Mercurial > repos > iuc > stacks_denovomap
changeset 12:fdbcc560c691 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 22:03:44 +0000 |
| parents | 9f9d39f582f3 |
| children | |
| files | macros.xml stacks_denovomap.xml |
| diffstat | 2 files changed, 17 insertions(+), 26 deletions(-) [+] |
line wrap: on
line diff
--- a/macros.xml Tue Mar 22 23:14:27 2022 +0000 +++ b/macros.xml Fri Apr 07 22:03:44 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_denovomap.xml Tue Mar 22 23:14:27 2022 +0000 +++ b/stacks_denovomap.xml Fri Apr 07 22:03:44 2023 +0000 @@ -1,9 +1,9 @@ <tool id="stacks_denovomap" name="Stacks: de novo map" version="@WRAPPER_VERSION@.0"> <description>the Stacks pipeline without a reference genome (denovo_map.pl)</description> - <expand macro="bio_tools"/> <macros> <import>macros.xml</import> </macros> + <expand macro="bio_tools"/> <expand macro="requirements"/> <expand macro="stdio"/> <command><![CDATA[ @@ -173,14 +173,13 @@ <!-- stack assembly options --> <section name="assembly_options" title="Assembly options" expanded="false"> - <param name="m" argument="-m" type="integer" value="" optional="true" label="Minimum number of identical raw reads required to create a stack" /> - <param name="P" argument="-P" type="integer" value="" optional="true" label="Minimum number of identical, raw reads required to create a stack in 'progeny' individuals" /> - <param name="M" argument="-M" type="integer" value="2" label="Number of mismatches allowed between loci when processing a single individual"/> - <param name="N" argument="-N" type="integer" value="" optional="true" label="Number of mismatches allowed when aligning secondary reads" help="default is [-M]+2" /> - <param name="n" argument="-n" type="integer" value="1" label="Number of mismatches allowed between loci when building the catalog"/> - - <param name="t" argument="-t" type="boolean" checked="false" truevalue="-t" falsevalue="" label="Remove, or break up, highly repetitive RAD-Tags in the ustacks program" /> - <param name="H" argument="-H" type="boolean" checked="false" truevalue="-H" falsevalue="" label="Disable calling haplotypes from secondary reads" /> + <param argument="-m" type="integer" value="" optional="true" label="Minimum number of identical raw reads required to create a stack" /> + <param argument="-P" type="integer" value="" optional="true" label="Minimum number of identical, raw reads required to create a stack in 'progeny' individuals" /> + <param argument="-M" type="integer" value="2" label="Number of mismatches allowed between loci when processing a single individual"/> + <param argument="-N" type="integer" value="" optional="true" label="Number of mismatches allowed when aligning secondary reads" help="default is [-M]+2" /> + <param argument="-n" type="integer" value="1" label="Number of mismatches allowed between loci when building the catalog"/> + <param argument="-t" type="boolean" checked="false" truevalue="-t" falsevalue="" label="Remove, or break up, highly repetitive RAD-Tags in the ustacks program" /> + <param argument="-H" type="boolean" checked="false" truevalue="-H" falsevalue="" label="Disable calling haplotypes from secondary reads" /> </section> <!-- SNP Model options --> @@ -190,32 +189,24 @@ </inputs> <outputs> <data format="txt" name="output_log" label="denovo_map.log with ${tool.name} on ${on_string}" from_work_dir="stacks_outputs/denovo_map.log" /> - <data format="html" name="output_summary" label="Summary from ${tool.name} on ${on_string}" from_work_dir="stacks_outputs/summary.html" /> - <data format="tabular" name="catalogtags" label="Catalog assembled loci (tags) with ${tool.name} on ${on_string}" from_work_dir="stacks_outputs/batch_1.catalog.tags.tsv" /> <data format="tabular" name="catalogsnps" label="Catalog model calls (snps) with ${tool.name} on ${on_string}" from_work_dir="stacks_outputs/batch_1.catalog.snps.tsv" /> <data format="tabular" name="catalogalleles" label="Catalog haplotypes (alleles) with ${tool.name} on ${on_string}" from_work_dir="stacks_outputs/batch_1.catalog.alleles.tsv" /> - <expand macro="genotypes_output_light"/> <expand macro="populations_output_light"/> - <collection name="tags" type="list" label="Assembled loci from ${on_string}"> <discover_datasets pattern="(?P<name>.+\.tags)\.tsv$" ext="tabular" directory="stacks_outputs" /> </collection> - <collection name="snps" type="list" label="Model calls from each locus on ${on_string}"> <discover_datasets pattern="(?P<name>.+\.snps)\.tsv$" ext="tabular" directory="stacks_outputs" /> </collection> - <collection name="alleles" type="list" label="Haplotypes/alleles recorded from each locus on ${on_string}"> <discover_datasets pattern="(?P<name>.+\.alleles)\.tsv$" ext="tabular" directory="stacks_outputs" /> </collection> - <collection name="matches" type="list" label="Matches to the catalog on ${on_string}"> <discover_datasets pattern="(?P<name>.+\.matches)\.tsv$" ext="tabular" directory="stacks_outputs" /> </collection> - <collection name="all_output" type="list" label="Full output from denovo_map on ${on_string}"> <discover_datasets pattern="(?P<name>.+\.(tags|snps|alleles|matches))\.tsv$" ext="tabular" directory="stacks_outputs" /> <discover_datasets pattern="(?P<name>.+\.(haplotypes|genotypes|markers|hapstats|sumstats|sumstats_summary))\.tsv$" ext="tabular" directory="stacks_outputs" />