comparison computeGCBias.xml @ 18:5ea8782d650c draft

Uploaded

17:ef65d6b68ccc

<tool id="deeptools_computeGCBias" name="computeGCBias" version="1.0.2">
    <description>to see whether your samples should be normalized for GC bias</description>
    <expand macro="requirements" />
    <expand macro="stdio" />
    <macros>
        <import>deepTools_macros.xml</import>
    </macros>
    <command>
        ln -s $bamInput local_bamInput.bam;
        ln -s $bamInput.metadata.bam_index local_bamInput.bam.bai;

                --effectiveGenomeSize $effectiveGenomeSize.effectiveGenomeSize
            #else:
                --effectiveGenomeSize $effectiveGenomeSize.effectiveGenomeSize_opt
            #end if

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

                --sampleSize '$advancedOpt.sampleSize'
                --regionSize '$advancedOpt.regionSize'

                #if $advancedOpt.filterOut:

        <expand macro="effectiveGenomeSize" />

        <param name="fragmentLength" type="integer" value="300" min="1"
            label="Fragment length used for the sequencing"
            help ="If paired-end reads are used, the fragment length is computed from the BAM file."/>
        <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="sampleSize" type="integer" value="50000000" min="1"
                    label="Number of sampling points to be considered" />

                <param name="regionSize" type="integer" value="300" min="1"
                    label="Region size"

usually shows a significant bias towards reads with high GC content (>50%)

.. image:: $PATH_TO_IMAGES/QC_GCplots_input.png


**Output files**:

- Diagnostic plot

  - box plot of absolute read numbers per genomic GC bin

  - to be used for GC correction with correctGCbias


-----

.. class:: infomark

@REFERENCES@

    </help>
</tool>

18:5ea8782d650c

<tool id="deeptools_computeGCBias" name="computeGCBias" version="1.0.3">
    <description>to see whether your samples should be normalized for GC bias</description>
    <expand macro="requirements" />
    <expand macro="stdio" />
    <macros>
        <token name="@BINARY@">computeGCBias</token>
        <import>deepTools_macros.xml</import>
    </macros>
    <command>
        ln -s $bamInput local_bamInput.bam;
        ln -s $bamInput.metadata.bam_index local_bamInput.bam.bai;

                --effectiveGenomeSize $effectiveGenomeSize.effectiveGenomeSize
            #else:
                --effectiveGenomeSize $effectiveGenomeSize.effectiveGenomeSize_opt
            #end if

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

            #if $advancedOpt.showAdvancedOpt == "yes":

                --sampleSize '$advancedOpt.sampleSize'
                --regionSize '$advancedOpt.regionSize'

                #if $advancedOpt.filterOut:

        <expand macro="effectiveGenomeSize" />

        <param name="fragmentLength" type="integer" value="300" min="1"
            label="Fragment length used for the sequencing"
            help ="If paired-end reads are used, the fragment length is computed from the BAM file."/>

        <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="sampleSize" type="integer" value="50000000" min="1"
                    label="Number of sampling points to be considered" />

                <param name="regionSize" type="integer" value="300" min="1"
                    label="Region size"

usually shows a significant bias towards reads with high GC content (>50%)

.. image:: $PATH_TO_IMAGES/QC_GCplots_input.png


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

.. _computeGCBias wiki: https://github.com/fidelram/deepTools/wiki/QC#wiki-computeGCbias


**Output files**:

- Diagnostic plot

  - box plot of absolute read numbers per genomic GC bin

  - to be used for GC correction with correctGCbias


-----

@REFERENCES@

    </help>
</tool>