comparison stacks_genotypes.xml @ 10:7a4de48964b6 draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 74ee33c6e30744a6da8deb7116d431d80ee80edb

9:d9a98a979632

<tool id="stacks_genotypes" name="Stacks: genotypes" version="@WRAPPER_VERSION@.0">
    <description>analyse haplotypes or genotypes in a genetic cross ('genotypes' program)</description>
    <expand macro="bio_tools"/>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements"/>
    <expand macro="stdio"/>
    <command><![CDATA[
        #import re

            #if $advanced_options.manual_cor
                --corr_path '$advanced_options.manual_cor'
            #end if

            #if $options_autocorr.corrections
                -c
                --min_hom_seqs $options_autocorr.hom
                --min_het_seqs $options_autocorr.het
                --max_het_seqs $options_autocorr.hetmax
            #end if

                </when>
            </conditional>
        </section>

        <conditional name="options_autocorr">
            <param name="corrections" argument="-c" type="boolean" checked="true" truevalue="-c" falsevalue="" label="Make automated corrections to the data" />
            <when value="-c">
                <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" />
                <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" />
                <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" />
            </when>

10:7a4de48964b6

<tool id="stacks_genotypes" name="Stacks: genotypes" version="@WRAPPER_VERSION@.0">
    <description>analyse haplotypes or genotypes in a genetic cross ('genotypes' program)</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="bio_tools"/>
    <expand macro="requirements"/>
    <expand macro="stdio"/>
    <command><![CDATA[
        #import re

            #if $advanced_options.manual_cor
                --corr_path '$advanced_options.manual_cor'
            #end if

            #if $options_autocorr.corrections != ""
                -c
                --min_hom_seqs $options_autocorr.hom
                --min_het_seqs $options_autocorr.het
                --max_het_seqs $options_autocorr.hetmax
            #end if

                </when>
            </conditional>
        </section>

        <conditional name="options_autocorr">
            <param name="corrections" argument="-c" type="select" label="Make automated corrections to the data">
                <option value="-c" selected="true">Yes</option>
                <option value="">No</option>
            </param>
            <when value="-c">
                <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" />
                <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" />
                <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" />
            </when>