| Previous changeset 11:3e43e51b3c3b (2022-03-22) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 74ee33c6e30744a6da8deb7116d431d80ee80edb |
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modified:
macros.xml stacks_rxstacks.xml |
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| diff -r 3e43e51b3c3b -r 8479d9a67998 macros.xml --- a/macros.xml Tue Mar 22 23:22:43 2022 +0000 +++ b/macros.xml Fri Apr 07 22:03:16 2023 +0000 |
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| @@ -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> |
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| diff -r 3e43e51b3c3b -r 8479d9a67998 stacks_rxstacks.xml --- a/stacks_rxstacks.xml Tue Mar 22 23:22:43 2022 +0000 +++ b/stacks_rxstacks.xml Fri Apr 07 22:03:16 2023 +0000 |
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| @@ -1,9 +1,9 @@ <tool id="stacks_rxstacks" name="Stacks: rxstacks" version="@WRAPPER_VERSION@.0"> <description>make corrections to genotype and haplotype calls</description> - <expand macro="bio_tools"/> <macros> <import>macros.xml</import> </macros> + <expand macro="bio_tools"/> <expand macro="requirements"/> <expand macro="stdio"/> <command><![CDATA[ @@ -69,18 +69,18 @@ <section name="options_filtering" title="Data filtering options" expanded="true"> <param name="lnl" type="float" value="" optional="true" argument="--lnl_lim" label="Filter loci with log likelihood values below this threshold" /> - <param name="lnl_dist" argument="--lnl_dist" truevalue="--lnl_dist" falsevalue="" type="boolean" checked="false" label="Print distribution of mean log likelihoods for catalog loci." /> + <param argument="--lnl_dist" truevalue="--lnl_dist" falsevalue="" type="boolean" checked="false" label="Print distribution of mean log likelihoods for catalog loci." /> <param name="conf" type="float" value="0.75" optional="true" argument="--conf_lim" min="0.0" max="1.0" label="Proportion of loci in population that must be confounded relative to the catalog locus (between 0.0 and 1.0)."/> <conditional name="prune"> - <param name="prune_haplo" argument="--prune_haplo" type="select" label="Prune out non-biological haplotypes unlikely to occur in the population."> + <param argument="--prune_haplo" type="select" label="Prune out non-biological haplotypes unlikely to occur in the population."> <option value="no" selected="true">No</option> <option value="yes">Yes</option> </param> <when value="no"/> <when value="yes"> - <param name="max_haplo" argument="--max_haplo" type="integer" value="" optional="true" label="Only consider haplotypes for pruning if they occur in fewer than this value."/> + <param argument="--max_haplo" type="integer" value="" optional="true" label="Only consider haplotypes for pruning if they occur in fewer than this value."/> </when> </conditional> </section> |