Mercurial > repos > iuc > bcftools_plugin_setgt
comparison bcftools_plugin_setgt.xml @ 16:40daf124be88 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit db275932cbb485cb44ae91e0b421d6f57698db49
author | iuc |
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date | Tue, 20 Sep 2022 13:03:05 +0000 |
parents | 99238dfb46cb |
children | a1aad8b559c6 |
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15:2c4941386820 | 16:40daf124be88 |
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1 <?xml version='1.0' encoding='utf-8'?> | 1 <?xml version='1.0' encoding='utf-8'?> |
2 <tool name="bcftools @EXECUTABLE@" id="bcftools_plugin_@PLUGIN_ID@" version="@TOOL_VERSION@"> | 2 <tool name="bcftools @EXECUTABLE@" id="bcftools_plugin_@PLUGIN_ID@" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@"> |
3 <description>plugin Sets genotypes</description> | 3 <description>plugin Sets genotypes</description> |
4 <macros> | 4 <macros> |
5 <token name="@EXECUTABLE@">setGT</token> | 5 <token name="@EXECUTABLE@">setGT</token> |
6 <token name="@PLUGIN_ID@">setgt</token> | 6 <token name="@PLUGIN_ID@">setgt</token> |
7 <import>macros.xml</import> | 7 <import>macros.xml</import> |
31 @INPUT_FILE@ | 31 @INPUT_FILE@ |
32 | 32 |
33 ## Plugin section | 33 ## Plugin section |
34 #set $section = $sec_plugin | 34 #set $section = $sec_plugin |
35 -- | 35 -- |
36 -t '$section.target_gt' | 36 --target-gt '$section.target_gt' |
37 --new-gt '$section.new_gt' | 37 --new-gt '$section.new_gt' |
38 > '$output_file' | 38 > '$output_file' |
39 ]]> | 39 ]]> |
40 </command> | 40 </command> |
41 <inputs> | 41 <inputs> |
42 <expand macro="macro_input" /> | 42 <expand macro="macro_input" /> |
43 <section name="sec_restrict" expanded="false" title="Restrict to"> | 43 <section name="sec_restrict" title="Restrict to"> |
44 <expand macro="macro_restrict" /> | 44 <expand macro="macro_restrict" /> |
45 <expand macro="macro_restrict" type="target" label_type="Target" /> | 45 <expand macro="macro_restrict" type="target" label_type="Target" /> |
46 <expand macro="macro_include" /> | 46 <expand macro="macro_include" /> |
47 <expand macro="macro_exclude" /> | 47 <expand macro="macro_exclude" /> |
48 </section> | 48 </section> |
50 <param name="target_gt" type="select" label="Target genotypes to change"> | 50 <param name="target_gt" type="select" label="Target genotypes to change"> |
51 <option value="./.">./. completely missing (. or ./., depending on ploidy)</option> | 51 <option value="./.">./. completely missing (. or ./., depending on ploidy)</option> |
52 <option value="./x">./x partially missing (./0 or .|1)</option> | 52 <option value="./x">./x partially missing (./0 or .|1)</option> |
53 <option value=".">. partially or completely missing</option> | 53 <option value=".">. partially or completely missing</option> |
54 <option value="a">a all genotypes</option> | 54 <option value="a">a all genotypes</option> |
55 <option value="b">b heterozygous genotypes failing two-tailed binomial test</option> | |
56 <option value="q">q select genotypes using -i/-e options</option> | |
55 </param> | 57 </param> |
56 <param name="new_gt" type="select" label="New genotypes to set"> | 58 <param name="new_gt" type="select" label="New genotypes to set"> |
57 <option value=".">. missing (. or ./., keeps ploidy)</option> | 59 <option value=".">. missing (. or ./., keeps ploidy)</option> |
58 <option value="0">0 reference allele</option> | 60 <option value="0">0 reference allele (e.g. 0/0 or 0, keeps ploidy)</option> |
61 <option value="c:GT">c:GT custom genotype (e.g. 0/0, 0, 0/1, m/M, overrides ploidy)</option> | |
59 <option value="M">M major allele</option> | 62 <option value="M">M major allele</option> |
63 <option value="m">m minor (the second most common) allele (e.g. 1/1 or 1, keeps ploidy)</option> | |
60 <option value="p">p phased genotype</option> | 64 <option value="p">p phased genotype</option> |
61 <option value="u">u unphase genotype and sort by allele (1|0 becomes 0/1)</option> | 65 <option value="u">u unphase genotype and sort by allele (1|0 becomes 0/1)</option> |
62 </param> | 66 </param> |
63 </section> | 67 </section> |
64 <expand macro="macro_select_output_type" /> | 68 <expand macro="macro_select_output_type" /> |