annotate tree.shared.xml @ 7:bf740ca1752a draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit ff56a4c9218ddea84ff5cd72fd98c62db212465d"

<tool profile="16.07" id="mothur_tree_shared" name="Tree.shared" version="@WRAPPER_VERSION@.0">
    <description>Generate a newick tree for dissimilarity among groups</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
ln -s '$input.dist' input_dist.dat &&
#if not $input.source == "shared":
    ln -s '$input.name' input_name.dat &&
#end if

echo 'tree.shared(
    #if $input.source == "shared":
        shared=input_dist.dat,
        #if $input.groups:
            groups=${ str($input.groups).replace(",","-") },
        #end if
        #if $input.label:
            label=${ str($input.label).replace(",","-") },
        #end if
        #if $input.subsampling.use == "yes":
            #if $input.subsampling.subsample:
                subsample=$input.subsampling.subsample,
            #else
                subsample=T,
            #end if
            #if $input.subsampling.iters:
                iters="$input.subsampling.iters,
            #end if
        #end if
    #elif $input.source == "column":
        column=input_dist.dat,
        name=input_name.dat,
    #elif $input.source == "phylip":
        phylip=input_dist.dat,
        #if $input.name:
            name=input_name.dat,
        #end if
    #else
        count=input_name.dat,
    #end if
    #if $calc:
        calc=${ str($calc).replace(",","-") },
    #end if
    processors='\${GALAXY_SLOTS:-8}'
)'
| sed 's/ //g'  ## mothur trips over whitespace
| mothur
| tee mothur.out.log
    ]]></command>
    <inputs>
        <conditional name="input">
            <param name="source" type="select" label="Select input format">
                <option value="shared">OTU Shared</option>
                <option value="column">Pairwise Column Distance Matrix</option>
                <option value="phylip">Phylip Distance Matrix</option>
                <option value="count">Count file</option>
            </param>
            <when value="column">
                <param name="dist" type="data" format="mothur.pair.dist" label="column - Distance Matrix"/>
                <param name="name" type="data" format="mothur.names" label="name - 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="name" type="data" format="mothur.names" optional="true" label="name - Names"/>
            </when>
            <when value="shared">
                <param name="dist" type="data" format="mothur.shared" label="shared - OTU Shared"/>
                <param name="label" type="select" label="label - OTU Labels" multiple="true">
                    <options>
                        <filter type="data_meta" ref="dist" key="labels"/>
                    </options>
                </param>
                <param name="groups" type="select" label="groups - Groups to consider" multiple="true">
                    <options>
                        <filter type="data_meta" ref="dist" key="groups"/>
                    </options>
                </param>
                <conditional name="subsampling">
                    <param name="use" type="select" label="subsample">
                        <option value="no" selected="true">no</option>
                        <option value="yes">yes</option>
                    </param>
                    <when value="yes">
                        <param name="subsample" type="integer" value="" min="0" optional="true" label="subsample (defaults to the size of the smallest group)" help="Should not exceed the number of sequences in any group"/>
                        <param name="iters" type="integer" value="" min="1" optional="true" label="iters - Number of iterations to try (default 1000)"/>
                    </when>
                    <when value="no"/>
                </conditional>
            </when>
            <when value="count">
                <param name="dist" type="data" format="mothur.pair.dist" label="column - Distance Matrix"/>
                <param name="name" type="data" format="mothur.count_table" label="count - count_table file"/>
            </when>
        </conditional>
        <param name="calc" type="select" label="calc - Calculators (Uses defaults if none selected)" multiple="true">
            <expand macro="calc-common"/>
            <!-- set default option(s) -->
            <option value="jclass" selected="true">jclass - Community Membership Similarity the traditional Jaccard similarity coefficient based on the observed richness</option>
            <option value="thetayc" selected="true">thetayc - Community Structure Similarity the Yue &amp; Clayton theta similarity coefficient</option>
        </param>
        <expand macro="param-savelog"/>
    </inputs>
    <outputs>
        <expand macro="logfile-output"/>
        <data name="tre" format="mothur.tre" from_work_dir="input_dist*.tre" label="${tool.name} on ${on_string}: tre">
            <filter>input['source'] != 'shared'</filter>
        </data>
        <collection name="trefiles" type="list" label="${tool.name} on ${on_string}: tre">
            <filter>input['source'] == 'shared'</filter>
        	<discover_datasets pattern=".*?\.(?P&lt;designation&gt;.*)\.tre" format="mothur.tre"/>
        </collection>
    </outputs>
    <tests>
        <test><!-- test with phylip and defaults -->
            <param name="source" value="phylip"/>
            <param name="dist" value="env.dist"/>
            <output name="tre" md5="c74a88ed448aad2d07059eda0b4161e9" ftype="mothur.tre"/>
            <param name="savelog" value="true"/>
            <expand macro="logfile-test"/>
        </test>
        <test><!-- test with shared and subsampling -->
            <param name="source" value="shared"/>
            <param name="dist" value="amazon.an.shared"/>
            <param name="use" value="yes"/>
            <param name="calc" value="jclass"/>
            <output_collection name="trefiles" count="108">
                <element name="jclass.0.32.all" md5="b8adfa6e41397b3815768f987836d102" ftype="mothur.tre"/>
            </output_collection>
            <param name="savelog" value="true"/>
            <expand macro="logfile-test"/>
        </test>
        <test><!-- test with shared and label and group select and all calculators -->
            <param name="source" value="shared"/>
            <param name="dist" value="amazon.an.shared"/>
            <param name="label" value="0.05,0.22,0.32"/>
            <param name="groups" value="forest,pasture"/>
            <param name="calc" value="sharedsobs,sharedchao,sharedace,anderberg,jclass,jest,kulczynski,kulczynskicody,kstest,lennon,ochiai,sorclass,sorest,whittaker,hamming,memchi2,memchord,memeuclidean,mempearson,braycurtis,jabund,morisitahorn,sorabund,thetan,thetayc,canberra,gower,hellinger,manhattan,odum,soergel,spearman,speciesprofile,structchi2,structchord,structeuclidean,structkulczynski,structpearson,sharednseqs,sharedobserved"/>
            <output_collection name="trefiles" count="117">
                <element name="canberra.0.32" md5="477b061d738d24a7476dd4c90d9666cf" ftype="mothur.tre"/>
            </output_collection>
            <param name="savelog" value="true"/>
            <expand macro="logfile-test"/>
        </test>
        <test><!-- test with column and name file -->
            <param name="source" value="column"/>
            <param name="dist" value="amazon.pair.dist"/>
            <param name="name" value="amazon1.names"/>
            <output name="tre" md5="33cc8cb433f123e49b33b998186b74ed" ftype="mothur.tre"/>
            <param name="savelog" value="true"/>
            <expand macro="logfile-test"/>
        </test>
    </tests>
    <help><![CDATA[

@MOTHUR_OVERVIEW@

**Command Documentation**

The tree.shared_ command will generate a newick-formatted tree file that describes the dissimilarity (1-similarity) among multiple groups.  For calc parameter choices see: https://www.mothur.org/wiki/Calculators

.. _tree.shared: https://www.mothur.org/wiki/Tree.shared

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