view macros.xml @ 3:bb6334253319 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit d578fad97ce545d68dde40155d36426a121e4447-dirty
author iuc
date Tue, 26 Sep 2017 06:02:07 -0400
parents 5773a57e91e6
children b18ce8713041
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<?xml version="1.0"?>
<macros>
    <xml name="requirements">
        <requirements>
            <requirement type="package" version="324">ucsc-wigtobigwig</requirement>
            <requirement type="package" version="0.2.2">crossmap</requirement>
            <yield/>
        </requirements>
    </xml>
    <token name="@WRAPPER_VERSION@">0.2.2</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>CrossMap.py 2&gt;&amp;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="0"/>
                    </options>
                </param>
            </when>
            <when value="history">
                <param type="data" format="csv" name="input_chain" label="LiftOver chain file"/>
            </when>
        </conditional>
    </xml>
    <xml name="source">
        <param name="index_source" type="select" label="Source for Input Data">
            <option value="cached">Local data (in galaxy)</option>
            <option value="history">From History</option>
        </param>
    </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>