Mercurial > repos > iuc > bcftools_plugin_fixploidy

comparison bcftools_plugin_fixploidy.xml @ 0:8eb720e59e15 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 06:57:28 -0400
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children 5a4073ad1140
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-1:000000000000 0:8eb720e59e15
1 <?xml version='1.0' encoding='utf-8'?>
2 <tool name="bcftools @EXECUTABLE@" id="bcftools_plugin_@PLUGIN_ID@" version="@VERSION@.0">
3 <description>plugin Fix ploidy</description>
4 <macros>
5 <token name="@EXECUTABLE@">fixploidy</token>
6 <token name="@PLUGIN_ID@">fixploidy</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 @PLOIDY_FILE@
36 #if $section.sex:
37 --sex "${section.sex}"
38 #end if
39 ## Only default tag GT is currently accepted
40 --tags "$section.tags"
41 > "$output_file"
42 ]]>
43 </command>
44 <inputs>
45 <expand macro="macro_input" />
46 <section name="sec_restrict" expanded="false" title="Restrict to">
47 <expand macro="macro_regions" />
48 <expand macro="macro_targets" />
49 <expand macro="macro_include" />
50 <expand macro="macro_exclude" />
51 </section>
52 <section name="sec_plugin" expanded="true" title="Plugin Options">
53 <expand macro="macro_ploidy_file" />
54 <param name="sex" type="data" format="tabular" label="Sample Sex file" optional="true"/>
55 <param name="tags" type="hidden" value="GT" label="tags"/>
56 </section>
57 <expand macro="macro_select_output_type" />
58 </inputs>
59 <outputs>
60 <expand macro="macro_vcf_output" />
61 </outputs>
62 <tests>
63 <test>
64 <param name="input_file" ftype="vcf" value="fixploidy.vcf" />
65 <param name="sex" ftype="tabular" value="fixploidy.samples" />
66 <param name="ploidy_file" ftype="tabular" value="fixploidy.ploidy" />
67 <param name="output_type" value="v" />
68 <output name="output_file">
69 <assert_contents>
70 <has_text_matching expression="3000004\txx\tC\tCTTTT\t11\tq11\tFLAG;IINT=11;IFLT=1.1;ISTR=xxx\tGT:FINT:FFLT:FSTR\t0/0/0/0/0/0:11:1.1:x\t0/0/0/0/0/0/0:11:1.1:xxx\t0|0|0|0|0|0|0|0:11:1.1:xxx" />
71 </assert_contents>
72 </output>
73 </test>
74 </tests>
75 <help><![CDATA[
76 =====================================
77 bcftools @EXECUTABLE@ plugin
78 =====================================
79
80 @REGIONS_HELP@
81 @TARGETS_HELP@
82 @EXPRESSIONS_HELP@
83
84 ]]></help>
85 <expand macro="citations" />
86 </tool>