comparison beta_diversity_through_plots.xml @ 5:2140c12755d0 draft

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

4:10810958c6b7

<tool id="qiime_beta_diversity_through_plots" name="Compute beta diversity distance matrices" version="@WRAPPER_VERSION@.0">
    <description>and generate PCoA plots</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements"/>
    <stdio>
        <regex match="VisibleDeprecationWarning" source="both" level="warning" description="VisibleDeprecationWarning on numpy for `rank`"/>
    </stdio>
    <version_command>beta_diversity_through_plots.py --version</version_command>
    <command detect_errors="aggressive"><![CDATA[
        beta_diversity_through_plots.py
            --otu_table_fp '$otu_table_fp'
            --mapping_fp '$mapping_fp'
            --output_dir beta_diversity_through_plots
            #if $tree_fp
                --tree_fp '$tree_fp'
            #end if
            #if $parameter_fp
                --parameter_fp '$parameter_fp'
            #end if
            $color_by_all_fields
            $parallel
            -O "\${GALAXY_SLOTS:-4}"
            #if $seqs_per_sample
                --seqs_per_sample '$seqs_per_sample'
            #end if
            $suppress_emperor_plots

        && python $__tool_directory__/beta_diversity_through_plots_html_generation.py
            --data_directory beta_diversity_through_plots
            --html_file '$beta_diversity_pcoa'
            --html_dir '$beta_diversity_pcoa.files_path'
    ]]></command>
    <inputs>
        <param argument="--otu_table_fp" type="data" format="tabular,txt,biom" multiple="True" label="OTU table"/>
        <param argument="--mapping_fp" type="data" format="tabular,txt" multiple="True" label="Mapping file" help=""/>
        <param argument="--tree_fp" type="data" format="txt" optional="True" label="Tree file (Optional)" help=""/>
        <param argument="--parameter_fp" type="data" format="txt" label="Parameter file (Optional)" help="It specifies changes to the default behavior, e.g. beta diversity metrics" optional="true"/>
        <param argument="--color_by_all_fields" type="text" optional="True" label="Colored mapping fields" help="Can be included only fields with greater than one value and fewer values than the number of samples"/>
        <param argument="--parallel" type="boolean" truevalue="--parallel" falsevalue="" checked="False" label="Run in parallel where available?" help=""/>
        <param argument="--seqs_per_sample" type="integer" optional="True" label="Depth of coverage for even sampling (Optional)" help=""/>
        <param argument="--suppress_emperor_plots" type="boolean" truevalue="" falsevalue="--suppress_emperor_plots" checked="True" label="Generate emperor plots?" help=""/>
    </inputs>
    <outputs>
        <collection name="beta_diversity_matrix" type="list" label="${tool.name} on ${on_string}: Distance matrix for each metrics">
            <discover_datasets pattern="(?P&lt;designation&gt;.+)_dm\.txt" ext="txt" directory="beta_diversity_through_plots"/>
        </collection>

5:2140c12755d0

<tool id="qiime_beta_diversity_through_plots" name="Compute beta diversity distance matrices and generate PCoA plots" version="@WRAPPER_VERSION@.0">
    <description>(beta_diversity_through_plots)</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements"/>
    <stdio>
        <regex match="VisibleDeprecationWarning" source="both" level="warning" description="VisibleDeprecationWarning on numpy for `rank`"/>
    </stdio>
    <version_command>beta_diversity_through_plots.py --version</version_command>
    <command detect_errors="aggressive"><![CDATA[
beta_diversity_through_plots.py
    --otu_table_fp '$otu_table_fp'
    --mapping_fp '$mapping_fp'
    --output_dir beta_diversity_through_plots
    #if $tree_fp
        --tree_fp '$tree_fp'
    #end if
    #if $parameter_fp
        --parameter_fp '$parameter_fp'
    #end if
    $color_by_all_fields
    $parallel
    -O "\${GALAXY_SLOTS:-4}"
    #if $seqs_per_sample
        --seqs_per_sample '$seqs_per_sample'
    #end if
    $suppress_emperor_plots

&& python $__tool_directory__/beta_diversity_through_plots_html_generation.py
    --data_directory beta_diversity_through_plots
    --html_file '$beta_diversity_pcoa'
    --html_dir '$beta_diversity_pcoa.files_path'
    ]]></command>
    <inputs>
        <param argument="--otu_table_fp" type="data" format="tabular,txt,biom" multiple="true" label="OTU table"/>
        <param argument="--mapping_fp" type="data" format="tabular,txt" multiple="true" label="Mapping file"/>
        <param argument="--tree_fp" type="data" format="txt" optional="true" label="Tree file (Optional)"/>
        <param argument="--parameter_fp" type="data" format="txt" label="Parameter file (Optional)" help="It specifies changes to the default behavior, e.g. beta diversity metrics" optional="true"/>
        <param argument="--color_by_all_fields" type="text" optional="true" label="Colored mapping fields" help="Can be included only fields with greater than one value and fewer values than the number of samples"/>
        <param argument="--parallel" type="boolean" truevalue="--parallel" falsevalue="" checked="false" label="Run in parallel where available?"/>
        <param argument="--seqs_per_sample" type="integer" optional="true" label="Depth of coverage for even sampling (Optional)"/>
        <param argument="--suppress_emperor_plots" type="boolean" truevalue="" falsevalue="--suppress_emperor_plots" checked="true" label="Generate emperor plots?" help=""/>
    </inputs>
    <outputs>
        <collection name="beta_diversity_matrix" type="list" label="${tool.name} on ${on_string}: Distance matrix for each metrics">
            <discover_datasets pattern="(?P&lt;designation&gt;.+)_dm\.txt" ext="txt" directory="beta_diversity_through_plots"/>
        </collection>