comparison pangolin.xml @ 26:007ffbb11881 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit d1c58058506d5eca398a43d8e5f98e59a2067739

25:ca337cce3888

<tool id="pangolin" name="Pangolin" version="@TOOL_VERSION@+galaxy0" profile="20.01">
    <description>Phylogenetic Assignment of Outbreak Lineages</description>
    <macros>
        <token name="@TOOL_VERSION@">4.1.2</token>
        <token name="@PANGOLIN_DATA_VERSION@">1.12</token>
        <token name="@CONSTELLATIONS_VERSION@">0.1.10</token>
        <token name="@MIN_COMPATIBLE_PANGOLIN_DATA_FORMAT@">4</token>
        <!-- a regex describing the scorpio versions that this wrapper version
        is backwards-compatible with; can be used with the min_scorpio_version
        column of the constellations data table to offer only compatible

        versions become available. Also, please check for updated dependencies
        when updating the wrapper for other reasons. -->
        <requirement type="package" version="0.3.17">scorpio</requirement>
        <requirement type="package" version="@PANGOLIN_DATA_VERSION@">pangolin-data</requirement>
        <requirement type="package" version="@CONSTELLATIONS_VERSION@">constellations</requirement>
        <requirement type="package" version="0.5.6">usher</requirement>
        <requirement type="package" version="1.1.0">gofasta</requirement>
        <requirement type="package" version="426">ucsc-fatovcf</requirement>
        <requirement type="package" version="2.24">minimap2</requirement>
        <!-- wrapper-specific requirements to turn pangolin's native
        comma-separated output into tab-separated one and to truncate
        pangolin's all-versions output. -->
        <requirement type="package" version="0.23.0">csvtk</requirement>
        <requirement type="package" version="3.4">grep</requirement>
    </requirements>
    <version_command><![CDATA[pangolin --version]]></version_command>
    <command detect_errors="exit_code"><![CDATA[
## Prepare a pangolin datadir if required:

    ]]></command>
    <inputs>
        <param type="data" name="input1" format="fasta,fasta.gz" label="Input FASTA File(s)" />
        <conditional name="engine">
            <param argument="--analysis-mode" type="select" label="Analysis mode"
            help="The analysis engine to use for lineage assignment. UShER is considered more accurate, but pangoLEARN is faster">
                <option value="usher">UShER</option>
                <option value="pangolearn">pangoLEARN</option>
            </param>
            <when value="usher">
                <expand macro="pangolin_data_sources">

        <data name="align1" format="fasta" label="pangolin alignment on ${on_string}">
            <filter>alignment</filter>
        </data>
    </outputs>
    <tests>
        <test expect_num_outputs="1">
            <param name="input1" value="test1.fasta"/>
            <conditional name="engine">
                <!-- Test only the default UShER mode for now since the
                pangolearn random forest model uses too much memory
                see https://github.com/cov-lineages/pangolin/issues/395
                <param name="analysis_mode" value="pangolearn" />
                -->
                <conditional name="pangolin_data">
                    <param name="source" value="default" />
                </conditional>
            </conditional>
            <output name="output1" ftype="tabular">

                    <has_text text="pass" />
                    <has_n_lines n="1" />
                </assert_contents>
            </output>
        </test>
        <test expect_num_outputs="1">
            <param name="input1" value="test1.fasta"/>
            <conditional name="engine">
                <conditional name="pangolin_data">
                    <param name="source" value="download" />
                </conditional>
            </conditional>
            <output name="output1" ftype="tabular">
                <assert_contents>
                    <has_text_matching expression="B\.1\.1.*\t\d\.\d\t*PUSHER" />
                    <has_text text="pass" />
                    <has_n_lines n="1" />
                </assert_contents>
            </output>
        </test>
        <test expect_num_outputs="2">
            <param name="input1" value="test1.fasta" />
            <conditional name="engine">
                <!-- Test only the default UShER mode for now since the
                pangolearn random forest model uses too much memory

26:007ffbb11881

<tool id="pangolin" name="Pangolin" version="@TOOL_VERSION@+galaxy0" profile="20.01">
    <description>Phylogenetic Assignment of Outbreak Lineages</description>
    <macros>
        <token name="@TOOL_VERSION@">4.1.3</token>
        <token name="@PANGOLIN_DATA_VERSION@">1.17</token>
        <token name="@CONSTELLATIONS_VERSION@">0.1.10</token>
        <token name="@MIN_COMPATIBLE_PANGOLIN_DATA_FORMAT@">4</token>
        <!-- a regex describing the scorpio versions that this wrapper version
        is backwards-compatible with; can be used with the min_scorpio_version
        column of the constellations data table to offer only compatible

        versions become available. Also, please check for updated dependencies
        when updating the wrapper for other reasons. -->
        <requirement type="package" version="0.3.17">scorpio</requirement>
        <requirement type="package" version="@PANGOLIN_DATA_VERSION@">pangolin-data</requirement>
        <requirement type="package" version="@CONSTELLATIONS_VERSION@">constellations</requirement>
        <requirement type="package" version="0.6.2">usher</requirement>
        <requirement type="package" version="1.1.0">gofasta</requirement>
        <requirement type="package" version="426">ucsc-fatovcf</requirement>
        <requirement type="package" version="2.24">minimap2</requirement>
        <!-- wrapper-specific requirements to turn pangolin's native
        comma-separated output into tab-separated one and to truncate
        pangolin's all-versions output. -->
        <requirement type="package" version="0.25.0">csvtk</requirement>
        <requirement type="package" version="3.4">grep</requirement>
    </requirements>
    <version_command><![CDATA[pangolin --version]]></version_command>
    <command detect_errors="exit_code"><![CDATA[
## Prepare a pangolin datadir if required:

    ]]></command>
    <inputs>
        <param type="data" name="input1" format="fasta,fasta.gz" label="Input FASTA File(s)" />
        <conditional name="engine">
            <param argument="--analysis-mode" type="select" label="Analysis mode"
            help="The analysis engine to use for lineage assignment. UShER is considered more accurate; pangoLEARN typically requires more memory, but might be faster in some cases.">
                <option value="usher">UShER</option>
                <option value="pangolearn">pangoLEARN</option>
            </param>
            <when value="usher">
                <expand macro="pangolin_data_sources">

        <data name="align1" format="fasta" label="pangolin alignment on ${on_string}">
            <filter>alignment</filter>
        </data>
    </outputs>
    <tests>
        <!-- Test only the default UShER mode for now since the
        pangolearn random forest model uses too much memory
        see https://github.com/cov-lineages/pangolin/issues/395
        <test expect_num_outputs="1">
            <param name="input1" value="test1.fasta"/>
            <conditional name="engine">
                <param name="analysis_mode" value="pangolearn" />
                <conditional name="pangolin_data">
                    <param name="source" value="default" />
                </conditional>
            </conditional>
            <output name="output1" ftype="tabular">

                    <has_text text="pass" />
                    <has_n_lines n="1" />
                </assert_contents>
            </output>
        </test>
        -->
        <test expect_num_outputs="1">
            <param name="input1" value="test1.fasta"/>
            <conditional name="engine">
                <conditional name="pangolin_data">
                    <param name="source" value="default" />
                </conditional>
            </conditional>
            <output name="output1" ftype="tabular">
                <assert_contents>
                    <has_text_matching expression="B\.1\.1.*\t\d\.\d+\t*PUSHER" />
                    <has_text text="pass" />
                    <has_n_lines n="1" />
                </assert_contents>
            </output>
        </test>
        <!-- test download and alignment options -->
        <test expect_num_outputs="2">
            <param name="input1" value="test1.fasta" />
            <conditional name="engine">
                <!-- Test only the default UShER mode for now since the
                pangolearn random forest model uses too much memory