<?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_file="liftOver.loc">
                        <column name="dbkey" index="0"/><!-- species/build 'from' -->
                        <column name="name" index="1"/><!-- species/build 'to' -->
                        <column name="value" index="2"/><!-- path of chain file -->
                        <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>