comparison computeMatrix.xml @ 29:2f7094a2cfd5 draft

planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b5fc4073c884a2d6a4092ea85150db1971010f28

28:62a2cfcca9d3

        <import>deepTools_macros.xml</import>
    </macros>
    <expand macro="requirements" />
    <command>
<![CDATA[
        #import re
        #import tempfile
        #set bw_files=[]
        #for $counter, $bigwig, in enumerate($scoreFileName):
            #set identifier = re.sub('[^\s\w\-]', '_', str($bigwig.element_identifier))
            ln -f -s "${bigwig}" "${identifier}_${counter}.bw" &&
            #silent $bw_files.append('%s_%s.bw' % ($identifier, $counter))
        #end for

        #set bed_files=[]
        #for $counter, $rf, in enumerate($regionsFiles):
            #set identifier = re.sub('[^\s\w\-]', '_', str($rf.regionsFile.element_identifier))
            ln -f -s "${rf.regionsFile}" "${identifier}_${counter}.bed" &&

        @BINARY@

            $mode.mode_select
            --regionsFileName '#echo "' '".join($bed_files)#'

            --scoreFileName '#echo "' '".join($bw_files)#'

            --outFileName '$outFileName'

            @THREADS@

                    --maxThreshold $advancedOpt.maxThreshold
                #end if
                #if $advancedOpt.scale is not None and str($advancedOpt.scale) != '':
                    --scale $advancedOpt.scale
                #end if

                @ADVANCED_OPTS_GTF@

                @blacklist@

        <repeat name="regionsFiles" title="Select regions" min="1">
            <param name="regionsFile" format="bed,gtf" type="data" label="Regions to plot"
                help="File, in BED format, containing the regions to plot."/>
        </repeat>

        <param name="scoreFileName" format="bigwig" type="data"
            label="Score file" multiple="True"
            help="You can generate a bigWig file from a BAM file using the
            bamCoverage tool. (--scoreFileName)"/>

        <conditional name="mode" >
            <param name="mode_select" type="select"
                label="computeMatrix has two main output options"
                help="In the scale-regions mode, all regions in the BED file are

                    numeric value will be skipped. The max threshold is useful to skip those
                    few regions with very high read counts (e.g. major satellites) that may
                    bias the average values. (--maxThreshold)"/>
                <param name="scale" type="float" optional="True" label="Scaling factor"
                    help="If set, all values are multiplied by this number. (--scale)"/>

                <expand macro="gtf_options" />

                <expand macro="blacklist" />
            </when>

        <expand macro="output_save_matrix_values" />
    </outputs>
    <tests>
        <test>
            <param name="regionsFile" value="computeMatrix1.bed" ftype="bed" />
            <param name="scoreFileName" value="bamCoverage_result4.bw" ftype="bigwig" />
            <param name="showAdvancedOpt" value="yes" />
            <param name="mode_select" value="reference-point" />
            <param name="binSize" value="10" />
            <param name="sortUsing" value="sum" />
            <param name="averageTypeBins" value="sum" />

            <param name="afterRegionStartLength" value="10" />
            <output name="outFileName" file="computeMatrix_result1.gz" ftype="deeptools_compute_matrix_archive" compare="sim_size" />
        </test>
        <test>
            <param name="regionsFile" value="computeMatrix2.bed" ftype="bed" />
            <param name="scoreFileName" value="computeMatrix2.bw" ftype="bigwig" />
            <param name="showAdvancedOpt" value="yes" />
            <param name="mode_select" value="reference-point" />
            <param name="binSize" value="10" />
            <param name="beforeRegionStartLength" value="10" />
            <param name="afterRegionStartLength" value="10" />
            <output name="outFileName" file="computeMatrix_result2.gz" ftype="deeptools_compute_matrix_archive" compare="sim_size" />
        </test>
        <test>
            <param name="regionsFile" value="computeMatrix2.bed" ftype="bed" />
            <param name="scoreFileName" value="computeMatrix2.bw" ftype="bigwig" />
            <param name="showAdvancedOpt" value="yes" />
            <param name="mode_select" value="scale-regions" />
            <param name="endLabel" value="END" />
            <param name="regionStartLength" value="yes" />
            <output name="outFileName" file="computeMatrix_result3.gz" ftype="deeptools_compute_matrix_archive" compare="sim_size" />

29:2f7094a2cfd5

        <import>deepTools_macros.xml</import>
    </macros>
    <expand macro="requirements" />
    <command>
<![CDATA[
        @multiple_input_bigwigs@

        #set bed_files=[]
        #for $counter, $rf, in enumerate($regionsFiles):
            #set identifier = re.sub('[^\s\w\-]', '_', str($rf.regionsFile.element_identifier))
            ln -f -s "${rf.regionsFile}" "${identifier}_${counter}.bed" &&

        @BINARY@

            $mode.mode_select
            --regionsFileName '#echo "' '".join($bed_files)#'

            --scoreFileName '#echo "' '".join($files)#'

            --outFileName '$outFileName'

            @THREADS@

                    --maxThreshold $advancedOpt.maxThreshold
                #end if
                #if $advancedOpt.scale is not None and str($advancedOpt.scale) != '':
                    --scale $advancedOpt.scale
                #end if
                #if $advancedOpt.samplesLabel is not None and str($advancedOpt.samplesLabel) != '':
                    --samplesLabel $advancedOpt.samplesLabel
                #end if

                @ADVANCED_OPTS_GTF@

                @blacklist@

        <repeat name="regionsFiles" title="Select regions" min="1">
            <param name="regionsFile" format="bed,gtf" type="data" label="Regions to plot"
                help="File, in BED format, containing the regions to plot."/>
        </repeat>

        <expand macro="multiple_input_bigwigs" MIN="1" LABEL="Score file" TITLE="Score files"/>

        <conditional name="mode" >
            <param name="mode_select" type="select"
                label="computeMatrix has two main output options"
                help="In the scale-regions mode, all regions in the BED file are

                    numeric value will be skipped. The max threshold is useful to skip those
                    few regions with very high read counts (e.g. major satellites) that may
                    bias the average values. (--maxThreshold)"/>
                <param name="scale" type="float" optional="True" label="Scaling factor"
                    help="If set, all values are multiplied by this number. (--scale)"/>
                <param argument="--samplesLabel" type="text" size="30"
                    label="Labels for the samples (each bigwig)"
                    help="The default is to use the history item label. The sample labels should be separated by
                    spaces and quoted if a label itself contains a space E.g. label-1 &quot;label 2&quot;">
                    <sanitizer>
                        <valid initial="string.printable">
                        </valid>
                    </sanitizer>
                </param>

                <expand macro="gtf_options" />

                <expand macro="blacklist" />
            </when>

        <expand macro="output_save_matrix_values" />
    </outputs>
    <tests>
        <test>
            <param name="regionsFile" value="computeMatrix1.bed" ftype="bed" />
            <param name="bigwigfiles" value="bamCoverage_result4.bw" ftype="bigwig" />
            <param name="showAdvancedOpt" value="yes" />
            <param name="mode_select" value="reference-point" />
            <param name="binSize" value="10" />
            <param name="sortUsing" value="sum" />
            <param name="averageTypeBins" value="sum" />

            <param name="afterRegionStartLength" value="10" />
            <output name="outFileName" file="computeMatrix_result1.gz" ftype="deeptools_compute_matrix_archive" compare="sim_size" />
        </test>
        <test>
            <param name="regionsFile" value="computeMatrix2.bed" ftype="bed" />
            <param name="bigwigfiles" value="computeMatrix2.bw" ftype="bigwig" />
            <param name="showAdvancedOpt" value="yes" />
            <param name="mode_select" value="reference-point" />
            <param name="binSize" value="10" />
            <param name="beforeRegionStartLength" value="10" />
            <param name="afterRegionStartLength" value="10" />
            <output name="outFileName" file="computeMatrix_result2.gz" ftype="deeptools_compute_matrix_archive" compare="sim_size" />
        </test>
        <test>
            <param name="regionsFile" value="computeMatrix2.bed" ftype="bed" />
            <param name="bigwigfiles" value="computeMatrix2.bw" ftype="bigwig" />
            <param name="showAdvancedOpt" value="yes" />
            <param name="mode_select" value="scale-regions" />
            <param name="endLabel" value="END" />
            <param name="regionStartLength" value="yes" />
            <output name="outFileName" file="computeMatrix_result3.gz" ftype="deeptools_compute_matrix_archive" compare="sim_size" />