Mercurial > repos > iuc > crossmap_bam

comparison macros.xml @ 1:8e5feca6a518 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit e365f2835488e73b870c73502c24ff23d28b76a5
author iuc
date Fri, 20 Oct 2017 02:48:57 -0400
parents d04d5afec2e0
children 083774cc8472
comparison
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0:d04d5afec2e0 1:8e5feca6a518
1 <?xml version="1.0"?> 1 <?xml version="1.0"?>
2 <macros> 2 <macros>
3 <xml name="requirements"> 3 <xml name="requirements">
4 <requirements> 4 <requirements>
5 <requirement type="package" version="324">ucsc-wigtobigwig</requirement> 5 <requirement type="package" version="0.2.5">crossmap</requirement>
6 <requirement type="package" version="0.2.2">crossmap</requirement>
7 <yield/> 6 <yield/>
8 </requirements> 7 </requirements>
9 </xml> 8 </xml>
10 <token name="@WRAPPER_VERSION@">0.2.2</token> 9 <token name="@WRAPPER_VERSION@">0.2.5</token>
11 <xml name="stdio"> 10 <xml name="stdio">
12 <stdio> 11 <stdio>
13 <regex match="Aborted (core dumped)" source="stdout" level="fatal"/> 12 <regex match="Aborted (core dumped)" source="stdout" level="fatal"/>
14 <regex match=".*" source="both" level="log"/> 13 <regex match=".*" source="both" level="log"/>
15 <exit_code range="1:"/> 14 <exit_code range="1:"/>
16 </stdio> 15 </stdio>
17 </xml> 16 </xml>
18 <xml name="version_command"> 17 <xml name="version_command">
19 <version_command>CrossMap.py 2&gt;&amp;1 | head -n 1 | grep -E --only-matching 'CrossMap.*'</version_command> 18 <version_command><![CDATA[
19 CrossMap.py 2>&1 | head -n 1 | grep -E --only-matching 'CrossMap.*'
20 ]]></version_command>
20 </xml> 21 </xml>
21 <xml name="chain"> 22 <xml name="chain">
22 <conditional name="chain_source"> 23 <conditional name="chain_source">
23 <param name="index_source" type="select" label="Source for LiftOver Data (chain file)"> 24 <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="cached">Local data (in galaxy)</option>
25 <option value="history">From History</option> 26 <option value="history">From History</option>
26 </param> 27 </param>
27 <when value="cached"> 28 <when value="cached">
28 <param name="input_chain" type="select" label="Lift Over To"> 29 <param name="input_chain" type="select" label="Lift Over To">
29 <options from_file="liftOver.loc"> 30 <options from_data_table="liftOver">
30 <column name="dbkey" index="0"/><!-- species/build 'from' --> 31 <!--
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"/> 32 <filter type="data_meta" ref="input" key="dbkey" column="0"/>
33 -->
34 </options> 34 </options>
35 </param> 35 </param>
36 </when> 36 </when>
37 <when value="history"> 37 <when value="history">
38 <param type="data" format="csv" name="input_chain" label="LiftOver chain file"/> 38 <param name="input_chain" type="data" format="csv" label="LiftOver chain file"/>
39 </when> 39 </when>
40 </conditional> 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> 41 </xml>
48 <token name="@HELP_GENERAL@"> 42 <token name="@HELP_GENERAL@">
49 CrossMap 43 CrossMap
50 -------- 44 --------
51 CrossMap is versatile tool to convert genome coordinates or annotation files between genome 45 CrossMap is versatile tool to convert genome coordinates or annotation files between genome