comparison stacks_ustacks.xml @ 12:4cce81af50a8 draft default tip

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

11:a4ec4f620a77

<tool id="stacks_ustacks" name="Stacks: ustacks" version="@WRAPPER_VERSION@.0">
    <description>align short reads into stacks</description>
    <expand macro="bio_tools"/>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements"/>
    <expand macro="stdio"/>
    <command><![CDATA[

        @CLEAN_EXT@

    ]]></command>

    <inputs>
        <param name="sample" argument="-f" format="fastqsanger,fastqsanger.gz,fasta" type="data" label="Input short reads from an individual" />

        <param name="m" argument="-m" type="integer" value="2" label="Minimum depth of coverage required to create a stack"/>
        <param name="M" argument="-M" type="integer" value="2" label="Maximum distance (in nucleotides) allowed between stacks"/>
        <param name="R" argument="-R" type="boolean" checked="false" truevalue="-R" falsevalue="" label="Retain unused reads" />
        <param name="H" argument="-H" type="boolean" checked="false" truevalue="-H" falsevalue="" label="Disable calling haplotypes from secondary reads" />

        <section name="assembly_options" title="SNP Model Options (ustacks options)" expanded="True">
            <param name="keep_high_cov" argument="--keep_high_cov" type="boolean" checked="false" truevalue="--keep-high-cov" falsevalue="" label="Disable the algorithm that removes highly-repetitive stacks and nearby errors. " />
            <param name="d" argument="-d" type="boolean" checked="false" truevalue="-d" falsevalue="" label="Enable the Deleveraging algorithm, used for resolving over merged tags" />
            <param name="max_locus_stacks" argument="--max_locus_stacks" type="integer" value="3" label="Maximum number of stacks at a single de novo locus"/>
            <param name="k_len" argument="--k_len" type="integer" value="" optional="true" label="K-mer size for matching between alleles and loci (automatically calculated by default)"/>
        </section>

        <conditional name="gapped">
            <param name="use_gapped" argument="--gapped" type="select" label="Perform gapped alignments between stacks">
                <option value="no" selected="true">No</option>
                <option value="yes">Yes</option>
            </param>
            <when value="no"/>
            <when value="yes">
                <param name="max_gaps" argument="--max_gaps" type="integer" value="2" label="Number of gaps allowed between stacks before merging"/>
                <param name="min_aln_len" argument="--min_aln_len" type="float" value="0.8" min="0.0" max="1.0" label="Minimum length of aligned sequence in a gapped alignment"/>
            </when>
        </conditional>

        <!-- SNP Model options -->
        <section name="snp_options" title="SNP Model Options (ustacks options)" expanded="False">

12:4cce81af50a8

<tool id="stacks_ustacks" name="Stacks: ustacks" version="@WRAPPER_VERSION@.0">
    <description>align short reads into stacks</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="bio_tools"/>
    <expand macro="requirements"/>
    <expand macro="stdio"/>
    <command><![CDATA[

        @CLEAN_EXT@

    ]]></command>

    <inputs>
        <param name="sample" argument="-f" format="fastqsanger,fastqsanger.gz,fasta" type="data" label="Input short reads from an individual" />

        <param argument="-m" type="integer" value="2" label="Minimum depth of coverage required to create a stack"/>
        <param argument="-M" type="integer" value="2" label="Maximum distance (in nucleotides) allowed between stacks"/>
        <param argument="-R" type="boolean" checked="false" truevalue="-R" falsevalue="" label="Retain unused reads" />
        <param argument="-H" type="boolean" checked="false" truevalue="-H" falsevalue="" label="Disable calling haplotypes from secondary reads" />

        <section name="assembly_options" title="SNP Model Options (ustacks options)" expanded="True">
            <param argument="--keep_high_cov" type="boolean" checked="false" truevalue="--keep-high-cov" falsevalue="" label="Disable the algorithm that removes highly-repetitive stacks and nearby errors. " />
            <param argument="-d" type="boolean" checked="false" truevalue="-d" falsevalue="" label="Enable the Deleveraging algorithm, used for resolving over merged tags" />
            <param argument="--max_locus_stacks" type="integer" value="3" label="Maximum number of stacks at a single de novo locus"/>
            <param argument="--k_len" type="integer" value="" optional="true" label="K-mer size for matching between alleles and loci (automatically calculated by default)"/>
        </section>

        <conditional name="gapped">
            <param name="use_gapped" argument="--gapped" type="select" label="Perform gapped alignments between stacks">
                <option value="no" selected="true">No</option>
                <option value="yes">Yes</option>
            </param>
            <when value="no"/>
            <when value="yes">
                <param argument="--max_gaps" type="integer" value="2" label="Number of gaps allowed between stacks before merging"/>
                <param argument="--min_aln_len" type="float" value="0.8" min="0.0" max="1.0" label="Minimum length of aligned sequence in a gapped alignment"/>
            </when>
        </conditional>

        <!-- SNP Model options -->
        <section name="snp_options" title="SNP Model Options (ustacks options)" expanded="False">