Mercurial > repos > iuc > stacks_genotypes
comparison stacks_genotypes.xml @ 12:62a4b8e5e139 draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 74ee33c6e30744a6da8deb7116d431d80ee80edb
author | iuc |
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date | Fri, 07 Apr 2023 22:01:52 +0000 |
parents | 46f061f3cfeb |
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11:46f061f3cfeb | 12:62a4b8e5e139 |
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1 <tool id="stacks_genotypes" name="Stacks: genotypes" version="@WRAPPER_VERSION@.0"> | 1 <tool id="stacks_genotypes" name="Stacks: genotypes" version="@WRAPPER_VERSION@.0"> |
2 <description>analyse haplotypes or genotypes in a genetic cross ('genotypes' program)</description> | 2 <description>analyse haplotypes or genotypes in a genetic cross ('genotypes' program)</description> |
3 <expand macro="bio_tools"/> | |
4 <macros> | 3 <macros> |
5 <import>macros.xml</import> | 4 <import>macros.xml</import> |
6 </macros> | 5 </macros> |
6 <expand macro="bio_tools"/> | |
7 <expand macro="requirements"/> | 7 <expand macro="requirements"/> |
8 <expand macro="stdio"/> | 8 <expand macro="stdio"/> |
9 <command><![CDATA[ | 9 <command><![CDATA[ |
10 #import re | 10 #import re |
11 | 11 |
56 | 56 |
57 #if $advanced_options.manual_cor | 57 #if $advanced_options.manual_cor |
58 --corr_path '$advanced_options.manual_cor' | 58 --corr_path '$advanced_options.manual_cor' |
59 #end if | 59 #end if |
60 | 60 |
61 #if $options_autocorr.corrections | 61 #if $options_autocorr.corrections != "" |
62 -c | 62 -c |
63 --min_hom_seqs $options_autocorr.hom | 63 --min_hom_seqs $options_autocorr.hom |
64 --min_het_seqs $options_autocorr.het | 64 --min_het_seqs $options_autocorr.het |
65 --max_het_seqs $options_autocorr.hetmax | 65 --max_het_seqs $options_autocorr.hetmax |
66 #end if | 66 #end if |
100 </when> | 100 </when> |
101 </conditional> | 101 </conditional> |
102 </section> | 102 </section> |
103 | 103 |
104 <conditional name="options_autocorr"> | 104 <conditional name="options_autocorr"> |
105 <param name="corrections" argument="-c" type="boolean" checked="true" truevalue="-c" falsevalue="" label="Make automated corrections to the data" /> | 105 <param name="corrections" argument="-c" type="select" label="Make automated corrections to the data"> |
106 <option value="-c" selected="true">Yes</option> | |
107 <option value="">No</option> | |
108 </param> | |
106 <when value="-c"> | 109 <when value="-c"> |
107 <param name="hom" argument="--min_hom_seqs" type="integer" value="5" label="Minimum number of reads required at a stack to call a homozygous genotype" /> | 110 <param name="hom" argument="--min_hom_seqs" type="integer" value="5" label="Minimum number of reads required at a stack to call a homozygous genotype" /> |
108 <param name="het" argument="--min_het_seqs:" type="float" value="0.05" label="Heterozygote minor allele minimum frequency" help="below this minor allele frequency a stack is called a homozygote, above it (but below --max_het_seqs) it is called unknown" /> | 111 <param name="het" argument="--min_het_seqs:" type="float" value="0.05" label="Heterozygote minor allele minimum frequency" help="below this minor allele frequency a stack is called a homozygote, above it (but below --max_het_seqs) it is called unknown" /> |
109 <param name="hetmax" argument="--max_het_seqs:" type="float" value="0.1" label="Heterozygote minor allele maximum frequency" help="minimum frequency of minor allele to call a heterozygote" /> | 112 <param name="hetmax" argument="--max_het_seqs:" type="float" value="0.1" label="Heterozygote minor allele maximum frequency" help="minimum frequency of minor allele to call a heterozygote" /> |
110 </when> | 113 </when> |