comparison stacks_rxstacks.xml @ 12:8479d9a67998 draft default tip

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

11:3e43e51b3c3b

<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="requirements"/>
    <expand macro="stdio"/>
    <command><![CDATA[

        mkdir stacks_inputs stacks_outputs

    <inputs>
        <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)" />

        <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 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.">
                    <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."/>
                </when>
            </conditional>
        </section>

        <!-- SNP Model options -->

12:8479d9a67998

<tool id="stacks_rxstacks" name="Stacks: rxstacks" version="@WRAPPER_VERSION@.0">
    <description>make corrections to genotype and haplotype calls</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="bio_tools"/>
    <expand macro="requirements"/>
    <expand macro="stdio"/>
    <command><![CDATA[

        mkdir stacks_inputs stacks_outputs

    <inputs>
        <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)" />

        <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 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 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 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>

        <!-- SNP Model options -->