comparison stacks_refmap.xml @ 12:d7a482f44e08 draft default tip

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

11:1ba1185929c1

<tool id="stacks_refmap" name="Stacks: reference map" version="@WRAPPER_VERSION@.0">
    <description>the Stacks pipeline with a reference genome (ref_map.pl)</description>
    <expand macro="bio_tools"/>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements"/>
    <expand macro="stdio"/>
    <command><![CDATA[

        @CLEAN_EXT@

                <param name="individual_sample" format="sam,bam" type="data" multiple="true" label="Files containing an individual sample from a population" argument="-s" help="Dataset names will be used as sample name (no space allowed)." />
                <param name="popmap" type="data" format="tabular,txt" label="Specify a population map" argument="-O" />
            </when>
        </conditional>

        <param name="m" type="integer" value="3" label="Minimum depth of coverage" help="specify the minimum depth of coverage to report a stack in pstacks" argument="-m" />
        <param name="P" type="integer" value="" optional="true" label="Minimum depth of coverage in 'progeny' individuals" help="specify the minimum depth of coverage to report a stack in pstacks for 'progeny' individuals" argument="-P" />

        <!-- SNP Model options -->
        <section name="snp_options" title="SNP_Model_Options" expanded="False">
            <expand macro="snp_options"/>
        </section>

12:d7a482f44e08

<tool id="stacks_refmap" name="Stacks: reference map" version="@WRAPPER_VERSION@.0">
    <description>the Stacks pipeline with a reference genome (ref_map.pl)</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="bio_tools"/>
    <expand macro="requirements"/>
    <expand macro="stdio"/>
    <command><![CDATA[

        @CLEAN_EXT@

                <param name="individual_sample" format="sam,bam" type="data" multiple="true" label="Files containing an individual sample from a population" argument="-s" help="Dataset names will be used as sample name (no space allowed)." />
                <param name="popmap" type="data" format="tabular,txt" label="Specify a population map" argument="-O" />
            </when>
        </conditional>

        <param argument="-m" type="integer" value="3" label="Minimum depth of coverage" help="specify the minimum depth of coverage to report a stack in pstacks" />
        <param argument="-P" type="integer" value="" optional="true" label="Minimum depth of coverage in 'progeny' individuals" help="specify the minimum depth of coverage to report a stack in pstacks for 'progeny' individuals" />

        <!-- SNP Model options -->
        <section name="snp_options" title="SNP_Model_Options" expanded="False">
            <expand macro="snp_options"/>
        </section>