Mercurial > repos > iuc > bcftools_plugin_fill_an_ac

comparison bcftools_plugin_fill_an_ac.xml @ 0:dccc7c3afddf 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 06:57:02 -0400
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children 14af5e9cb493
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-1:000000000000 0:dccc7c3afddf
1 <?xml version='1.0' encoding='utf-8'?>
2 <tool name="bcftools @EXECUTABLE@" id="bcftools_plugin_@PLUGIN_ID@" version="@VERSION@.0">
3 <description>plugin Fill INFO fields AN and AC</description>
4 <macros>
5 <token name="@EXECUTABLE@">fill-AN-AC</token>
6 <token name="@PLUGIN_ID@">fill_an_ac</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 ## VCF input section
19 #set $section = $sec_restrict
20 @INCLUDE@
21 @EXCLUDE@
22 @REGIONS@
23 @TARGETS@
24
25 @OUTPUT_TYPE@
26 @THREADS@
27
28 ## Primary Input/Outputs
29 @INPUT_FILE@
30 > "$output_file"
31 ]]>
32 </command>
33 <inputs>
34 <expand macro="macro_input" />
35 <section name="sec_restrict" expanded="false" title="Restrict to">
36 <expand macro="macro_regions" />
37 <expand macro="macro_targets" />
38 <expand macro="macro_include" />
39 <expand macro="macro_exclude" />
40 </section>
41 <expand macro="macro_select_output_type" />
42 </inputs>
43 <outputs>
44 <expand macro="macro_vcf_output" />
45 </outputs>
46 <tests>
47 <test>
48 <param name="input_file" ftype="vcf" value="plugin1.vcf" />
49 <param name="output_type" value="v" />
50 <output name="output_file">
51 <assert_contents>
52 <has_text text="AN=0;AC=0" />
53 </assert_contents>
54 </output>
55 </test>
56 </tests>
57 <help><![CDATA[
58 =====================================
59 bcftools @EXECUTABLE@ plugin
60 =====================================
61
62 @REGIONS_HELP@
63 @TARGETS_HELP@
64 @EXPRESSIONS_HELP@
65
66 ]]></help>
67 <expand macro="citations" />
68 </tool>