comparison intervene_pairwise.xml @ 2:33b8c5eedc04 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/intervene commit bf6d77a84f796430a6b4530209d0f21e1d40d25a

1:08780101bc36

<tool id="intervene_pairwise" name="Pairwise intersection" version="@TOOL_VERSION@">
    <description>and heatmap for genomic intervals</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <requirements>
        <requirement type="package" version="@TOOL_VERSION@">intervene</requirement>

        <param argument="--fontsize" type="integer" value="8" label="Label font size"/>
        <param argument="--title" type="text" label="Heatmap main title" value="Pairwise intersection">
            <expand macro="quote_sanitizer"/>
        </param>
        <expand macro="figure_params"/>
    </inputs>
    <outputs>
        <data name="plot" format="pdf" label="Pairwise plot on ${on_string}" from_work_dir="results/Intervene_pairwise.plot">
            <actions>
                <action type="format">
                    <option type="from_param" name="figtype"/>
                </action>
            </actions>
        </data>
    </outputs>
    <tests>
        <test>
            <param name="input" value="a.bed,b.bed,c.bed"/>
            <output name="plot" value="bed_pairwise.pdf" compare="sim_size"/>
        </test>
    </tests>
    <help><![CDATA[
**What it does**

2:33b8c5eedc04

<tool id="intervene_pairwise" name="Pairwise intersection" version="@TOOL_VERSION@+galaxy1">
    <description>and heatmap for genomic intervals</description>
    <xrefs>
        <xref type="bio.tools">intervene</xref>
    </xrefs>
    <macros>
        <import>macros.xml</import>
    </macros>
    <requirements>
        <requirement type="package" version="@TOOL_VERSION@">intervene</requirement>

        <param argument="--fontsize" type="integer" value="8" label="Label font size"/>
        <param argument="--title" type="text" label="Heatmap main title" value="Pairwise intersection">
            <expand macro="quote_sanitizer"/>
        </param>
        <expand macro="figure_params"/>
        <param name="out_matrix" type="boolean" truevalue="true" falsevalue="false" label="Output the intervene matrix file?"/>
    </inputs>
    <outputs>
        <data name="plot" format="pdf" label="Pairwise plot on ${on_string}" from_work_dir="results/Intervene_pairwise.plot">
            <actions>
                <action type="format">
                    <option type="from_param" name="figtype"/>
                </action>
            </actions>
        </data>
        <data name="matrix" format="txt" label="Matrix on ${on_string}" from_work_dir="results/Intervene_pairwise_frac_matrix.txt">
            <filter>out_matrix</filter>
        </data>
    </outputs>
    <tests>
        <test expect_num_outputs="2">
            <param name="input" value="a.bed,b.bed,c.bed"/>
            <param name="out_matrix" value="true"/>
            <output name="plot" value="bed_pairwise.pdf" compare="sim_size"/>
            <output name="matrix" value="matrix.txt" />
        </test>
    </tests>
    <help><![CDATA[
**What it does**