comparison correctGCBias.xml @ 0:09b65c12a75a draft

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0:09b65c12a75a

<tool id="correctGCBias" name="correctGCBias" version="1.0">
  <description>
  </description>
  <requirements>
    <requirement type="package" version="1.5.1_98e5d8a61431ea8605c0643d991a1a5d8999b4dc">deepTools</requirement>
    <requirement type="package" version="0.1">ucsc_tools</requirement>
  </requirements>
  <command>
  correctGCBias
  --bamfile '$bamInput'
  --species '$species'
  --GCbiasFrequenciesFile $GCbiasFrequenciesFile
  
  #if $source.ref_source=="history":
    --genome $source.input1
  #else:
    --genome "${source.input1_2bit.fields.path}"
  #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

  </command>

  <inputs>
  
  <param name="GCbiasFrequenciesFile" type="data" format="tabular" label="Output of computeGCBias" />
  
  <param name="bamInput" format="bam" type="data" label="Input BAM file" help="The BAM file must be sorted and indexed."/>
  
  <param name="species" type="text" value="" label="Species name abbreviation" />
  
  <conditional name="source">
    <param name="ref_source" type="select" label="Reference genome">
        <option value="cached">locally cached</option>
        <option value="history">in your history</option>
    </param>
    <when value="cached">
        <param name="input1_2bit" type="select" label="Using reference genome" help="If your genome of interest is not listed, contact your Galaxy team">
            <options from_data_table="deepTools_seqs" />
        </param>
    </when>
    <when value="history">
        <param name="input1" type="data" format="twobit" label="Select a reference dataset in 2bit format" />
    </when>
  </conditional>
     
  <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 &quot;chr10&quot; or &quot;chr10:456700:891000&quot;" />
           
           <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**

Computes the GC bias ussing Benjamini's method [citation]. The resulting GC
bias can later be used to plot the bias or to correct the bias.

-----

.. class:: infomark

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`_.

This tool is developed by the `Bioinformatics and Deep-Sequencing Unit`_ at the `Max Planck Institute for Immunobiology and Epigenetics`_.


.. _Bioinformatics and Deep-Sequencing Unit: http://www3.ie-freiburg.mpg.de/facilities/research-facilities/bioinformatics-and-deep-sequencing-unit/
.. _Max Planck Institute for Immunobiology and Epigenetics: http://www3.ie-freiburg.mpg.de
.. _Fidel Ramirez: [e-mail]

  </help>
  
</tool>