Mercurial > repos > iuc > bcftools_plugin_color_chrs
comparison bcftools_plugin_color_chrs.xml @ 8:47ee1925fe9e draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5
author | iuc |
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date | Wed, 05 Jun 2019 12:59:21 -0400 |
parents | |
children | 71dfde92fd57 |
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7:78a435cb9900 | 8:47ee1925fe9e |
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1 <?xml version='1.0' encoding='utf-8'?> | |
2 <tool name="bcftools @EXECUTABLE@" id="bcftools_plugin_@PLUGIN_ID@" version="@TOOL_VERSION@+galaxy1"> | |
3 <description>plugin Color shared chromosomal segments, requires phased GTs</description> | |
4 <macros> | |
5 <token name="@EXECUTABLE@">color-chrs</token> | |
6 <token name="@PLUGIN_ID@">color_chrs</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 @PREPARE_REGIONS_FILE@ | |
17 | |
18 bcftools plugin @EXECUTABLE@ | |
19 | |
20 ## VCF input section | |
21 #set $section = $sec_restrict | |
22 @REGIONS@ | |
23 @TARGETS@ | |
24 @INCLUDE@ | |
25 @EXCLUDE@ | |
26 | |
27 @THREADS@ | |
28 | |
29 ## Primary Input/Outputs | |
30 @INPUT_FILE@ | |
31 | |
32 ## Plugin options | |
33 #if $sample_relation.sample_rel_sel == 'trio': | |
34 -- --trio '${sample_relation.mother},${sample_relation.father},${sample_relation.child}' | |
35 #else: | |
36 -- --unrelated '${sample_relation.sample_a},${sample_relation.sample_b}' | |
37 #end if | |
38 -p output_tmp | |
39 && color-chrs.pl output_tmp.dat -p output_tmp | |
40 && mv output_tmp.dat '$output_data' | |
41 && mv output_tmp.svg '$output_svg' | |
42 ]]> | |
43 </command> | |
44 <inputs> | |
45 <expand macro="macro_input" /> | |
46 <conditional name="sample_relation"> | |
47 <param name="sample_rel_sel" type="select" label="Sample relationship"> | |
48 <option value="trio">trio - mother,father,child</option> | |
49 <option value="unrelated">unrelated sample pair</option> | |
50 </param> | |
51 <when value="trio"> | |
52 <param name="mother" type="text" value="" label="name of mother"/> | |
53 <param name="father" type="text" value="" label="name of father"/> | |
54 <param name="child" type="text" value="" label="name of child"/> | |
55 </when> | |
56 <when value="unrelated"> | |
57 <param name="sample_a" type="text" value="" label="name of sample A"/> | |
58 <param name="sample_b" type="text" value="" label="name of sample B"/> | |
59 </when> | |
60 </conditional> | |
61 <section name="sec_restrict" expanded="false" title="Restrict analysis to"> | |
62 <expand macro="macro_include" /> | |
63 <expand macro="macro_exclude" /> | |
64 <expand macro="macro_restrict" /> | |
65 <expand macro="macro_restrict" type="target" label_type="Target" /> | |
66 </section> | |
67 </inputs> | |
68 <outputs> | |
69 <data name="output_data" format="tabular" /> | |
70 <data name="output_svg" format="svg" /> | |
71 </outputs> | |
72 <tests> | |
73 <test expect_num_outputs="2"> | |
74 <param name="input_file" ftype="vcf" value="stats.a.vcf" /> | |
75 <conditional name="sample_relation"> | |
76 <param name="sample_rel_sel" value="trio" /> | |
77 <param name="mother" value="A" /> | |
78 <param name="father" value="C" /> | |
79 <param name="child" value="B" /> | |
80 </conditional> | |
81 <output name="output_data" ftype="tabular" file="color_chrs.dat" /> | |
82 </test> | |
83 <test expect_num_outputs="2"> | |
84 <param name="input_file" ftype="vcf" value="stats.a.vcf" /> | |
85 <conditional name="sample_relation"> | |
86 <param name="sample_rel_sel" value="unrelated" /> | |
87 <param name="sample_a" value="A" /> | |
88 <param name="sample_b" value="B" /> | |
89 </conditional> | |
90 <output name="output_data" ftype="tabular" file="color_chrs_unrelated.dat" /> | |
91 </test> | |
92 </tests> | |
93 <help><![CDATA[ | |
94 ===================================== | |
95 bcftools @EXECUTABLE@ plugin | |
96 ===================================== | |
97 | |
98 @REGIONS_HELP@ | |
99 @TARGETS_HELP@ | |
100 @EXPRESSIONS_HELP@ | |
101 | |
102 ]]> | |
103 </help> | |
104 <expand macro="citations" /> | |
105 </tool> |