view assess_poliovirus_alignment.xml @ 2:31ca16290d4f draft

planemo upload for repository https://github.com/pvanheus/polio_report commit a99e10fec2fac5aae70974c977eb3b362a1a8429-dirty

<tool id="assess_poliovirus_alignment" name="Assess poliovirus alignment" version="0.2.0+galaxy0" profile="21.05">
    <requirements>
        <requirement type="package" version="3.9">python</requirement>
    </requirements>
    <command detect_errors="exit_code"><![CDATA[
        #set $dataset_names = ','.join([ dataset.name for dataset in $tracy_results ])
        python $__tool_directory__/assess_alignment.py 
            --dataset_names '$dataset_names'
            --output_filename '$output1'
            --sample_name '$tracy_results.name'
            --datasets
        #for $dataset in $tracy_results
             '$dataset' 
        #end for

    ]]></command>
    <inputs>
        <!-- input is list of reports for poliovirus sabin 1, 2 and 3 -->
        <param name="tracy_results" format="json" type="data_collection" collection_type="list" label="Tracy JSON reports" help="Input is a list of tracy assemble JSON reports for assembly guided by there reference sequences for poliovirus sabin 1, 2 and 3" />
    </inputs>
    <outputs>
        <data name="output1" format="json" label="Poliovirus alignment assessment on ${on_string}" />
    </outputs>
    <tests>
        <test expect_num_outputs="1">
            <param name="tracy_results" ftype="json">
                <collection type="list">
                    <element name="poliovirus1sabin" value="sample1/poliovirus1sabin.json" />
                    <element name="poliovirus2sabin" value="sample1/poliovirus2sabin.json" />
                    <element name="poliovirus3sabin" value="sample1/poliovirus3sabin.json" />
                </collection>
            </param>
            <output name="output1" ftype="json" file="sample1_output.json" />
        </test>
    </tests>
    <help><![CDATA[
        Given the output of the poliovirus pipeline, make a JSON summarising the comparison against the three poliovirus Sabin reference genomes.
    ]]></help>
    <citations>
        <citation type="bibtex"><![CDATA[
            @software{van_Heusden_Poliovirus_variation_reporting_2022,
                author = {van Heusden, Peter},
                month = {7},
                title = {{Poliovirus variation reporting scripts}},
                url = {https://github.com/pvanheus/polio_report},
                version = {0.1.0},
                year = {2022}
                }
        ]]></citation>
    </citations>
</tool>