Mercurial > repos > iuc > crossmap_bw

comparison macros.xml @ 0:fb5401ff7ca2 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 8564863eaad7bb9f9c8c273d471511979a2c96aa
author iuc
date Sat, 01 Jul 2017 17:45:36 -0400
parents
children 9b8ee2aedca4
comparison
equal deleted inserted replaced
-1:000000000000 0:fb5401ff7ca2
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="name" index="1"/>
31 <column name="value" index="2"/>
32 <column name="dbkey" index="0"/>
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>