comparison macros.xml @ 0:bc72094f7ce9 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit d578fad97ce545d68dde40155d36426a121e4447
author iuc
date Tue, 26 Sep 2017 05:44:37 -0400
parents
children 1e881a00d8ff
comparison
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-1:000000000000 0:bc72094f7ce9
1 <?xml version="1.0"?>
2 <macros>
3 <xml name="requirements">
4 <requirements>
5 <requirement type="package" version="324">ucsc-wigtobigwig</requirement>
6 <requirement type="package" version="0.2.2">crossmap</requirement>
7 <yield/>
8 </requirements>
9 </xml>
10 <token name="@WRAPPER_VERSION@">0.2.2</token>
11 <xml name="stdio">
12 <stdio>
13 <regex match="Aborted (core dumped)" source="stdout" level="fatal"/>
14 <regex match=".*" source="both" level="log"/>
15 <exit_code range="1:"/>
16 </stdio>
17 </xml>
18 <xml name="version_command">
19 <version_command>CrossMap.py 2&gt;&amp;1 | head -n 1 | grep -E --only-matching 'CrossMap.*'</version_command>
20 </xml>
21 <xml name="chain">
22 <conditional name="chain_source">
23 <param name="index_source" type="select" label="Source for LiftOver Data (chain file)">
24 <option value="cached">Local data (in galaxy)</option>
25 <option value="history">From History</option>
26 </param>
27 <when value="cached">
28 <param name="input_chain" type="select" label="Lift Over To">
29 <options from_file="liftOver.loc">
30 <column name="dbkey" index="0"/><!-- species/build 'from' -->
31 <column name="name" index="1"/><!-- species/build 'to' -->
32 <column name="value" index="2"/><!-- path of chain file -->
33 <filter type="data_meta" ref="input" key="dbkey" column="0"/>
34 </options>
35 </param>
36 </when>
37 <when value="history">
38 <param type="data" format="csv" name="input_chain" label="LiftOver chain file"/>
39 </when>
40 </conditional>
41 </xml>
42 <xml name="source">
43 <param name="index_source" type="select" label="Source for Input Data">
44 <option value="cached">Local data (in galaxy)</option>
45 <option value="history">From History</option>
46 </param>
47 </xml>
48 <token name="@HELP_GENERAL@">
49 CrossMap
50 --------
51 CrossMap is versatile tool to convert genome coordinates or annotation files between genome
52 assemblies. It supports mostly commonly used file types, including BAM, BED,BigWig, GFF,
53 GTF, SAM, Wiggle, and VCF formats. For large plain text file types, such as BED, GFF, GTF
54 and VCF, reading from remote servers and file compression are supported.
55 </token>
56 </macros>