view correctGCBias.xml @ 1:21d563d5f2b2 draft

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−<tool id="correctGCBias" name="correctGCBias" version="1.0.1">
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−  <description>
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−  </description>
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−  <requirements>
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−    <requirement type="package" version="1.5.1_59e067cce039cb93add04823c9f51cab202f8c2b">deepTools</requirement>
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−    <requirement type="package" version="0.1">ucsc_tools</requirement>
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−  </requirements>
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−  <command>
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−    #import tempfile
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−    #set $temp_dir = os.path.abspath(tempfile.mkdtemp())
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−
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−    #set $temp_bam_handle = tempfile.NamedTemporaryFile( dir=$temp_dir )
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−    #set $temp_bam_path = $temp_bam_handle.name + '.bam'
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−    #silent $temp_bam_handle.close()
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−    #silent os.system("ln -s %s %s" % (str($bamInput), $temp_bam_path))
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−    #silent os.system("ln -s %s %s.bai" % (str($bamInput.metadata.bam_index), $temp_bam_path))
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−
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−
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−  correctGCBias
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−  --bamfile '$temp_bam_path'
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−  --species '$species'
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−  --GCbiasFrequenciesFile $GCbiasFrequenciesFile
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−  
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−  #if $source.ref_source=="history":
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−    --genome $source.input1
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−  #else:
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−    --genome "${source.input1_2bit.fields.path}"
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−  #end if
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−  
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−  #if $advancedOpt.showAdvancedOpt == "yes":
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−    #if str($advancedOpt.region.value) != '':
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−      --region '$advancedOpt.region'
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−    #end if
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−    
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−    --binSize '$advancedOpt.binSize'  
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−  #end if
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−  
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−  #set newoutFileName="corrected."+str($outFileFormat)
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−  
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−  --correctedFile $newoutFileName; mv $newoutFileName $outFileName
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−
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−  </command>
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−
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−  <inputs>
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−
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−  <param name="GCbiasFrequenciesFile" type="data" format="tabular" label="Output of computeGCBias" />
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−
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−  <param name="bamInput" format="bam" type="data" label="Input BAM file" help="The BAM file must be sorted and indexed."/>
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−
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−  <param name="species" type="select" label="Species name abbreviation">
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−    <option value="hg19">hg19</option>
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−    <option value="ce10">ce10</option>
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−    <option value="dm3">dm3</option>
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−    <option value="mm9">mm9</option>
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−  </param>
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−
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−  <conditional name="source">
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−    <param name="ref_source" type="select" label="Reference genome">
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−        <option value="cached">locally cached</option>
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−        <option value="history">in your history</option>
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−    </param>
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−    <when value="cached">
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−        <param name="input1_2bit" type="select" label="Using reference genome" help="If your genome of interest is not listed, contact your Galaxy team">
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−            <options from_data_table="deepTools_seqs" />
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−        </param>
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−    </when>
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−    <when value="history">
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−        <param name="input1" type="data" format="twobit" label="Select a reference dataset in 2bit format" />
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−    </when>
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−  </conditional>
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−     
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−  <param name="outFileFormat" type="select" label="File format of the output">
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−    <option value="bam">bam</option>
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−    <option value="bw">bigwig</option>
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−    <option value="bg">bedgraph</option>
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−  </param>
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−  
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−  <conditional name="advancedOpt">
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−    <param name="showAdvancedOpt" type="select" label="Show advanced options" >
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−        <option value="no" selected="true">no</option>
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−        <option value="yes">yes</option>
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−      </param>
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−      <when value="no" />
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−      <when value="yes">
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−          <param name="region" type="text" value=""
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−            label="Region of the genome to limit the operation to"
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−            help="This is useful when testing parameters to reduce the computing time. The format is chr:start:end, for example &quot;chr10&quot; or &quot;chr10:456700:891000&quot;" />
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−           
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−           <param name="binSize" type="integer" value="50" min="1" 
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−             label="Bin size in bp"
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−             help="Size of the bins in bp for the ouput of the bigwig/bedgraph file."/>
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−      </when>
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−  </conditional>
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−  </inputs>
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−  
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−  <outputs>
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−    <data format="bam" name="outFileName">
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−    <change_format>
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−        <when input="outFileFormat" value="bw" format="bigwig" />
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−        <when input="outFileFormat" value="bam" format="bam" />
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−        <when input="outFileFormat" value="bg" format="bedgraph" />
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−    </change_format>
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−    </data>
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−  </outputs>
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−  <help>
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−
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−**What it does**
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−
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−Computes the GC bias ussing Benjamini's method [citation]. The resulting GC
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−bias can later be used to plot the bias or to correct the bias.
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−
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−-----
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−
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−.. class:: infomark
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−
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−Please acknowledge that this tool **is still in development** and we will be very happy to receive feedback from the users. If you run into any trouble please sent an email to `Fidel Ramirez`_.
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−
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−This tool is developed by the `Bioinformatics and Deep-Sequencing Unit`_ at the `Max Planck Institute for Immunobiology and Epigenetics`_.
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−
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−
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−.. _Bioinformatics and Deep-Sequencing Unit: http://www3.ie-freiburg.mpg.de/facilities/research-facilities/bioinformatics-and-deep-sequencing-unit/
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−.. _Max Planck Institute for Immunobiology and Epigenetics: http://www3.ie-freiburg.mpg.de
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−.. _Fidel Ramirez: [e-mail]
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−
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−  </help>
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−  
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−</tool>