comparison bamCoverage.xml @ 3:10e697ec9bfb draft

planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2e8510e4f4015f51f7726de5697ba2de9b4e2f4c

2:8145727ba0f0

                $advancedOpt.skipNAs

                #if str($advancedOpt.ignoreForNormalization).strip() != '':
                    --ignoreForNormalization $advancedOpt.ignoreForNormalization
                #end if
            #end if
]]>
    </command>

    <inputs>
        <param name="bamInput" format="bam" type="data" label="BAM file"
            help="The BAM file must be sorted."/>

        <param name="binSize" type="integer" value="50" min="1"
            label="Bin size in bases"
            help="The genome will be divided into bins of the specified size. For each bin, the overlaping number of fragments (or reads)  will be reported. If only half a fragment overlaps, this fraction will be reported. "/>

                <param argument="--MNase" type="boolean" truevalue="--MNase" falsevalue=""
                    label="Determine nucleosome positions from MNase-seq data"
                    help="Only the 3 nucleotides at the center of each fragment are counted. The fragment ends are defined by the two mate reads. *NOTE*: Requires paired-end data." />

            </when>
        </conditional>
    </inputs>
    <outputs>
        <data format="bigwig" name="outFileName">

            <param name="outFileFormat" value="bedgraph" />
            <param name="showAdvancedOpt" value="yes" />
            <param name="binSize" value="10" />
            <output name="outFileName" file="bamCoverage_result4.bg" ftype="bedgraph" />
        </test>
    </tests>
    <help>
<![CDATA[

What it does

3:10e697ec9bfb

                $advancedOpt.skipNAs

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

                #if str($advancedOpt.filterRNAstrand) != 'no':
                    --filterRNAstrand '$advancedOpt.filterRNAstrand'
                #end if
            #end if
]]>
    </command>

    <inputs>
        <param name="bamInput" format="bam" type="data" label="BAM file"
            help=""/>

        <param name="binSize" type="integer" value="50" min="1"
            label="Bin size in bases"
            help="The genome will be divided into bins of the specified size. For each bin, the overlaping number of fragments (or reads)  will be reported. If only half a fragment overlaps, this fraction will be reported. "/>

                <param argument="--MNase" type="boolean" truevalue="--MNase" falsevalue=""
                    label="Determine nucleosome positions from MNase-seq data"
                    help="Only the 3 nucleotides at the center of each fragment are counted. The fragment ends are defined by the two mate reads. *NOTE*: Requires paired-end data." />

                <param argument="filterRNAstrand" type="select" label="Only include reads originating from fragments from the forward or reverse strand." 
                    help="By default (the no option), all reads are processed, regardless of the strand they originated from. For RNAseq, it can be useful to separately create bigWig files for the forward or reverse strands.
                          Note that this tools assumes that a dUTP-based method was used, so fragments will be assigned to the reverse strand if the second read in a pair is reverse complemented.">
                    <option value="no" selected="true">no</option>
                    <option value="forward">forward</option>
                    <option value="reverse">reverse</option>
                </param>

            </when>
        </conditional>
    </inputs>
    <outputs>
        <data format="bigwig" name="outFileName">

            <param name="outFileFormat" value="bedgraph" />
            <param name="showAdvancedOpt" value="yes" />
            <param name="binSize" value="10" />
            <output name="outFileName" file="bamCoverage_result4.bg" ftype="bedgraph" />
        </test>
        <test>
            <param name="bamInput" value="phiX.bam" ftype="bam" />
            <param name="outFileFormat" value="bigwig" />
            <param name="showAdvancedOpt" value="yes" />
            <param name="filterRNAstrand" value="reverse" />
            <param name="binSize" value="10" />
            <output name="outFileName" file="bamCoverage_result5.bw" ftype="bigwig" />
        </test>
    </tests>
    <help>
<![CDATA[

What it does