comparison snippy-core.xml @ 5:0aa87d97847f draft

"planemo upload commit 13d17dd18915767d3ca5bbd92ce3e5e80a287112"

4:9bccc8404a3c

<?xml version="1.0" encoding="utf-8"?>
<tool id="snippy_core" name="snippy-core" version="@VERSION@">
    <description>
        Combine multiple Snippy outputs into a core SNP alignment
    </description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements" />
    <command detect_errors="exit_code"><![CDATA[
        #for $indir in $indirs
            #set $sample_name = os.path.splitext(os.path.basename(str($indir.name)))[0]
            mkdir '$sample_name' && tar -xf '$indir' -C '$sample_name' --strip-components=1 &&
        #end for
        #set snippy_dirs = " ".join(["'{0}'".format(os.path.splitext(os.path.basename(str($indir.name)))[0]) for $indir in $indirs])
        snippy-core
            --ref '$ref'
            ${snippy_dirs}
    ]]></command>

    <inputs>
        <param name="indirs" type="data" multiple="true" format="zip" label="Snippy input zipped dirs" help="Select all the snippy inputs for alignment" />
        <param name="ref" type="data" format="fasta,genbank" label="Reference File (either in fasta or genbank format)" help="Fasta or Genbank file to use as the reference" />
        <param name="outputs" type="select" multiple="true" display="checkboxes" label="Output selection">
            <option value="outaln" selected="True">A core SNP alignment in the fasta format</option>
            <option value="outfull" selected="False">A whole genome SNP alignment (includes invariant sites)</option>
            <option value="outtab" selected="False">Tab-separated columnar list of core SNP sites with alleles and annotations</option>
            <option value="outtxt" selected="False">Tab-separated columnar list of alignment/core-size statistics</option>

    </outputs>

    <tests>
        <test><!-- Test #1 - test with 3 zipped directories -->
            <param name="indirs" value="a.tgz,b.tgz,c.tgz" />
            <param name="ref" value="reference.fasta" />
            <param name="outputs" value="outtxt" />
            <output name="alignment_summary" ftype="txt" file="a_b_c.core.txt" />
        </test>
    </tests>

5:0aa87d97847f

<?xml version="1.0" encoding="utf-8"?>
<tool id="snippy_core" name="snippy-core" version="@VERSION@+galaxy0">
    <description>
        Combine multiple Snippy outputs into a core SNP alignment
    </description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements" />
    <command detect_errors="exit_code"><![CDATA[
        @REFERENCE_SOURCE_FILE@
        #for $indir in $indirs
            #set $sample_name = os.path.splitext(os.path.basename(str($indir.name)))[0]
            mkdir '$sample_name' && tar -xf '$indir' -C '$sample_name' --strip-components=1 &&
        #end for
        #set snippy_dirs = " ".join(["'{0}'".format(os.path.splitext(os.path.basename(str($indir.name)))[0]) for $indir in $indirs])
        snippy-core
            @REFERENCE_COMMAND@
            ${snippy_dirs}
    ]]></command>

    <inputs>
        <param name="indirs" type="data" multiple="true" format="zip" label="Snippy input zipped dirs" help="Select all the snippy inputs for alignment" />
        <expand macro="reference_selector" />
        <param name="outputs" type="select" multiple="true" display="checkboxes" label="Output selection">
            <option value="outaln" selected="True">A core SNP alignment in the fasta format</option>
            <option value="outfull" selected="False">A whole genome SNP alignment (includes invariant sites)</option>
            <option value="outtab" selected="False">Tab-separated columnar list of core SNP sites with alleles and annotations</option>
            <option value="outtxt" selected="False">Tab-separated columnar list of alignment/core-size statistics</option>

    </outputs>

    <tests>
        <test><!-- Test #1 - test with 3 zipped directories -->
            <param name="indirs" value="a.tgz,b.tgz,c.tgz" />
            <conditional name="reference_source">
                <param name="reference_source_selector" value="history"/>
                <param name="ref_file" value="reference.fasta" ftype="fasta"/>
            </conditional>
            <param name="outputs" value="outtxt" />
            <output name="alignment_summary" ftype="txt" file="a_b_c.core.txt" />
        </test>
        <test><!-- Test #2 - test with 3 zipped directories -->
            <param name="indirs" value="a.tgz,b.tgz,c.tgz" />
            <conditional name="reference_source">
                <param name="reference_source_selector" value="cached"/>
                <param name="ref_file" value="test_id"/>
            </conditional>
            <param name="outputs" value="outtxt" />
            <output name="alignment_summary" ftype="txt" file="a_b_c.core.txt" />
        </test>
    </tests>