comparison computeGCBias.xml @ 65:9bee2c86eeb1 draft

planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit ab1ab06323702186cf0c883d5774720cbb822cb5-dirty

64:627004611e98

<tool id="deeptools_computeGCBias" name="computeGCBias" version="@WRAPPER_VERSION@.0">
    <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>
<![CDATA[
        ln -s $bamInput local_bamInput.bam;
        ln -s $bamInput.metadata.bam_index local_bamInput.bam.bai;

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

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

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

                #if $advancedOpt.filterOut:
                    --filterOut $advancedOpt.filterOut

            <when value="yes">
                <param name="sampleSize" type="integer" value="50000000" min="1"
                    label="Number of sampling points to be considered" help="(--sampleSize)" />
                <param name="regionSize" type="integer" value="300" min="1"
                    label="Region size"
                    help ="To plot the reads per GC over a region, the size of the region is required (see below for more details of the mthod). By default, the bin size is set to 300 bp, which is close to the standard fragment size many sequencing applications. However, if the depth of sequencing is low, a larger bin size will be required, otherwise many bins will not overlap with any read. (--regionSize)"/>
                <param name="filterOut" type="data" format="bed" optional="true"
                    label="BED file containing genomic regions to be excluded from the estimation of the correction"
                    help="Such regions  usually contain repetitive regions and peaks that if included will bias the correction. It is recommended to filter out known repetitive regions if multi-reads (reads that map to more than one genomic position) were excluded. In the case of ChIP-seq data, it is recommended to first use a peak caller to identify and filter out the identified peaks. (--filterOut)" />
                <param name="extraSampling" type="data" format="bed" optional="true"
                    label="BED file containing genomic regions for which extra sampling is required because they are underrepresented in the genome"
                    help="(--extraSampling)" />
            </when>
        </conditional>

65:9bee2c86eeb1

<tool id="deeptools_computeGCBias" name="computeGCBias" version="@WRAPPER_VERSION@.0">
    <description>to see whether your samples should be normalized for GC bias</description>
    <macros>
        <token name="@BINARY@">computeGCBias</token>
        <import>deepTools_macros.xml</import>
    </macros>
    <expand macro="requirements" />
    <command>
<![CDATA[
        ln -s $bamInput local_bamInput.bam;
        ln -s $bamInput.metadata.bam_index local_bamInput.bam.bai;

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

            #if $advancedOpt.showAdvancedOpt == "yes":
                --sampleSize '$advancedOpt.sampleSize'
                --regionSize '$advancedOpt.regionSize'

                #if $advancedOpt.filterOut:
                    --filterOut $advancedOpt.filterOut

            <when value="yes">
                <param name="sampleSize" type="integer" value="50000000" min="1"
                    label="Number of sampling points to be considered" help="(--sampleSize)" />
                <param name="regionSize" type="integer" value="300" min="1"
                    label="Region size"
                    help ="To plot the reads per GC over a region, the size of the region is
                    required (see below for more details of the mthod). By default, the bin size
                    is set to 300 bp, which is close to the standard fragment size many sequencing
                    applications. However, if the depth of sequencing is low, a larger bin size will
                    be required, otherwise many bins will not overlap with any read. (--regionSize)"/>
                <param name="filterOut" type="data" format="bed" optional="true"
                    label="BED file containing genomic regions to be excluded from the estimation of the correction"
                    help="Such regions  usually contain repetitive regions and peaks that if included will
                    bias the correction. It is recommended to filter out known repetitive regions if multi-reads
                    (reads that map to more than one genomic position) were excluded. In the case of ChIP-seq data,
                    it is recommended to first use a peak caller to identify and filter out the identified peaks. (--filterOut)" />
                <param name="extraSampling" type="data" format="bed" optional="true"
                    label="BED file containing genomic regions for which extra sampling is required because they are underrepresented in the genome"
                    help="(--extraSampling)" />
            </when>
        </conditional>