comparison macros.xml @ 1:81986a56b281 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit e365f2835488e73b870c73502c24ff23d28b76a5

0:0e6f675cea09

<?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

1:81986a56b281

<?xml version="1.0"?>
<macros>
    <xml name="requirements">
        <requirements>
            <requirement type="package" version="0.2.5">crossmap</requirement>
            <yield/>
        </requirements>
    </xml>
    <token name="@WRAPPER_VERSION@">0.2.5</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="0"/>
                        -->
                    </options>
                </param>
            </when>
            <when value="history">
                <param name="input_chain" type="data" format="csv" 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