annotate cluster.split.xml @ 0:e70a33ec8f3b draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d

<tool profile="16.07" id="mothur_cluster_split" name="Cluster.split" version="@WRAPPER_VERSION@.0">
    <description>Assign sequences to OTUs (Operational Taxonomic Unit) splits large matrices</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements"/>
    <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
            #if $method:
                method=$method,
            #end if
            #if float($cutoff) > 0.0:
                cutoff=$cutoff,
            #end if
            hard=$hard,
            #if $precision
                precision=$precision,
            #end if
            large=$large,
            cluster=$cluster,
            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="">
                <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" help="">
                        <option value="column">Pairwise Column Matrix</option>
                        <option value="phylip">Phylip Distance Matrix</option>
                    </param>
                    <when value="column">
                        <param name="dist" 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" 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>
            </when>
            <when value="classify">
                <param name="dist" type="data" format="mothur.pair.dist" label="column - Distance Matrix"/>
                <param name="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 name="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"/>
            </when>
            <when value="fasta">
                <param name="fasta" type="data" format="mothur.align,fasta" label="fasta - Aligned Sequences" help="must be aligned sequences (mothur.align)"/>
                <param name="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 name="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 name="classic" type="boolean" checked="false" truevalue="true" falsevalue="false" label="classic - Use cluster.classic"/>
            </when>
        </conditional>
        <param name="method" type="select" label="method - Select a Clustering Method" help="">
            <option value="furthest">Furthest neighbor</option>
            <option value="nearest">Nearest neighbor</option>
            <option value="average" selected="true">Average neighbor</option>
        </param>
        <param name="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 name="hard" type="boolean" checked="true" truevalue="true" falsevalue="false" label="hard - Use hard cutoff instead of rounding" help=""/>
        <param name="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 name="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 name="cluster" type="boolean" falsevalue="false" truevalue="true" checked="true" label="The cluster parameter allows you to indicate whether you want to run the clustering or just split the distance matrix, default=T"/>
    </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>
    </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"/>
            <output name="otulist" md5="2613ef0a1805ba9de012a41e938d8947" ftype="mothur.list"/>
            <output name="rabund" md5="4df813ec2d51c373a846a82380c7a1f8" ftype="mothur.rabund"/>
            <output name="sabund" md5="8d6813a5e8d2ad426a0ee5fdd99f1a19" ftype="mothur.sabund"/>
            <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"/>
            <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="4">
                <element name="0" md5="27037eeb3e696888b24653d0996261cd" ftype="mothur.names"/>
            </output_collection>
            <output_collection name="splitdist" count="3">
                <element name="4" md5="f751aee00b598d3b6691d34f67dbc8d5" ftype="mothur.dist"/>
            </output_collection>
            <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"/>
            <output name="otulist" md5="d6eba624ad79759c530b9bc3285a1361" ftype="mothur.list"/>
            <output name="rabund" md5="2a165e1e40644fccb8cc9f53d8915bc3" ftype="mothur.rabund"/>
            <output name="sabund" md5="7aad8a9ca0eade414d6eba1f8bef960f" ftype="mothur.sabund"/>
            <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"/>
            <output name="otulist" md5="c5c28330434d3e773221f635d04d6af9" ftype="mothur.list"/>
            <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"/>
            <output name="otulist" md5="a1279248cf2bc1094e0046b2cff1b785" ftype="mothur.list"/>
            <output name="rabund" md5="65ec9f326cd92fc607679b9902ec8430" ftype="mothur.rabund"/>
            <output name="sabund" md5="854d3acd15f64299c5d9d9e18f2d51b4" ftype="mothur.sabund"/>
            <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>