comparison snippy-core.xml @ 9:e4d0231d8595 draft

"planemo upload commit 02413e02c9484cdb604bda2c09931599f9259792"

8:32f2211eeec3

<?xml version="1.0" encoding="utf-8"?>
<tool id="snippy_core" name="snippy-core" version="@VERSION@+galaxy1">
    <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" />

9:e4d0231d8595

<?xml version="1.0" encoding="utf-8"?>
<tool id="snippy_core" name="snippy-core" version="@VERSION@+galaxy2">
    <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@
        mkdir 'snippy_dirs' && cd 'snippy_dirs' &&
        #for $indir in $indirs
            tar -xf '$indir' -C . &&
        #end for
        cd - &&
        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" />