comparison plotFingerprint.xml @ 20:d0390db2a666 draft

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

19:37403b3340c9

                #if $output.saveQualityMetrics:
                    --outQualityMetrics '$outFileQualityMetrics'
                    #if $output.JSDsample:
                        #if "'{}'".format($output.JSDsample.display_name) in $labels:
                            #set JSDidx = $labels.index("'{}'".format($output.JSDsample.display_name))
                            --JSDsample "./${JSDidx}.bam"
                        #end if
                    #end if
                #end if
            #else
                --plotFileFormat 'png'

            #end if
]]>
    </command>

    <inputs>
        <expand macro="multiple_input_bams" />
        <expand macro="region_limit_operation" />

        <conditional name="advancedOpt">
            <param name="showAdvancedOpt" type="select" label="Show advanced options" >
                <option value="no" selected="true">no</option>

            <when value="yes">
                <expand macro="input_image_file_format" />
                <param name="saveRawCounts" type="boolean" label="Save the bin counts" help="(--outRawCounts)"/>
                <param name="saveQualityMetrics" type="boolean" label="Save quality metrics"
                   help="The file will have one row per input BAM file and columns containing a variety of QC metrics. For the full description of all metrics and their interpretation, please see our online documentation: http://deeptools.readthedocs.io/en/latest/content/feature/plotFingerprint_QC_metrics.html. (--outQualityMetrics)"/>
                <param name="JSDsample" type="data" format="bam"
                   label="Jensen-Shannon distance reference sample"
                   help="If output metrics should be saved, then use this sample as the reference for computing the Jensen-Shannon distance and CHANCE metrics of all other samples. Normally this is an input sample. If you don't specify this, then these metrics will not be computed. This is only applicable if quality metrics are being saved. (--JSDsample)" />
            </when>
        </conditional>
    </inputs>

20:d0390db2a666

                #if $output.saveQualityMetrics:
                    --outQualityMetrics '$outFileQualityMetrics'
                    #if $output.JSDsample:
                        #if "'{}'".format($output.JSDsample.display_name) in $labels:
                            #set JSDidx = $labels.index("'{}'".format($output.JSDsample.display_name))
                            --JSDsample "${JSDidx}.bam"
                        #end if
                    #end if
                #end if
            #else
                --plotFileFormat 'png'

            #end if
]]>
    </command>

    <inputs>
        <expand macro="multiple_input_bams" MIN="1"/>
        <expand macro="region_limit_operation" />

        <conditional name="advancedOpt">
            <param name="showAdvancedOpt" type="select" label="Show advanced options" >
                <option value="no" selected="true">no</option>

            <when value="yes">
                <expand macro="input_image_file_format" />
                <param name="saveRawCounts" type="boolean" label="Save the bin counts" help="(--outRawCounts)"/>
                <param name="saveQualityMetrics" type="boolean" label="Save quality metrics"
                   help="The file will have one row per input BAM file and columns containing a variety of QC metrics. For the full description of all metrics and their interpretation, please see our online documentation: http://deeptools.readthedocs.io/en/latest/content/feature/plotFingerprint_QC_metrics.html. (--outQualityMetrics)"/>
                <param name="JSDsample" type="data" format="bam" optional="true"
                   label="Jensen-Shannon distance reference sample"
                   help="If output metrics should be saved, then use this sample as the reference for computing the Jensen-Shannon distance and CHANCE metrics of all other samples. Normally this is an input sample. If you don't specify this, then these metrics will not be computed. This is only applicable if quality metrics are being saved. (--JSDsample)" />
            </when>
        </conditional>
    </inputs>