view macros.xml @ 12:88d180fb6d67 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit ce9efed8c15240a269107ff356aeb18b52eb383f"
author iuc
date Wed, 30 Sep 2020 13:59:51 +0000
parents 09c6a9e067f9
children 4d97434ea0fb
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<?xml version="1.0"?>
<macros>
    <xml name="requirements">
        <requirements>
            <requirement type="package" version="@TOOL_VERSION@">crossmap</requirement>
            <yield/>
        </requirements>
    </xml>
    <token name="@TOOL_VERSION@">0.3.7</token>
    <token name="@WRAPPER_VERSION@">@TOOL_VERSION@+galaxy1</token>
    <xml name="stdio">
        <stdio>
            <regex match="Aborted (core dumped)" source="stdout" level="fatal"/>
            <regex match=".*" source="both" level="log"/>
            <exit_code range="1:"/>
        </stdio>
    </xml>
    <xml name="version_command">
        <version_command><![CDATA[
CrossMap.py 2>&1 | head -n 1 | grep -E --only-matching 'CrossMap.*'
        ]]></version_command>
    </xml>
    <xml name="chain">
        <conditional name="chain_source">
            <param name="index_source" type="select" label="Source for LiftOver Data (chain file)">
                <option value="cached">Local data (in galaxy)</option>
                <option value="history">From History</option>
            </param>
            <when value="cached">
                <param name="input_chain" type="select" label="Lift Over To">
                    <options from_data_table="liftOver">
                        <filter type="data_meta" ref="input" key="dbkey" column="dbkey"/>
                    </options>
                </param>
            </when>
            <when value="history">
                <param name="input_chain" type="data" format="txt" label="LiftOver chain file"/>
            </when>
        </conditional>
    </xml>
    <token name="@HELP_GENERAL@">
CrossMap
--------
CrossMap is versatile tool to convert genome coordinates or annotation files between genome
assemblies. It supports mostly commonly used file types, including BAM, BED,BigWig, GFF,
GTF, SAM, Wiggle, and VCF formats. For large plain text file types, such as BED, GFF, GTF
and VCF, reading from remote servers and file compression are supported.
    </token>
</macros>