comparison stacks_refmap.xml @ 2:39ebc7633942 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 8b047549e9e8791a5ca9424b1ef391e8980aba79-dirty

1:a8d93e132d3b

<tool id="stacks2_refmap" name="Stacks2: reference map" version="@WRAPPER_VERSION@">
    <description>the Stacks pipeline with a reference genome (ref_map.pl)</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements"/>

            <param name="add_log" value="yes" />
            <output ftype="txt" name="output_log"><assert_contents><has_text text="ref_map.pl is done." /></assert_contents></output>
            <!-- TODO test for outputs -->
        </test>
        <test>
            <param name="input_type|input_type_selector" value="manual"/>
            <param name="input_type|input_bam" value="refmap/PopA_01.bam,refmap/PopA_02.bam"/>
            <param name="popmap" ftype="tabular" value="denovo_map/popmap_cstacks.tsv" />
            <param name="paired_select" value="--unpaired"/>
            <param name="model_options|var_alpha" value="0.1" />
            <param name="model_options|gt_alpha" value="0.1" />
            <assert_command>

2:39ebc7633942

<tool id="stacks2_refmap" name="Stacks2: reference map" version="@STACKS_VERSION@+galaxy@WRAPPER_VERSION@">
    <description>the Stacks pipeline with a reference genome (ref_map.pl)</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements"/>

            <param name="add_log" value="yes" />
            <output ftype="txt" name="output_log"><assert_contents><has_text text="ref_map.pl is done." /></assert_contents></output>
            <!-- TODO test for outputs -->
        </test>
        <test>
            <param name="input_bam" value="refmap/PopA_01.bam,refmap/PopA_02.bam"/>
            <param name="popmap" ftype="tabular" value="denovo_map/popmap_cstacks.tsv" />
            <param name="paired_select" value="--unpaired"/>
            <param name="model_options|var_alpha" value="0.1" />
            <param name="model_options|gt_alpha" value="0.1" />
            <assert_command>