Mercurial > repos > iuc > bcftools_plugin_fill_tags
comparison bcftools_plugin_fill_tags.xml @ 0:d7cba58e3b72 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
author | iuc |
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date | Wed, 06 Jul 2016 07:05:50 -0400 |
parents | |
children | b365f9164cdf |
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-1:000000000000 | 0:d7cba58e3b72 |
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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 INFO tags AF, AN, AC, AC_Hom, AC_Het, AC_Hemi</description> | |
4 <macros> | |
5 <token name="@EXECUTABLE@">fill-tags</token> | |
6 <token name="@PLUGIN_ID@">fill_tags</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 #set $section = $sec_plugin | |
33 #if $section.tags: | |
34 -- --tags "${section.tags}" | |
35 #end if | |
36 > "$output_file" | |
37 ]]> | |
38 </command> | |
39 <inputs> | |
40 <expand macro="macro_input" /> | |
41 <section name="sec_restrict" expanded="false" title="Restrict to"> | |
42 <expand macro="macro_regions" /> | |
43 <expand macro="macro_targets" /> | |
44 <expand macro="macro_include" /> | |
45 <expand macro="macro_exclude" /> | |
46 </section> | |
47 <section name="sec_plugin" expanded="true" title="Plugin Options"> | |
48 <param name="tags" type="select" multiple="true" label="TAGs to set"> | |
49 <option value="AF">AF</option> | |
50 <option value="AN">AN</option> | |
51 <option value="AC">AC</option> | |
52 <option value="AC_Hom">AC_Hom</option> | |
53 <option value="AC_Het">AC_Het</option> | |
54 <option value="AC_Hemi">AC_Hemi</option> | |
55 </param> | |
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="plugin1.vcf" /> | |
65 <param name="output_type" value="v" /> | |
66 <output name="output_file"> | |
67 <assert_contents> | |
68 <has_text text="AN=0" /> | |
69 <has_text text="AC=0" /> | |
70 <has_text text="AC_Het=0" /> | |
71 <has_text text="AC_Hom=0" /> | |
72 <has_text text="AC_Hemi=0" /> | |
73 </assert_contents> | |
74 </output> | |
75 </test> | |
76 <test> | |
77 <param name="input_file" ftype="vcf" value="plugin1.vcf" /> | |
78 <param name="output_type" value="v" /> | |
79 <param name="tags" value="AC_Het,AC_Hom" /> | |
80 <output name="output_file"> | |
81 <assert_contents> | |
82 <has_text text="AC_Het=0" /> | |
83 <has_text text="AC_Hom=0" /> | |
84 <not_has_text text="AC_Hemi=0" /> | |
85 </assert_contents> | |
86 </output> | |
87 </test> | |
88 | |
89 </tests> | |
90 | |
91 <help><![CDATA[ | |
92 ===================================== | |
93 bcftools @EXECUTABLE@ plugin | |
94 ===================================== | |
95 | |
96 @REGIONS_HELP@ | |
97 @TARGETS_HELP@ | |
98 @EXPRESSIONS_HELP@ | |
99 | |
100 ]]></help> | |
101 <expand macro="citations" /> | |
102 </tool> |