Mercurial > repos > iuc > stacks_rxstacks

comparison stacks_rxstacks.xml @ 12:8479d9a67998 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 22:03:16 +0000
parents 3e43e51b3c3b
children
comparison
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11:3e43e51b3c3b 12:8479d9a67998
1 <tool id="stacks_rxstacks" name="Stacks: rxstacks" version="@WRAPPER_VERSION@.0"> 1 <tool id="stacks_rxstacks" name="Stacks: rxstacks" version="@WRAPPER_VERSION@.0">
2 <description>make corrections to genotype and haplotype calls</description> 2 <description>make corrections to genotype and haplotype calls</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 10
11 mkdir stacks_inputs stacks_outputs 11 mkdir stacks_inputs stacks_outputs
67 <inputs> 67 <inputs>
68 <param name="input_col" format="tabular,txt" type="data_collection" collection_type="list" label="Output from previous Stacks pipeline steps (e.g. denovo_map or refmap)" /> 68 <param name="input_col" format="tabular,txt" type="data_collection" collection_type="list" label="Output from previous Stacks pipeline steps (e.g. denovo_map or refmap)" />
69 69
70 <section name="options_filtering" title="Data filtering options" expanded="true"> 70 <section name="options_filtering" title="Data filtering options" expanded="true">
71 <param name="lnl" type="float" value="" optional="true" argument="--lnl_lim" label="Filter loci with log likelihood values below this threshold" /> 71 <param name="lnl" type="float" value="" optional="true" argument="--lnl_lim" label="Filter loci with log likelihood values below this threshold" />
72 <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." /> 72 <param argument="--lnl_dist" truevalue="--lnl_dist" falsevalue="" type="boolean" checked="false" label="Print distribution of mean log likelihoods for catalog loci." />
73 73
74 <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)."/> 74 <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)."/>
75 75
76 <conditional name="prune"> 76 <conditional name="prune">
77 <param name="prune_haplo" argument="--prune_haplo" type="select" label="Prune out non-biological haplotypes unlikely to occur in the population."> 77 <param argument="--prune_haplo" type="select" label="Prune out non-biological haplotypes unlikely to occur in the population.">
78 <option value="no" selected="true">No</option> 78 <option value="no" selected="true">No</option>
79 <option value="yes">Yes</option> 79 <option value="yes">Yes</option>
80 </param> 80 </param>
81 <when value="no"/> 81 <when value="no"/>
82 <when value="yes"> 82 <when value="yes">
83 <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."/> 83 <param argument="--max_haplo" type="integer" value="" optional="true" label="Only consider haplotypes for pruning if they occur in fewer than this value."/>
84 </when> 84 </when>
85 </conditional> 85 </conditional>
86 </section> 86 </section>
87 87
88 <!-- SNP Model options --> 88 <!-- SNP Model options -->