comparison bamFingerprint.xml @ 18:5ea8782d650c draft

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17:ef65d6b68ccc

<tool id="deeptools_bamFingerprint" name="bamFingerprint" version="1.0.2">
    <description>plots profiles of BAM files; useful for assesing ChIP signal strength</description>
    <expand macro="requirements" />
    <expand macro="stdio" />
    <macros>
        <import>deepTools_macros.xml</import>
    </macros>
    <command>
        @multiple_input_bams@

          #end if
      #else
        --plotFileFormat 'png'
      #end if

      #if $advancedOpt.showAdvancedOpt == "yes":
        
        #if str($advancedOpt.region.value) != '':
          --region '$advancedOpt.region'
        #end if

        --binSize '$advancedOpt.binSize'
        --numberOfSamples '$advancedOpt.numberOfSamples'

        $advancedOpt.doNotExtendPairedEnds
        $advancedOpt.ignoreDuplicates

    </command>

    <inputs>
        <expand macro="multiple_input_bams" />

        <param name="fragmentLength" type="integer" value="200" min="1"
           label="Length of the average fragment size"/>
        <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="10000" min="1" 
                   label="Bin size in bp"
                   help="Length in base pairs for a window used to sample the genome."/>
                
                <param name="numberOfSamples" type="integer" value="100000" min="1" 

.. image:: $PATH_TO_IMAGES/QC_fingerprint.png


**Output files**:

- Diagnostic plot
- Data matrix of raw counts

-----

.. class:: infomark

@REFERENCES@

    </help>
</tool>

18:5ea8782d650c

<tool id="deeptools_bamFingerprint" name="bamFingerprint" version="1.0.3">
    <description>plots profiles of BAM files; useful for assesing ChIP signal strength</description>
    <expand macro="requirements" />
    <expand macro="stdio" />
    <macros>
        <token name="@BINARY@">bamFingerprint</token>
        <import>deepTools_macros.xml</import>
    </macros>
    <command>
        @multiple_input_bams@

          #end if
      #else
        --plotFileFormat 'png'
      #end if

      #if str(region).strip() != '':
          --region 'region'
      #end if

      #if $advancedOpt.showAdvancedOpt == "yes":
        --binSize '$advancedOpt.binSize'
        --numberOfSamples '$advancedOpt.numberOfSamples'

        $advancedOpt.doNotExtendPairedEnds
        $advancedOpt.ignoreDuplicates

    </command>

    <inputs>
        <expand macro="multiple_input_bams" />


        <param name="fragmentLength" type="integer" value="200" min="1"
           label="Length of the average fragment size"/>

        <expand macro="region_limit_operation" />

        <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="binSize" type="integer" value="10000" min="1" 
                   label="Bin size in bp"
                   help="Length in base pairs for a window used to sample the genome."/>
                
                <param name="numberOfSamples" type="integer" value="100000" min="1" 

.. image:: $PATH_TO_IMAGES/QC_fingerprint.png


You can find more details in the `bamFingerprint wiki`_.

.. _bamFingerprint wiki: https://github.com/fidelram/deepTools/wiki/QC#wiki-bamFingerprint


**Output files**:

- Diagnostic plot
- Data matrix of raw counts

-----

@REFERENCES@

    </help>
</tool>