comparison macs2_callpeak.xml @ 10:f0b351e734b8 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit e9415c8ba21c77f848a57d60ee6be78dff4b49a6

9:acbd3fb47f90

<tool id="macs2_callpeak" name="MACS2 callpeak" version="@VERSION_STRING@.2">
    <description>Call peaks from alignment results</description>
    <macros>
        <import>macs2_macros.xml</import>
    </macros>
    <expand macro="requirements">

            &&
            cp MACS2_peaks.xls '${ output_tabular }'
        #end if

        ## run R to create pdf from model script
        #if $nomodel_type.nomodel_type_selector == "create_model" and "pdf" in str($outputs).split(','):
            &&
            Rscript MACS2_model.r > MACS2_model.r.log
        #end if

        #if 'html' in str($outputs).split(','):

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

        <section name="advanced_options" title="Advanced Options">
                <param name="to_large" type="boolean" truevalue="--to-large" falsevalue="" checked="False" optional="True"
                    label="When set, scale the small sample up to the bigger sample"

        </data>
        <data name="output_plot" format="pdf" from_work_dir="MACS2_model.pdf" label="${tool.name} on ${on_string} (plot)">
            <filter>
            ((
              outputs and 'pdf' in outputs and
              nomodel_type['nomodel_type_selector'] == "create_model"
            ))
            </filter>
        </data>
        <data name="output_treat_pileup" format="bedgraph" from_work_dir="MACS2_treat_pileup.bdg" label="${tool.name} on ${on_string} (Bedgraph Treatment)">
            <filter>outputs and 'bdg' in outputs</filter>

            <param name="format" value="BAMPE" />
            <param name="effective_genome_size_options_selector" value="user_defined"/>
            <param name="gsize" value="3300000000"/>
            <param name="nomodel_type_selector" value="nomodel"/>
            <param name="nolambda" value="True"/>
            <output name="output_narrowpeaks" file="callpeak_bampe_narrow.bed"/>
        </test>
    </tests>
    <help><![CDATA[

10:f0b351e734b8

<tool id="macs2_callpeak" name="MACS2 callpeak" version="@VERSION_STRING@.3">
    <description>Call peaks from alignment results</description>
    <macros>
        <import>macs2_macros.xml</import>
    </macros>
    <expand macro="requirements">

            &&
            cp MACS2_peaks.xls '${ output_tabular }'
        #end if

        ## run R to create pdf from model script
        #if $nomodel_type.nomodel_type_selector == "create_model" and "pdf" in str($outputs).split(',') and $format != "BAMPE":
            &&
            Rscript MACS2_model.r > MACS2_model.r.log
        #end if

        #if 'html' in str($outputs).split(','):

        <param name="outputs" type="select" display="checkboxes" multiple="True" optional="True" label="Additional Outputs" help="PDF is only created when the model is built">
            <option value="peaks_tabular">Peaks as tabular file</option>
            <option value="summits">Peak summits</option>
            <option value="bdg" >Scores in bedGraph files (--bdg)</option>
            <option value="html">Summary page (html)</option>
            <option value="pdf">Plot in PDF (only available if a model is created and if BAMPE is not used)</option>
        </param>

        <section name="advanced_options" title="Advanced Options">
                <param name="to_large" type="boolean" truevalue="--to-large" falsevalue="" checked="False" optional="True"
                    label="When set, scale the small sample up to the bigger sample"

        </data>
        <data name="output_plot" format="pdf" from_work_dir="MACS2_model.pdf" label="${tool.name} on ${on_string} (plot)">
            <filter>
            ((
              outputs and 'pdf' in outputs and
              nomodel_type['nomodel_type_selector'] == "create_model" and
              format != "BAMPE"
            ))
            </filter>
        </data>
        <data name="output_treat_pileup" format="bedgraph" from_work_dir="MACS2_treat_pileup.bdg" label="${tool.name} on ${on_string} (Bedgraph Treatment)">
            <filter>outputs and 'bdg' in outputs</filter>

            <param name="format" value="BAMPE" />
            <param name="effective_genome_size_options_selector" value="user_defined"/>
            <param name="gsize" value="3300000000"/>
            <param name="nomodel_type_selector" value="nomodel"/>
            <param name="nolambda" value="True"/>
            <!-- we select PDF as output, but since we are in BAMPE mode, this will not ignored and the expect_num_outputs stays one. -->
            <param name="outputs" value="pdf"/>
            <output name="output_narrowpeaks" file="callpeak_bampe_narrow.bed"/>
        </test>
    </tests>
    <help><![CDATA[