comparison repmatch_gff3.xml @ 7:1807688a8a5f draft

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6:6df81aade62c

        --output_summary "$output_summary"
        #if str($output_files_cond.output_files) in ["all", "simple_orphan"]:
            --output_orphan "$output_orphan"
        #end if
        #if str($output_files_cond.output_files) =="all":
            --plot_format $output_files_cond.plot_format
            --output_detail "$output_detail"
            --output_key "$output_key"
            --output_histogram "$output_histogram"
        #end if
    </command>

                <option value="simple">matched pairs only</option>
                <option value="simple_orphan">matched pairs and orphans only</option>
            </param>
            <when value="simple" />
            <when value="simple_orphan" />
            <when value="all">
                <param name="plot_format" type="select" label="Output format for graph">
                    <option value="pdf" selected="True">Pdf</option>
                    <option value="png">Png</option>
                    <option value="svg">Svg</option>
                </param>
            </when>
        </conditional>
    </inputs>
    <outputs>
        <data name="output_summary" format="gff" label="Matched pairs: ${tool.name} on ${on_string}" />
        <data name="output_orphan" format="tabular" label="Orphans: ${tool.name} on ${on_string}">

        <data name="output_key" format="tabular" label="Key: ${tool.name} on ${on_string}">
            <filter>output_files_cond["output_files"] == "all"</filter>
       </data>
        <data name="output_histogram" format="pdf" label="Histogram: ${tool.name} on ${on_string}">
            <filter>output_files_cond["output_files"] == "all"</filter>
            <actions>
                <action type="format">
                    <option type="from_param" name="output_files_cond.plot_format" />
                 </action>
           </actions>
       </data>
    </outputs>
    <tests>
        <param name="input" value="closest_s_input1.gff" ftype="gff" />
        <param name="input" value="largest_s_input1.gff" ftype="gff" />

        <param name="step" value="0" />
        <param name="replicates" value="2" />
        <param name="low_limit" value="-1000" />
        <param name="up_limit" value="1000" />
        <param name="output_files" value="all" />
        <param name="plot_format" value="png" />
        <output name="output_summary" file="summary_out1.gff" ftype="gff" />
        <output name="output_orphan" file="orphan_out1.tabular" ftype="tabular" />
        <output name="output_detail" file="orphan_detail1.tabular" ftype="tabular" />
        <output name="output_key" file="key_out1.tabular" ftype="tabular" />
        <output name="output_histogram" file="histogram_out1.pdf" ftype="pdf" compare="sim_size" />

7:1807688a8a5f

        --output_summary "$output_summary"
        #if str($output_files_cond.output_files) in ["all", "simple_orphan"]:
            --output_orphan "$output_orphan"
        #end if
        #if str($output_files_cond.output_files) =="all":
            --output_detail "$output_detail"
            --output_key "$output_key"
            --output_histogram "$output_histogram"
        #end if
    </command>

                <option value="simple">matched pairs only</option>
                <option value="simple_orphan">matched pairs and orphans only</option>
            </param>
            <when value="simple" />
            <when value="simple_orphan" />
            <when value="all" />
        </conditional>
    </inputs>
    <outputs>
        <data name="output_summary" format="gff" label="Matched pairs: ${tool.name} on ${on_string}" />
        <data name="output_orphan" format="tabular" label="Orphans: ${tool.name} on ${on_string}">

        <data name="output_key" format="tabular" label="Key: ${tool.name} on ${on_string}">
            <filter>output_files_cond["output_files"] == "all"</filter>
       </data>
        <data name="output_histogram" format="pdf" label="Histogram: ${tool.name} on ${on_string}">
            <filter>output_files_cond["output_files"] == "all"</filter>
       </data>
    </outputs>
    <tests>
        <param name="input" value="closest_s_input1.gff" ftype="gff" />
        <param name="input" value="largest_s_input1.gff" ftype="gff" />

        <param name="step" value="0" />
        <param name="replicates" value="2" />
        <param name="low_limit" value="-1000" />
        <param name="up_limit" value="1000" />
        <param name="output_files" value="all" />
        <output name="output_summary" file="summary_out1.gff" ftype="gff" />
        <output name="output_orphan" file="orphan_out1.tabular" ftype="tabular" />
        <output name="output_detail" file="orphan_detail1.tabular" ftype="tabular" />
        <output name="output_key" file="key_out1.tabular" ftype="tabular" />
        <output name="output_histogram" file="histogram_out1.pdf" ftype="pdf" compare="sim_size" />