> - - <param name="binSize" type="integer" value="50" min="1" - label="Bin size in bp" - help="Size of the bins in bp for the ouput of the bigwig/bedgraph file."/> - </when> - </conditional> - </inputs> - - <outputs> - <data format="bam" name="outFileName"> - <change_format> - <when input="outFileFormat" value="bw" format="bigwig" /> - <when input="outFileFormat" value="bam" format="bam" /> - <when input="outFileFormat" value="bg" format="bedgraph" /> - </change_format> - </data> - </outputs> - <help> + <param name="outFileFormat" type="select" label="File format of the output"> + <option value="bam">bam</option> + <option value="bw">bigwig</option> + <option value="bg">bedgraph</option> + </param> + + <conditional name="advancedOpt"> + <param name="showAdvancedOpt" type="select" label="Show advanced options" > + <option value="no" selected="true">no</option> + <option value="yes">yes</option> + </param> + <when value="no" /> + <when value="yes"> + <param name="region" type="text" value="" + label="Region of the genome to limit the operation to" + help="This is useful when testing parameters to reduce the computing time. The format is chr:start:end, for example "chr10" or "chr10:456700:891000"" /> + + <param name="binSize" type="integer" value="50" min="1" + label="Bin size in bp" + help="Size of the bins in bp for the ouput of the bigwig/bedgraph file."/> + </when> + </conditional> + </inputs> + <outputs> + <data format="bam" name="outFileName"> + <change_format> + <when input="outFileFormat" value="bw" format="bigwig" /> + <when input="outFileFormat" value="bam" format="bam" /> + <when input="outFileFormat" value="bg" format="bedgraph" /> + </change_format> + </data> + </outputs> + <help> **What it does**