comparison macs2_callpeak.xml @ 4:56e104999978 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 9df9b52baf62b70fbcfc3fbe965d7197d4e8738e

3:6d4babad010f

            --qvalue "${ cutoff_options.qvalue }"
        #elif str( $cutoff_options.cutoff_options_selector ) == 'pvalue':
            #if str($cutoff_options.pvalue).strip() != '':
                --pvalue "${ cutoff_options.pvalue }"
            #end if
        #else:
            --foldenrichment "${ cutoff_options.foldenrichment }"
        #end if

        ## model options
        #if $nomodel_type.nomodel_type_selector == 'nomodel':
            --nomodel

        <conditional name="cutoff_options">
            <param name="cutoff_options_selector" type="select" label="Peak detection based on" help="default uses q-value">
                <option value="qvalue" selected="true">q-value</option>
                <option value="pvalue">p-value</option>
                <option value="foldenrichment">foldenrichment</option>
            </param>
            <when value="pvalue">
                <param name="pvalue" type="float" value="" label="p-value cutoff for peak detection"
                    help="default: not set (--pvalue)"/>
            </when>
            <when value="qvalue">
                <param name="qvalue" type="float" value="0.05" label="Minimum FDR (q-value) cutoff for peak detection"
                    help="default: 0.05 (--qvalue)"/>
            </when>
            <when value="foldenrichment">
                <param name="foldenrichment" value="" type="integer" label="Foldenrichment cutoff for peak detection"
                    help="(--foldenrichment)"/>
            </when>
        </conditional>

        <conditional name="nomodel_type">
            <param name="nomodel_type_selector" type="select" label="Build Model">

                <param name="extsize" type="integer" value="100" label="The arbitrary extension size in bp"
                    help="MACS will use this value as fragment size to extend each read towards 3' end, then pile them up. It's exactly twice the number of legacy shiftsize. In previous language, each read is moved 3' direction to middle of fragment by 1/2 d, then extended to both direction with 1/2 d. This is equivalent to say each read is extended towards 3' into a d size fragment. DEFAULT: 200 (--extsize)"/>
            </when>
        </conditional>

        <param name="outputs" type="select" display="checkboxes" multiple="True" label="Outputs" help="PDF only created when model is build">
            <option value="peaks_tabular" selected="True">Peaks as tabular file</option>
            <!--<option value="narrow">narrow Peaks</option>-->
            <option value="summits" selected="true">summits</option>
            <option value="bdg" selected="true">Scores in bedGraph files (--bdg)</option>
            <option value="html">Summary page (html)</option>
            <option value="pdf">Plot in PDF</option>
            <validator type="no_options" message="Please select at least one output file." />
        </param>

        <conditional name="advanced_options">
            <param name="advanced_options_selector" type="select" label="Advanced options">
                <option value="off" selected="true">Hide advanced options</option>

4:56e104999978

            --qvalue "${ cutoff_options.qvalue }"
        #elif str( $cutoff_options.cutoff_options_selector ) == 'pvalue':
            #if str($cutoff_options.pvalue).strip() != '':
                --pvalue "${ cutoff_options.pvalue }"
            #end if
        #end if

        ## model options
        #if $nomodel_type.nomodel_type_selector == 'nomodel':
            --nomodel

        <conditional name="cutoff_options">
            <param name="cutoff_options_selector" type="select" label="Peak detection based on" help="default uses q-value">
                <option value="qvalue" selected="true">q-value</option>
                <option value="pvalue">p-value</option>
            </param>
            <when value="pvalue">
                <param name="pvalue" type="float" value="" label="p-value cutoff for peak detection"
                    help="default: not set (--pvalue)"/>
            </when>
            <when value="qvalue">
                <param name="qvalue" type="float" value="0.05" label="Minimum FDR (q-value) cutoff for peak detection"
                    help="default: 0.05 (--qvalue)"/>
            </when>
        </conditional>

        <conditional name="nomodel_type">
            <param name="nomodel_type_selector" type="select" label="Build Model">

                <param name="extsize" type="integer" value="100" label="The arbitrary extension size in bp"
                    help="MACS will use this value as fragment size to extend each read towards 3' end, then pile them up. It's exactly twice the number of legacy shiftsize. In previous language, each read is moved 3' direction to middle of fragment by 1/2 d, then extended to both direction with 1/2 d. This is equivalent to say each read is extended towards 3' into a d size fragment. DEFAULT: 200 (--extsize)"/>
            </when>
        </conditional>

        <param name="outputs" type="select" display="checkboxes" multiple="True" optional="false" label="Outputs" help="PDF only created when model is build">
            <option value="peaks_tabular" selected="True">Peaks as tabular file</option>
            <!--<option value="narrow">narrow Peaks</option>-->
            <option value="summits" selected="true">summits</option>
            <option value="bdg" selected="true">Scores in bedGraph files (--bdg)</option>
            <option value="html">Summary page (html)</option>
            <option value="pdf">Plot in PDF</option>
        </param>

        <conditional name="advanced_options">
            <param name="advanced_options_selector" type="select" label="Advanced options">
                <option value="off" selected="true">Hide advanced options</option>