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comparison stacks_genotypes.xml @ 12:62a4b8e5e139 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 74ee33c6e30744a6da8deb7116d431d80ee80edb
author iuc
date Fri, 07 Apr 2023 22:01:52 +0000
parents 46f061f3cfeb
children
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equal deleted inserted replaced
11:46f061f3cfeb 12:62a4b8e5e139
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>