annotate cluster.split.xml @ 2:3c24b99497db draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3

<tool profile="16.07" id="mothur_cluster_split" name="Cluster.split" version="@WRAPPER_VERSION@.0">
    <description>Assign sequences to OTUs and split large matrices</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements">
        <requirement type="package" version="2.6.0">vsearch</requirement>
    </expand>
    <expand macro="stdio"/>
    <expand macro="version_command"/>
    <command><![CDATA[
@SHELL_OPTIONS@

## create symlinks to input datasets
#if $splitby.splitmethod == "distance":
    ln -s '$splitby.matrix.dist' splitby.matrix.dist.dat &&
    ln -s '$splitby.matrix.nameOrCount' splitby.matrix.nameOrCount.dat &&
#elif $splitby.splitmethod == "classify":
    ln -s '$splitby.dist' splitby.dist.dat &&
    ln -s '$splitby.nameOrCount' splitby.nameOrCount.dat &&
    ln -s '$splitby.taxonomy' splitby.taxonomy.dat &&
#elif $splitby.splitmethod == "fasta":
    ln -s '$splitby.fasta' splitby.fasta.dat &&
    ln -s '$splitby.nameOrCount' splitby.nameOrCount.dat &&
    ln -s '$splitby.taxonomy' splitby.taxonomy.dat &&
#end if

echo 'cluster.split(
    splitmethod=$splitby.splitmethod,
    #if $splitby.splitmethod == "distance":
        #if $splitby.matrix.format == "column":
            column=splitby.matrix.dist.dat,
            #if $splitby.matrix.nameOrCount.is_of_type("mothur.names"):
                name=splitby.matrix.nameOrCount.dat,
            #elif $splitby.matrix.nameOrCount.is_of_type("mothur.count_table"):
                count=splitby.matrix.nameOrCount.dat,
            #end if
        #elif $splitby.matrix.format == "phylip":
            phylip=splitby.matrix.dist.dat,
            #if $splitby.matrix.nameOrCount:
                #if $splitby.matrix.nameOrCount.is_of_type("mothur.names"):
                    name=splitby.matrix.nameOrCount.dat,
                #elif $splitby.matrix.nameOrCount.is_of_type("mothur.count_table"):
                    count=splitby.matrix.nameOrCount.dat,
                #end if
            #end if
        #end if
    #elif $splitby.splitmethod == "classify":
        column=splitby.dist.dat,
        taxonomy=splitby.taxonomy.dat,
        #if $splitby.nameOrCount.is_of_type("mothur.names"):
            name=splitby.nameOrCount.dat,
        #elif $splitby.nameOrCount.is_of_type("mothur.count_table"):
            count=splitby.nameOrCount.dat,
        #end if
        #if $splitby.taxlevel:
            taxlevel=$splitby.taxlevel,
        #end if
    #elif $splitby.splitmethod == "fasta":
        fasta=splitby.fasta.dat,
        taxonomy=splitby.taxonomy.dat,
        #if $splitby.nameOrCount.is_of_type("mothur.names"):
            name=splitby.nameOrCount.dat,
        #elif $splitby.nameOrCount.is_of_type("mothur.count_table"):
            count=splitby.nameOrCount.dat,
        #end if
        #if $splitby.taxlevel:
            taxlevel=$splitby.taxlevel,
        #end if
        classic=$splitby.classic,
    #end if
    method=$splitby.condmethod.method,
    #if $splitby.condmethod.method == "opti":
        metric=$splitby.condmethod.metric,
        initialize=$splitby.condmethod.initialize,
        delta=$splitby.condmethod.delta,
        iters=$splitby.condmethod.iters,
    #end if
    #if float($cutoff) > 0.0:
        cutoff=$cutoff,
    #end if
    #if $precision
        precision=$precision,
    #end if
    large=$large,
    cluster=$cluster,
    runsensspec=$runsensspec,
    processors='\${GALAXY_SLOTS:-8}'
)'
| sed 's/ //g'  ## mothur trips over whitespace
| mothur
| tee mothur.out.log
    ]]></command>
    <inputs>
        <conditional name="splitby">
            <param name="splitmethod" type="select" label="Split by" help="VSEARCH methods (agc and dgc) require a fasta file">
                <option value="distance">Distance</option>
                <option value="classify">Classification</option>
                <option value="fasta">Classification using fasta</option>
            </param>
            <when value="distance">
                <conditional name="matrix">
                    <param name="format" type="select" label="Select a Distance Matrix Format">
                        <option value="column">Pairwise Column Matrix</option>
                        <option value="phylip">Phylip Distance Matrix</option>
                    </param>
                    <when value="column">
                        <param name="dist" argument="column" type="data" format="mothur.pair.dist" label="column - Distance Matrix"/>
                        <param name="nameOrCount" type="data" format="mothur.names,mothur.count_table" label="name file or count table - Sequences Name reference"/>
                    </when>
                    <when value="phylip">
                        <param name="dist" argument="phylip" type="data" format="mothur.dist,mothur.lower.dist,mothur.square.dist" label="phylip - Distance Matrix"/>
                        <param name="nameOrCount" type="data" format="mothur.names,mothur.count_table" optional="true" label="name file or count table - Sequences Name reference"/>
                    </when>
                </conditional>
                <conditional name="condmethod">
                    <expand macro="param-clustermethods"/>
                    <when value="furthest"/>
                    <when value="nearest"/>
                    <when value="average"/>
                    <when value="opti">
                        <expand macro="params-opticlust"/>
                    </when>
                </conditional>
            </when>
            <when value="classify">
                <param name="dist" argument="column" type="data" format="mothur.pair.dist" label="column - Distance Matrix"/>
                <param argument="taxonomy" type="data" format="mothur.seq.taxonomy" label="taxonomy - Taxonomy (from Classify.seqs)"/>
                <param name="nameOrCount" type="data" format="mothur.names,mothur.count_table" label="name file or count table - Sequences Name reference"/>
                <param argument="taxlevel" type="integer" value="1" min="1" label="taxlevel - taxonomy level for split (default=1)"
                    help="taxonomy level you want to use to split the distance file, default=1, meaning use the first taxon in each list"/>
                <conditional name="condmethod">
                    <expand macro="param-clustermethods"/>
                    <when value="furthest"/>
                    <when value="nearest"/>
                    <when value="average"/>
                    <when value="opti">
                        <expand macro="params-opticlust"/>
                    </when>
                </conditional>
            </when>
            <when value="fasta">
                <param argument="fasta" type="data" format="mothur.align,fasta" label="Fasta"/>
                <param argument="taxonomy" type="data" format="mothur.seq.taxonomy" label="Taxonomy" help="can be obtained by running classify.seqs"/>
                <param name="nameOrCount" type="data" format="mothur.names,mothur.count_table" label="name file or count table - Sequences Name reference"/>
                <param argument="taxlevel" type="integer" value="3" min="1" label="taxlevel - taxonomy level for split (default=3)"
                    help="taxonomy level you want to use to split the distance file, default=1, meaning use the first taxon in each list"/>
                <param argument="classic" type="boolean" checked="false" truevalue="true" falsevalue="false" label="classic - Use cluster.classic"/>
                <conditional name="condmethod">
                    <expand macro="param-clustermethods">
                        <expand macro="option-vsearch-clustermethods"/>
                    </expand>
                    <when value="furthest"/>
                    <when value="nearest"/>
                    <when value="average"/>
                    <when value="agc"/>
                    <when value="dgc"/>
                    <when value="opti">
                        <expand macro="params-opticlust"/>
                    </when>
                </conditional>
            </when>
        </conditional>
        <param argument="cutoff" type="float" value="0.0" min="0.0" label="cutoff - Distance Cutoff threshold - ignored if not > 0"
            help="Ignore pairwise distances larger than this, a common value would be 0.25"/>
        <param argument="precision" type="select" optional="true" label="precision - Precision for rounding distance values"
            help="Set higher precision for longer genome scale sequence lengths">
            <option value="10">.1</option>
            <option value="100" selected="true">.01</option>
            <option value="1000">.001</option>
            <option value="10000">.0001</option>
            <option value="100000">.00001</option>
            <option value="1000000">.000001</option>
        </param>
        <param argument="large" type="boolean" checked="false" truevalue="true" falsevalue="false" label="large - distance matrix is too large to fit in RAM"
            help="If your job fails due to not enough memory error, set this to true to rerun"/>
        <param argument="cluster" type="boolean" falsevalue="false" truevalue="true" checked="true" label="perform clustering?"
            help="indicate whether you want to run the clustering or just split the distance matrix"/>
        <param argument="runsensspec" type="boolean" truevalue="true" falsevalue="false" checked="true" label="runsensspec" help="run the sens.spec command on the completed list file"/>
        <expand macro="param-savelog"/>
    </inputs>
    <outputs>
        <expand macro="logfile-output"/>
        <data name="rabund" format="mothur.rabund" from_work_dir="splitby.*.rabund" label="${tool.name} on ${on_string}: rabund (Rank Abundance)">
             <filter>splitby['nameOrCount'].ext != "mothur.count_table"</filter>
             <filter>splitby['matrix']['nameOrCount'].ext != "mothur.count_table"</filter>
        </data>
        <data name="sabund" format="mothur.sabund" from_work_dir="splitby.*.sabund" label="${tool.name} on ${on_string}: sabund (Species Abundance)">
             <filter>splitby['nameOrCount'].ext != "mothur.count_table"</filter>
             <filter>splitby['matrix']['nameOrCount'].ext != "mothur.count_table"</filter>
        </data>
        <data name="otulist" format="mothur.list" from_work_dir="splitby.*.list" label="${tool.name} on ${on_string}: list (OTU List)"/>
        <collection name="splitdist" type="list" label="${tool.name} on ${on_string}: split dist">
            <filter>not cluster</filter>
            <discover_datasets pattern=".*?\.column\.dist\.(?P&lt;designation&gt;.*)\.temp" format="mothur.dist"/>
        </collection>
        <collection name="splitnames" type="list" label="${tool.name} on ${on_string}: split names">
            <filter>not cluster</filter>
            <discover_datasets pattern=".*?\.names\.(?P&lt;designation&gt;.*)\.temp" format="mothur.names"/>
        </collection>
        <data name="splitfile" format="txt" from_work_dir="splitby.*.file" label="${tool.name} on ${on_string}: split.file">
            <filter>not cluster</filter>
        </data>
        <data name="sensspec" format="txt" from_work_dir="splitby.*.sensspec" label="${tool.name} on ${on_string}: sensspec">
            <filter>runsensspec and splitby['condmethod']['method'] == "opti"</filter>
        </data>
    </outputs>
    <tests>
        <test><!-- test with distance method -->
            <param name="splitmethod" value="distance"/>
            <param name="format" value="phylip"/>
            <param name="dist" value="98_sq_phylip_amazon.dist" ftype="mothur.square.dist"/>
            <param name="method" value="average"/>
            <output name="otulist" ftype="mothur.list">
                <assert_contents>
                    <expand macro="test-list-format"/>
                    <has_text text="unique"/>
                    <has_text text="U68680"/>
                </assert_contents>
            </output>
            <output name="rabund" ftype="mothur.rabund">
                <assert_contents>
                    <has_line_matching expression="^unique(\t\d+)+$"/>
                    <has_text text="0.03"/>
                </assert_contents>
            </output>
            <output name="sabund" ftype="mothur.sabund">
                <assert_contents>
                    <has_line_matching expression="^unique(\t\d+)+$"/>
                    <has_text text="0.03"/>
                </assert_contents>
            </output>
            <param name="savelog" value="true"/>
            <expand macro="logfile-test"/>
        </test>
        <test><!-- test with cluster false -->
            <param name="splitmethod" value="distance"/>
            <param name="format" value="phylip"/>
            <param name="dist" value="98_sq_phylip_amazon.dist" ftype="mothur.square.dist"/>
            <param name="cluster" value="false"/>
            <param name="method" value="average"/>
            <output name="splitfile" ftype="txt">
                <assert_contents>
                    <has_text text="column"/>
                    <has_text text="dist"/>
                    <has_text text="names"/>
                    <has_text text="temp"/>
                </assert_contents>
            </output>
            <output_collection name="splitnames" count="14">
                <element name="0" ftype="mothur.names">
                    <assert_contents>
                        <has_text text="U68591"/>
                        <has_text text="U68600"/>
                    </assert_contents>
                </element>
            </output_collection>
            <output_collection name="splitdist" count="13">
                <element name="4" ftype="mothur.dist">
                    <assert_contents>
                        <has_line_matching expression="^U\d+\tU\d+\t\d+\.\d+$"/>
                    </assert_contents>
                </element>
            </output_collection>
            <param name="savelog" value="true"/>
            <expand macro="logfile-test"/>
        </test>
        <test><!-- test with classify method (mothur.names input file) -->
            <param name="splitmethod" value="classify"/>
            <param name="format" value="column"/>
            <param name="dist" value="amazon.pair.dist" ftype="mothur.pair.dist"/>
            <param name="nameOrCount" value="amazon.names" ftype="mothur.names"/>
            <param name="taxonomy" value="amazon.wang.wang.taxonomy" ftype="mothur.seq.taxonomy"/>
            <param name="method" value="average"/>
            <output name="otulist" md5="d6eba624ad79759c530b9bc3285a1361" ftype="mothur.list"/>
            <output name="rabund" md5="2a165e1e40644fccb8cc9f53d8915bc3" ftype="mothur.rabund"/>
            <output name="sabund" md5="7aad8a9ca0eade414d6eba1f8bef960f" ftype="mothur.sabund"/>
            <param name="savelog" value="true"/>
            <expand macro="logfile-test"/>
        </test>
        <test><!-- test with classify method (mothur.count_table input file) -->
            <param name="splitmethod" value="classify"/>
            <param name="format" value="column"/>
            <param name="dist" value="amazon.pair.dist" ftype="mothur.pair.dist"/>
            <param name="nameOrCount" value="amazon.count_table" ftype="mothur.count_table"/>
            <param name="taxonomy" value="amazon.wang.wang.taxonomy" ftype="mothur.seq.taxonomy"/>
            <param name="method" value="average"/>
            <output name="otulist" md5="c5c28330434d3e773221f635d04d6af9" ftype="mothur.list"/>
            <param name="savelog" value="true"/>
            <expand macro="logfile-test"/>
        </test>
        <test><!-- test with fasta -->
            <param name="splitmethod" value="fasta"/>
            <param name="fasta" value="amazon.align_head" ftype="mothur.align"/>
            <param name="nameOrCount" value="amazon.align_head.names" ftype="mothur.names"/>
            <param name="taxonomy" value="amazon.align_head.wang.taxonomy" ftype="mothur.seq.taxonomy"/>
            <param name="cutoff" value="9999"/>
            <param name="method" value="average"/>
            <output name="otulist" md5="a1279248cf2bc1094e0046b2cff1b785" ftype="mothur.list"/>
            <output name="rabund" md5="65ec9f326cd92fc607679b9902ec8430" ftype="mothur.rabund"/>
            <output name="sabund" md5="854d3acd15f64299c5d9d9e18f2d51b4" ftype="mothur.sabund"/>
            <param name="savelog" value="true"/>
            <expand macro="logfile-test"/>
        </test>
        <test><!-- test with vsearch executable (agc/dgc method) -->
            <param name="splitmethod" value="fasta"/>
            <param name="fasta" value="amazon.align_head" ftype="mothur.align"/>
            <param name="nameOrCount" value="amazon.align_head.names" ftype="mothur.names"/>
            <param name="taxonomy" value="amazon.align_head.wang.taxonomy" ftype="mothur.seq.taxonomy"/>
            <param name="method" value="agc"/>
            <output name="otulist" md5="0fbc5bf21331538dd50b6586c4005edc" ftype="mothur.list"/>
            <output name="rabund" md5="dcccca11d9fa7a186cd93e9d4592f832" ftype="mothur.rabund"/>
            <output name="sabund" md5="167815924b1b2b4d4e5e7468d41256cb" ftype="mothur.sabund"/>
            <param name="savelog" value="true"/>
            <expand macro="logfile-test"/>
        </test>
        <test><!-- test with opticlust method -->
            <param name="splitmethod" value="distance"/>
            <param name="format" value="phylip"/>
            <param name="dist" value="98_sq_phylip_amazon.dist" ftype="mothur.square.dist"/>
            <param name="method" value="opti"/>
            <output name="otulist" ftype="mothur.list">
                <assert_contents>
                    <expand macro="test-list-format"/>
                    <has_text text="0.03"/>
                </assert_contents>
            </output>
            <output name="rabund" ftype="mothur.rabund">
                <assert_contents>
                    <expand macro="test-rabund-format"/>
                    <has_text text="0.03"/>
                </assert_contents>
            </output>
            <output name="sabund" ftype="mothur.sabund">
                <assert_contents>
                    <expand macro="test-sabund-format"/>
                    <has_text text="0.03"/>
                </assert_contents>
            </output>
            <output name="sensspec" ftype="txt">
                <assert_contents>
                    <expand macro="test-sensspec-format"/>
                    <has_text text="0.03"/>
                </assert_contents>
            </output>
            <param name="savelog" value="true"/>
            <expand macro="logfile-test"/>
        </test>
    </tests>
    <help><![CDATA[

@MOTHUR_OVERVIEW@


**Command Documentation**

The cluster.split_ command assign sequences to OTUs (Operational Taxonomy Unit).

.. _cluster.split: https://www.mothur.org/wiki/Cluster.split

v1.28.0: Upgraded to Mothur 1.33, introduced cluster boolean.

    ]]></help>
    <expand macro="citations"/>
</tool>