comparison stacks_pstacks.xml @ 12:a9ff3d0184b8 draft default tip

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

11:67cbd80b83f5

<tool id="stacks_pstacks" name="Stacks: pstacks" version="@WRAPPER_VERSION@.0">
    <description>find stacks from short reads mapped to a reference genome</description>
    <expand macro="bio_tools"/>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements"/>
    <expand macro="stdio"/>
    <command><![CDATA[

        @CLEAN_EXT@

            stacks_summary.py --stacks-prog pstacks --res-dir stacks_outputs --logfile pstacks.log --summary stacks_outputs/summary.html
    ]]></command>

    <inputs>
        <param name="sample" argument="-f" format="sam,bam" type="data" label="Input short reads from an individual" />

        <param name="sample_id" argument="-i" type="integer" value="" label="Give a unique numeric ID to this sample"/>

        <param name="m" argument="-m" type="integer" value="1" label="Minimum depth of coverage required to create a stack"/>

        <param name="max_clipped" argument="--max_clipped" type="float" value="0.15" min="0.0" max="1.0" label="Alignments with more than this fraction of soft-clipped bases are discarded"/>

        <param name="min_mapq" argument="--min_mapq" type="integer" value="10" label="Minimum required mapping quality"/>

        <param name="keep_sec_alns" argument="--keep_sec_alns" type="boolean" checked="false" truevalue="--keep_sec_alns" falsevalue="" label="Keep secondary alignments" />

        <!-- SNP Model options -->
        <section name="snp_options" title="SNP Model Options (pstacks options)" expanded="False">
            <expand macro="snp_options_full"/>
        </section>
    </inputs>

    <outputs>
        <data format="txt" name="output_log" label="pstacks.log with ${tool.name} on ${on_string}" from_work_dir="pstacks.log" />

        <data format="html" name="output_summary" label="Summary from ${tool.name} on ${on_string}" from_work_dir="stacks_outputs/summary.html" />

        <collection name="tabs" type="list" label="Stacks from ${on_string}">
            <discover_datasets pattern="(?P&lt;name&gt;.+\.tags)\.tsv$" ext="tabular" directory="stacks_outputs" />
            <discover_datasets pattern="(?P&lt;name&gt;.+\.snps)\.tsv$" ext="tabular" directory="stacks_outputs" />
            <discover_datasets pattern="(?P&lt;name&gt;.+\.alleles)\.tsv$" ext="tabular" directory="stacks_outputs" />
            <discover_datasets pattern="(?P&lt;name&gt;.+\.models)\.tsv$" ext="tabular" directory="stacks_outputs" />

12:a9ff3d0184b8

<tool id="stacks_pstacks" name="Stacks: pstacks" version="@WRAPPER_VERSION@.0">
    <description>find stacks from short reads mapped to a reference genome</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="bio_tools"/>
    <expand macro="requirements"/>
    <expand macro="stdio"/>
    <command><![CDATA[

        @CLEAN_EXT@

            stacks_summary.py --stacks-prog pstacks --res-dir stacks_outputs --logfile pstacks.log --summary stacks_outputs/summary.html
    ]]></command>

    <inputs>
        <param name="sample" argument="-f" format="sam,bam" type="data" label="Input short reads from an individual" />
        <param name="sample_id" argument="-i" type="integer" value="" label="Give a unique numeric ID to this sample"/>
        <param argument="-m" type="integer" value="1" label="Minimum depth of coverage required to create a stack"/>
        <param argument="--max_clipped" type="float" value="0.15" min="0.0" max="1.0" label="Alignments with more than this fraction of soft-clipped bases are discarded"/>
        <param argument="--min_mapq" type="integer" value="10" label="Minimum required mapping quality"/>
        <param argument="--keep_sec_alns" type="boolean" checked="false" truevalue="--keep_sec_alns" falsevalue="" label="Keep secondary alignments" />
        <!-- SNP Model options -->
        <section name="snp_options" title="SNP Model Options (pstacks options)" expanded="False">
            <expand macro="snp_options_full"/>
        </section>
    </inputs>

    <outputs>
        <data format="txt" name="output_log" label="pstacks.log with ${tool.name} on ${on_string}" from_work_dir="pstacks.log" />
        <data format="html" name="output_summary" label="Summary from ${tool.name} on ${on_string}" from_work_dir="stacks_outputs/summary.html" />
        <collection name="tabs" type="list" label="Stacks from ${on_string}">
            <discover_datasets pattern="(?P&lt;name&gt;.+\.tags)\.tsv$" ext="tabular" directory="stacks_outputs" />
            <discover_datasets pattern="(?P&lt;name&gt;.+\.snps)\.tsv$" ext="tabular" directory="stacks_outputs" />
            <discover_datasets pattern="(?P&lt;name&gt;.+\.alleles)\.tsv$" ext="tabular" directory="stacks_outputs" />
            <discover_datasets pattern="(?P&lt;name&gt;.+\.models)\.tsv$" ext="tabular" directory="stacks_outputs" />