comparison macros.xml @ 1:f193fef5b19d draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cojac commit 5b54fc7af13196445abda407054e01dd3e5603c6

0:d04ea6b052c5

<?xml version="1.0"?>
<macros>
    <token name="@TOOL_VERSION@">0.2</token>
    <token name="@VERSION_SUFFIX@">0</token>
    <token name="@PROFILE@">21.01</token>
    <xml name="biotools">
        <xrefs>
            <xref type="bio.tools">cojac</xref>

    </xml>
    <xml name="version">
        <version_command>echo @TOOL_VERSION@</version_command>
    </xml>
    <xml name="vocdir_input">
        <conditional name="vocdir_option">
            <param name="choice" type="select"
                   label="Source of YAML files with definition of the variant of concerns"
                   help="Cojac ships with a directory with variant definitions yaml files (https://github.com/cbg-ethz/cojac/tree/master/voc), which the tool can access internally. You can also download the latest version of the yaml files from https://github.com/phe-genomics/variant_definitions and use it as a custom yamls defining the variant of concerns.">
                <option value="cache">Definitions shipped with the tool (can be outdated)</option>
                <option value="custom">From history</option>
            </param>
            <when value="cache"/>
            <when value="custom">
                <param name="voc_file" type="data" format="yaml" multiple="true"
                       label="YAML defining the variant of concern"/>
            </when>
        </conditional>
    </xml>
    <token name="@VOCDIR_COMMAND@"><![CDATA[
#if $vocdir_option.choice == 'custom'
    #set vocdir = 'voc/'
    #set file_paths1 = []
    mkdir -p voc &&
    #for $input_file in $voc_file
        #set $file_path = $vocdir + $input_file.element_identifier
        ln -s '$input_file' '$file_path' &&
        $file_paths1.append($file_path)
    #end for
#else
    DB_PATH="\$(dirname "\$(dirname "\$(which cooc-mutbamscan)")")/share/cojac" &&
    ln -s "\$DB_PATH" db &&
    #set $vocdir = 'db/voc'
#end if
]]></token>
    <token name="@HELP_HEADER@"><![CDATA[
What it does
============

1:f193fef5b19d

<?xml version="1.0"?>
<macros>
    <token name="@TOOL_VERSION@">0.9</token>
    <token name="@VERSION_SUFFIX@">0</token>
    <token name="@PROFILE@">21.01</token>
    <xml name="biotools">
        <xrefs>
            <xref type="bio.tools">cojac</xref>

    </xml>
    <xml name="version">
        <version_command>echo @TOOL_VERSION@</version_command>
    </xml>
    <xml name="vocdir_input">
        <conditional name="voc_source">
            <param name="choice" type="select"
                   label="Source of lineage definitions"
                   help="Cojac detects lineage evidence based on lineage mutation patterns deined in tool-specific yaml format. You can choose between the (possibly outdated) definitions shipped with the tool or definitions provided as a collection of yaml datasets in your history. See the tool help below for more details.">
                <option value="builtin">Lineage definitions shipped with the tool</option>
                <option value="custom">YAML dataset collection in history</option>
            </param>
            <when value="builtin"/>
            <when value="custom">
                <param name="collection" type="data_collection" collection_type="list" format="yaml" label="Collection of lineage definitions" />
            </when>
        </conditional>
    </xml>
    <token name="@VOCDIR_COMMAND@"><![CDATA[
#if $voc_config.choice == 'custom'
    mkdir -p voc &&
    #for $input_file in $voc_config.collection
        ln -s '$input_file' 'voc/$input_file.element_identifier' &&
    #end for
#else
    DB_PATH="\$(dirname "\$(dirname "\$(which cojac)")")/share/cojac/voc" &&
    ln -s "\$DB_PATH" voc &&
#end if
]]></token>
    <token name="@HELP_HEADER@"><![CDATA[
What it does
============