comparison jackknifed_beta_diversity.xml @ 5:205f4c9739c0 draft

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

4:89823e3721a0

<tool id="qiime_jackknifed_beta_diversity" name="Perform jackknifed UPGMA clustering" version="@WRAPPER_VERSION@.0">
    <description>and building jackknifed 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`"/>
        <regex match="RuntimeWarning: The result contains negative eigenvalues" source="both" level="warning" description="Presence of negative eigenvalues"/>
    </stdio>
    <version_command>jackknifed_beta_diversity.py --version</version_command>
    <command detect_errors="aggressive"><![CDATA[
        jackknifed_beta_diversity.py
            --otu_table_fp '$otu_table_fp'
            --mapping_fp '$mapping_fp'
            -o jackknifed_beta_diversity
            --seqs_per_sample '$seqs_per_sample'
            #if $tree_fp
                --tree_fp '$tree_fp'
            #end if
            #if $parameter_fp
                --parameter_fp '$parameter_fp'
            #end if
            --master_tree '$master_tree'
            $parallel
            -O "\${GALAXY_SLOTS:-4}"

        && python $__tool_directory__/jackknifed_beta_diversity_output_management.py
            --data_directory jackknifed_beta_diversity
            --html_file '$jackknifed_beta_diversity_report'
            --html_dir '$jackknifed_beta_diversity_report.files_path'
    ]]></command>
    <inputs>
        <param argument="--otu_table_fp" type="data" format="tabular,txt,biom" label="OTU table" multiple="True"/>
        <param argument="--mapping_fp" type="data" format="tabular,txt,tsv" label="Mapping file" multiple="True"/>
        <param argument="--seqs_per_sample" type="integer" value="" label="Number of sequences to include in each jackknifed subset"/>

        <param argument="--parameter_fp" type="data" format="txt" label="Parameter file" help="It specifies changes to the default behavior, e.g. beta diversity metrics" optional="true"/>
        <param argument="--master_tree" type="select" label="Method for computing master trees in jackknife analysis">
            <option value="consensus" selected="True">Consensus of trees from jackknifed otu tables</option>
            <option value="full">Tree generated from input (unsubsambled) otu table</option>
        </param>
        <param argument="--parallel" type="boolean" label="Run in parallel where available?" truevalue="--parallel" falsevalue="" checked="true"/>
    </inputs>
    <outputs>
        <collection name="unrarefied_beta_div_dist_matrix" type="list" label="${tool.name} on ${on_string}: Distance matrix for unrarefied beta diversity">
            <discover_datasets pattern="(?P&lt;designation&gt;.+)\.txt" directory="jackknifed_beta_diversity/unrarefied_bdiv/"/>
        </collection>

5:205f4c9739c0

<tool id="qiime_jackknifed_beta_diversity" name="Perform jackknifed UPGMA clustering" version="@WRAPPER_VERSION@.0">
    <description> and building jackknifed PCoA plots (jackknifed_beta_diversity)</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements"/>
    <stdio>
        <regex match="VisibleDeprecationWarning" source="both" level="warning" description="VisibleDeprecationWarning on numpy for `rank`"/>
        <regex match="RuntimeWarning: The result contains negative eigenvalues" source="both" level="warning" description="Presence of negative eigenvalues"/>
    </stdio>
    <version_command>jackknifed_beta_diversity.py --version</version_command>
    <command detect_errors="aggressive"><![CDATA[
jackknifed_beta_diversity.py
    --otu_table_fp '$otu_table_fp'
    --mapping_fp '$mapping_fp'
    -o jackknifed_beta_diversity
    --seqs_per_sample '$seqs_per_sample'
    #if $tree_fp
        --tree_fp '$tree_fp'
    #end if
    #if $parameter_fp
        --parameter_fp '$parameter_fp'
    #end if
    --master_tree '$master_tree'
    $parallel
    -O "\${GALAXY_SLOTS:-4}"

&& python $__tool_directory__/jackknifed_beta_diversity_output_management.py
    --data_directory jackknifed_beta_diversity
    --html_file '$jackknifed_beta_diversity_report'
    --html_dir '$jackknifed_beta_diversity_report.files_path'
    ]]></command>
    <inputs>
        <param argument="--otu_table_fp" type="data" format="tabular,txt,biom" label="OTU table" multiple="True"/>
        <param argument="--mapping_fp" type="data" format="tabular,txt,tsv" label="Mapping file" multiple="True"/>
        <param argument="--seqs_per_sample" type="integer" value="" label="Number of sequences to include in each jackknifed subset"/>

        <param argument="--parameter_fp" type="data" format="txt" label="Parameter file" help="It specifies changes to the default behavior, e.g. beta diversity metrics" optional="true"/>
        <param argument="--master_tree" type="select" label="Method for computing master trees in jackknife analysis">
            <option value="consensus" selected="True">Consensus of trees from jackknifed otu tables</option>
            <option value="full">Tree generated from input (unsubsambled) otu table</option>
        </param>
        <param argument="--parallel" type="boolean" truevalue="--parallel" falsevalue="" checked="true" label="Run in parallel where available?"/>
    </inputs>
    <outputs>
        <collection name="unrarefied_beta_div_dist_matrix" type="list" label="${tool.name} on ${on_string}: Distance matrix for unrarefied beta diversity">
            <discover_datasets pattern="(?P&lt;designation&gt;.+)\.txt" directory="jackknifed_beta_diversity/unrarefied_bdiv/"/>
        </collection>