Mercurial > repos > iuc > bcftools_plugin_impute_info

comparison bcftools_plugin_impute_info.xml @ 0:981086ab0e3d draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
author iuc
date Wed, 06 Jul 2016 07:06:43 -0400
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children c6071203aaa0
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-1:000000000000 0:981086ab0e3d
1 <?xml version='1.0' encoding='utf-8'?>
2 <tool name="bcftools @EXECUTABLE@" id="bcftools_plugin_@PLUGIN_ID@" version="@VERSION@.0">
3 <description>plugin Add imputation information metrics to the INFO field</description>
4 <macros>
5 <token name="@EXECUTABLE@">impute-info</token>
6 <token name="@PLUGIN_ID@">impute_info</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 = $sec_restrict
21 @INCLUDE@
22 @EXCLUDE@
23 @REGIONS@
24 @TARGETS@
25
26 @OUTPUT_TYPE@
27 @THREADS@
28
29 ## Primary Input/Outputs
30 @INPUT_FILE@
31 > "$output_file"
32 ]]>
33 </command>
34 <inputs>
35 <expand macro="macro_input" />
36 <section name="sec_restrict" expanded="false" title="Restrict to">
37 <expand macro="macro_regions" />
38 <expand macro="macro_targets" />
39 <expand macro="macro_include" />
40 <expand macro="macro_exclude" />
41 </section>
42 <expand macro="macro_select_output_type" />
43 </inputs>
44 <outputs>
45 <expand macro="macro_vcf_output" />
46 </outputs>
47 <tests>
48 <test>
49 <param name="input_file" ftype="vcf" value="convert.vcf" />
50 <param name="output_type" value="v" />
51 <output name="output_file">
52 <assert_contents>
53 <has_text text="IMPUTE2" />
54 <has_text text="INFO=1" />
55 </assert_contents>
56 </output>
57 </test>
58 </tests>
59 <help><![CDATA[
60 =====================================
61 bcftools @EXECUTABLE@ plugin
62 =====================================
63
64 @REGIONS_HELP@
65 @TARGETS_HELP@
66 @EXPRESSIONS_HELP@
67
68 ]]></help>
69 <expand macro="citations" />
70 </tool>