Mercurial > repos > jjohnson > bcftools_plugin_missing2ref

comparison bcftools_plugin_missing2ref.xml @ 0:ff65d6e0809b draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 21c66fb27c7e2fd21c7f7607b3b29e77e64fb86d-dirty
author jjohnson
date Sat, 25 Jun 2016 20:51:04 -0400
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-1:000000000000 0:ff65d6e0809b
1 <?xml version='1.0' encoding='utf-8'?>
2 <tool name="bcftools @EXECUTABLE@" id="bcftools_plugin_@PLUGIN_ID@" version="@VERSION@.0">
3 <description>plugin Set missing genotypes</description>
4 <macros>
5 <token name="@EXECUTABLE@">missing2ref</token>
6 <token name="@PLUGIN_ID@">missing2ref</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 #if $section.phased or $section.major:
35 --
36 ${section.phased}
37 ${section.major}
38 #end if
39 > "$output_file"
40 ]]>
41 </command>
42 <inputs>
43 <expand macro="macro_input" />
44 <section name="sec_restrict" expanded="false" title="Restrict to">
45 <expand macro="macro_regions" />
46 <expand macro="macro_targets" />
47 <expand macro="macro_include" />
48 <expand macro="macro_exclude" />
49 </section>
50 <section name="sec_plugin" expanded="true" title="Plugin Options">
51 <param name="phased" type="boolean" truevalue="--phased" falsevalue="" checked="false" label="Phased" help="Set to 0|0" />
52 <param name="major" type="boolean" truevalue="--major" falsevalue="" checked="false" label="Major" help="Set to major allele" />
53 </section>
54 <expand macro="macro_select_output_type" />
55 </inputs>
56 <outputs>
57 <expand macro="macro_vcf_output" />
58 </outputs>
59 <tests>
60 <test>
61 <param name="input_file" ftype="vcf" value="plugin1.vcf" />
62 <param name="output_type" value="v" />
63 <output name="output_file">
64 <assert_contents>
65 <has_text text="0/0:245" />
66 </assert_contents>
67 </output>
68 </test>
69 </tests>
70 <help><![CDATA[
71 =====================================
72 bcftools @EXECUTABLE@ plugin
73 =====================================
74
75 @REGIONS_HELP@
76 @TARGETS_HELP@
77 @EXPRESSIONS_HELP@
78
79 ]]></help>
80 <expand macro="citations" />
81 </tool>