comparison compare_categories.xml @ 5:21abe2afb7cf draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380

4:0bb58d2f80a3

<tool id="qiime_compare_categories" name="Analyzes statistical significance" version="@WRAPPER_VERSION@.0">
    <description>of sample groupings using distance matrices</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements">
        <requirement type="package" version="1.3.2">r-optparse</requirement>
        <requirement type="package" version="2.3_4">r-vegan</requirement>
        <requirement type="package" version="3.3">r-base</requirement>
    </expand>
    <version_command>compare_categories.py --version</version_command>
    <command detect_errors="aggressive"><![CDATA[
        compare_categories.py
            --method '$method'
            --input_dm '$input_dm'
            --mapping_file '$mapping_file'
            --categories '$categories'
            -o compare_categories
            #if $num_permutations
                --num_permutations '$num_permutations'
            #end if
        ]]></command>
    <inputs>
        <param argument="--method" label="Select the statistical method to use" type="select">
            <option value="adonis">adonis</option>
            <option value="anosim">anosim</option>
            <option value="bioenv">bioenv</option>
            <option value="morans_i">morans_i</option>
            <option value="mrpp">mrpp</option>

            <option value="dbrda">dbrda</option>
        </param>
        <param argument="--input_dm" type="data" format="txt,tabular,tsv" label="Input distance matrix" help="Only symmetric, hollow distance matrices may be used as input. Asymmetric distance matrices, such as those obtained by the UniFrac Gain metric (i.e. beta_diversity.py -m unifrac_g), should not be used as input"/>
        <param argument="--mapping_file" type="data" format="tabular,txt,tsv" label="Mapping file"/>
        <param argument="--categories" type="text" label="Comma-delimited list of categories from the mapping file" help="All methods except for BIO-ENV accept just a single category. If multiple categories are provided, only the first will be used"/>
        <param argument="--num_permutations" type="integer" label="Number of permutations to use when calculating statistical significance" help="Only applies to adonis, ANOSIM, MRPP, PERMANOVA, PERMDISP, and db-RDA. Must be greater than or equal to zero" optional="True" value="999" min="0"/>
    </inputs>
    <outputs>
        <data name="test_results" format="txt" from_work_dir="compare_categories/*_results.txt" label="${tool.name} on ${on_string}: Test resuts"/>
        <data name="dbrda_plot" format="pdf" from_work_dir="compare_categories/dbrda_plot.pdf" label="${tool.name} on ${on_string}: Ordination plot">
            <filter>(method == 'dbrda')</filter>

5:21abe2afb7cf

<tool id="qiime_compare_categories" name="Analyze statistical significance of sample groupings" version="@WRAPPER_VERSION@.0">
    <description> using distance matrices (compare_categories)</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements">
        <requirement type="package" version="1.3.2">r-optparse</requirement>
        <requirement type="package" version="2.3_4">r-vegan</requirement>
        <requirement type="package" version="3.3">r-base</requirement>
    </expand>
    <version_command>compare_categories.py --version</version_command>
    <command detect_errors="aggressive"><![CDATA[
compare_categories.py
    --method '$method'
    --input_dm '$input_dm'
    --mapping_file '$mapping_file'
    --categories '$categories'
    -o compare_categories
    #if $num_permutations
        --num_permutations '$num_permutations'
    #end if
    ]]></command>
    <inputs>
        <param argument="--method" type="select" label="Select the statistical method to use">
            <option value="adonis">adonis</option>
            <option value="anosim">anosim</option>
            <option value="bioenv">bioenv</option>
            <option value="morans_i">morans_i</option>
            <option value="mrpp">mrpp</option>

            <option value="dbrda">dbrda</option>
        </param>
        <param argument="--input_dm" type="data" format="txt,tabular,tsv" label="Input distance matrix" help="Only symmetric, hollow distance matrices may be used as input. Asymmetric distance matrices, such as those obtained by the UniFrac Gain metric (i.e. beta_diversity.py -m unifrac_g), should not be used as input"/>
        <param argument="--mapping_file" type="data" format="tabular,txt,tsv" label="Mapping file"/>
        <param argument="--categories" type="text" label="Comma-delimited list of categories from the mapping file" help="All methods except for BIO-ENV accept just a single category. If multiple categories are provided, only the first will be used"/>
        <param argument="--num_permutations" type="integer" value="999" min="0" optional="True" label="Number of permutations to use when calculating statistical significance" help="Only applies to adonis, ANOSIM, MRPP, PERMANOVA, PERMDISP, and db-RDA. Must be greater than or equal to zero"/>
    </inputs>
    <outputs>
        <data name="test_results" format="txt" from_work_dir="compare_categories/*_results.txt" label="${tool.name} on ${on_string}: Test resuts"/>
        <data name="dbrda_plot" format="pdf" from_work_dir="compare_categories/dbrda_plot.pdf" label="${tool.name} on ${on_string}: Ordination plot">
            <filter>(method == 'dbrda')</filter>