comparison summarize_poliovirus_alignment.xml @ 5:7bcfc97b9284 draft default tip

planemo upload for repository https://github.com/pvanheus/polio_report commit 753aad311378b064f2152c8e99e7c8097c7f4321-dirty

4:eae57366bc55

<tool id="summarize_poliovirus_alignment" name="Summarize poliovirus alignment" version="0.2.0+galaxy1" 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

        <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}">
            <actions>
                <action name="column_names" type="metadata" default="sample name,best matching reference,num variants,perc variants,quality,variant list" />
            </actions>
        </data>
        <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>

5:7bcfc97b9284

<tool id="summarize_poliovirus_alignment" name="Summarize poliovirus alignment" version="0.3.0+galaxy1" 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

        <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}">
            <actions>
                <action name="column_names" type="metadata" default="sample name,best matching reference,num variants,perc variants,quality,vp1 coverage,variant list" />
            </actions>
        </data>
        <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>