view summarize_poliovirus_alignment.xml @ 0:7e49c6b19f5e draft

planemo upload commit a99e10fec2fac5aae70974c977eb3b362a1a8429

<tool id="summarize_poliovirus_alignment" name="Summarize poliovirus alignment" version="0.1.0+galaxy0" profile="21.05">
    <requirements>
        <requirement type="package" version="3.9">python</requirement>
    </requirements>
    <command detect_errors="exit_code"><![CDATA[
        python $__tool_directory__/summarize_alignment.py
            --summary_output_filename '$output1'
            --variant_list_outputs
        #for $key in $variant_list.keys()
            '$variant_list[$key]' 
        #end for
            --datasets
        #for $dataset in $alignment_assessments
             '$dataset' 
        #end for
        
    ]]></command>
    <inputs>
        <!-- input is list of reports for poliovirus sabin 1, 2 and 3 -->
        <param name="alignment_assessments" format="json" type="data_collection" collection_type="list" label="Poliovius alignment assessments" help="Input is a list of JSON reports from the assess_poliovirus_alignment tool" />
    </inputs>
    <outputs>
        <data name="output1" format="tabular" label="Poliovirus variant summary on ${on_string}" />
        <collection name="variant_list" type="list" label="Poliovirus variant lists on ${on_string}" structured_like="alignment_assessments" format="tabular">
            <!-- todo - find a way to set the metadata columns for the tabular datasets -->
        </collection>
    </outputs>
    <tests>
        <test expect_num_outputs="3">
            <param name="alignment_assessments" ftype="json">
                <collection type="list">
                    <element name="sample1" value="sample1_output.json" />
                </collection>
            </param>
            <output name="output1" ftype="tabular">
                <assert_contents>
                    <has_text text="23:G:A;26:G:A;38:A:G;40:T:C;59:C:T;65:T:C;72:A:G;" />
                </assert_contents>
            </output>
            <output_collection name="variant_list">
                <element name="sample1" file="sample1_variants.tabular" ftype="tabular" />
            </output_collection>
        </test>
    </tests>
    <help><![CDATA[
        Given a list of outputs of the assess_poliovirus_alignment tool, make a final summary.
    ]]></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>