comparison computeMatrix.xml @ 23:f305afa8ff0d draft

planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 3cefc7d64faa53ef9a4e5984c7b275fc47cbdaaf

22:a2e50c362097

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

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

            --outFileName '$outFileName'

            @THREADS@

            #if $output.showOutputSettings == "yes"
                #if $output.saveMatrix:

                    --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@

            <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>

23:f305afa8ff0d

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

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

            --outFileName '$outFileName'
            --samplesLabel #echo ' '.join($labels)#

            @THREADS@

            #if $output.showOutputSettings == "yes"
                #if $output.saveMatrix:

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

                @ADVANCED_OPTS_GTF@

                @blacklist@

            <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"/>
        <expand macro="custom_sample_labels" />

        <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>