Mercurial > repos > iuc > stacks_sstacks
changeset 12:96de7538bf0c draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 74ee33c6e30744a6da8deb7116d431d80ee80edb
| author | iuc |
|---|---|
| date | Fri, 07 Apr 2023 22:05:37 +0000 |
| parents | 563af4497055 |
| children | |
| files | macros.xml stacks_sstacks.xml |
| diffstat | 2 files changed, 19 insertions(+), 14 deletions(-) [+] |
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--- a/macros.xml Tue Mar 22 23:15:15 2022 +0000 +++ b/macros.xml Fri Apr 07 22:05:37 2023 +0000 @@ -343,7 +343,7 @@ <option value="fixed">Fixed</option> </param> <when value="snp"> - <param name="alpha" argument="--alpha" type="select" label="Chi square significance level required to call a heterozygote or homozygote" > + <param argument="--alpha" type="select" label="Chi square significance level required to call a heterozygote or homozygote" > <option value="0.1">0.1</option> <option value="0.05" selected="True">0.05</option> <option value="0.01">0.01</option> @@ -351,9 +351,9 @@ </param> </when> <when value="bounded"> - <param name="bound_low" argument="--bound_low" type="float" value="0.0" min="0.0" max="1.0" label="lower bound for epsilon, the error rate" help="between 0 and 1.0"/> - <param name="bound_high" argument="--bound_high" type="float" value="1.0" min="0.0" max="1.0" label="upper bound for epsilon, the error rate" help="between 0 and 1.0" /> - <param name="alpha" argument="--alpha" type="select" label="Chi square significance level required to call a heterozygote or homozygote" > + <param argument="--bound_low" type="float" value="0.0" min="0.0" max="1.0" label="lower bound for epsilon, the error rate" help="between 0 and 1.0"/> + <param argument="--bound_high" type="float" value="1.0" min="0.0" max="1.0" label="upper bound for epsilon, the error rate" help="between 0 and 1.0" /> + <param argument="--alpha" type="select" label="Chi square significance level required to call a heterozygote or homozygote" > <option value="0.1">0.1</option> <option value="0.05" selected="True">0.05</option> <option value="0.01">0.01</option> @@ -373,7 +373,7 @@ <option value="fixed">Fixed</option> </param> <when value="snp"> - <param name="alpha" argument="--alpha" type="select" label="Chi square significance level required to call a heterozygote or homozygote" > + <param argument="--alpha" type="select" label="Chi square significance level required to call a heterozygote or homozygote" > <option value="0.1">0.1</option> <option value="0.05" selected="True">0.05</option> <option value="0.01">0.01</option> @@ -381,9 +381,9 @@ </param> </when> <when value="bounded"> - <param name="bound_low" argument="--bound_low" type="float" value="0.0" min="0.0" max="1.0" label="lower bound for epsilon, the error rate" help="between 0 and 1.0"/> - <param name="bound_high" argument="--bound_high" type="float" value="1.0" min="0.0" max="1.0" label="upper bound for epsilon, the error rate" help="between 0 and 1.0" /> - <param name="alpha" argument="--alpha" type="select" label="Chi square significance level required to call a heterozygote or homozygote" > + <param argument="--bound_low" type="float" value="0.0" min="0.0" max="1.0" label="lower bound for epsilon, the error rate" help="between 0 and 1.0"/> + <param argument="--bound_high" type="float" value="1.0" min="0.0" max="1.0" label="upper bound for epsilon, the error rate" help="between 0 and 1.0" /> + <param argument="--alpha" type="select" label="Chi square significance level required to call a heterozygote or homozygote" > <option value="0.1">0.1</option> <option value="0.05" selected="True">0.05</option> <option value="0.01">0.01</option> @@ -391,7 +391,7 @@ </param> </when> <when value="fixed"> - <param name="bc_err_freq" argument="--bc_err_freq" type="float" value="0.1" min="0.0" max="1.0" label="Barcode error frequency" help="between 0 and 1.0"/> + <param argument="--bc_err_freq" type="float" value="0.1" min="0.0" max="1.0" label="Barcode error frequency" help="between 0 and 1.0"/> </when> </conditional> </xml>
--- a/stacks_sstacks.xml Tue Mar 22 23:15:15 2022 +0000 +++ b/stacks_sstacks.xml Fri Apr 07 22:05:37 2023 +0000 @@ -1,9 +1,9 @@ -<tool id="stacks_sstacks" name="Stacks: sstacks" version="@WRAPPER_VERSION@.0"> +<tool id="stacks_sstacks" name="Stacks: sstacks" version="@WRAPPER_VERSION@.1"> <description>match stacks to a catalog</description> - <expand macro="bio_tools"/> <macros> <import>macros.xml</import> </macros> + <expand macro="bio_tools"/> <expand macro="requirements"/> <expand macro="stdio"/> <command><![CDATA[ @@ -35,7 +35,12 @@ #set $filename = $filename + ".tsv" #end if #if not re.search('catalog\.[a-z]+(\.tsv)?$', $filename) - ln -s '${input_file}' 'stacks_inputs/$filename' && + ## When using a popmap, stacks write to the input dir (see also below) + #if $popmap + cp '${input_file}' 'stacks_inputs/$filename' && + #else + ln -s '${input_file}' 'stacks_inputs/$filename' && + #end if #if $filename.endswith('.tags.tsv') #set samples += " -s 'stacks_inputs/"+$filename[:-9] + "'" @@ -82,11 +87,11 @@ <param name="popmap" type="data" format="tabular,txt" label="Population map" help="If set, matching will be done only for samples listed in this file" optional="true" argument="-M" /> - <param name="g" argument="-g" type="boolean" checked="false" truevalue="-g" falsevalue="" label="Base catalog matching on genomic location, not sequence identity" /> + <param argument="-g" type="boolean" checked="false" truevalue="-g" falsevalue="" label="Base catalog matching on genomic location, not sequence identity" /> <param name="check_haplo" argument="-x" type="boolean" checked="false" truevalue="-x" falsevalue="" label="Don't verify haplotype of matching locus" /> - <param name="gapped" argument="--gapped" type="boolean" checked="false" truevalue="--gapped" falsevalue="" label="Perform gapped alignments between stacks" /> + <param argument="--gapped" type="boolean" checked="false" truevalue="--gapped" falsevalue="" label="Perform gapped alignments between stacks" /> </inputs> <outputs>