Mercurial > repos > iuc > bcftools_plugin_tag2tag

comparison bcftools_plugin_tag2tag.xml @ 0:702c96a52e74 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/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
author iuc
date Wed, 06 Jul 2016 07:07:45 -0400
parents
children 09533c5972fb
comparison
equal deleted inserted replaced
-1:000000000000 0:702c96a52e74
1 <?xml version='1.0' encoding='utf-8'?>
2 <tool name="bcftools @EXECUTABLE@" id="bcftools_plugin_@PLUGIN_ID@" version="@VERSION@.0">
3 <description>plugin Convert between similar tags, such as GL and GP</description>
4 <macros>
5 <token name="@EXECUTABLE@">tag2tag</token>
6 <token name="@PLUGIN_ID@">tag2tag</token>
7 <import>macros.xml</import>
8 </macros>
9 <expand macro="requirements" />
10 <expand macro="version_command" />
11 <command detect_errors="aggressive"><![CDATA[
12 @PREPARE_ENV@
13 @PREPARE_INPUT_FILE@
14 #set $section = $sec_restrict
15 @PREPARE_TARGETS_FILE@
16
17 bcftools plugin @EXECUTABLE@
18
19 ## VCF input section
20 #set $section = $sec_restrict
21 @INCLUDE@
22 @EXCLUDE@
23 @REGIONS@
24 @TARGETS@
25
26 @OUTPUT_TYPE@
27 @THREADS@
28
29 ## Primary Input/Outputs
30 @INPUT_FILE@
31
32 ## Plugin section
33 #set $section = $sec_plugin
34 --
35 ${section.conversion}
36 ${section.replace}
37 > "$output_file"
38 ]]>
39 </command>
40 <inputs>
41 <expand macro="macro_input" />
42 <section name="sec_restrict" expanded="false" title="Restrict to">
43 <expand macro="macro_regions" />
44 <expand macro="macro_targets" />
45 <expand macro="macro_include" />
46 <expand macro="macro_exclude" />
47 </section>
48 <section name="sec_plugin" expanded="true" title="Plugin Options">
49 <param name="conversion" type="select" label="Tag conversion">
50 <option value="--gp-to-gl" selected="true">convert FORMAT/GP to FORMAT/GL</option>
51 <option value="--gl-to-pl">convert FORMAT/GL to FORMAT/PL</option>
52 </param>
53 <param name="replace" type="boolean" truevalue="--replace" falsevalue="" checked="true" label="drop the source tag" help="(\-\-replace)" />
54 </section>
55 <expand macro="macro_select_output_type" />
56 </inputs>
57 <outputs>
58 <expand macro="macro_vcf_output" />
59 </outputs>
60 <tests>
61 <test>
62 <param name="input_file" ftype="vcf" value="view.GL.vcf" />
63 <param name="replace" value="True" />
64 <param name="conversion" value="--gp-to-gl" />
65 <param name="output_type" value="v" />
66 <output name="output_file">
67 <assert_contents>
68 </assert_contents>
69 </output>
70 </test>
71 </tests>
72 <help><![CDATA[
73 =====================================
74 bcftools @EXECUTABLE@ plugin
75 =====================================
76
77 @REGIONS_HELP@
78 @TARGETS_HELP@
79 @EXPRESSIONS_HELP@
80
81 ]]></help>
82 <expand macro="citations" />
83 </tool>