Mercurial > repos > iuc > bcftools_plugin_fill_an_ac
comparison bcftools_plugin_fill_an_ac.xml @ 0:7dfc3bbbe973 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 07:05:33 -0400 |
parents | |
children | 0124b2fa5f59 |
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-1:000000000000 | 0:7dfc3bbbe973 |
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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 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> |