annotate classify.otu.xml @ 2:1ae93cdb2383 draft

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

<tool profile="16.07" id="mothur_classify_otu" name="Classify.otu" version="@WRAPPER_VERSION@.0">
    <description>Assign sequences to taxonomy</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 '$otu' otu.dat &&
ln -s '$tax.taxonomy' tax.taxonomy.dat &&
ln -s '$name' name.dat &&
ln -s '$count' count.dat &&
ln -s '$group' group.dat &&

echo 'classify.otu(
    list=otu.dat,
    taxonomy=tax.taxonomy.dat,
    #if $name:
        name=name.dat,
    #end if
    #if $count:
        count=count.dat,
    #end if
    #if $label:
        label=${ str($label).replace(",","-") },
    #end if
    #if $group:
        group=group.dat,
    #end if
    basis=$basis,
    probs=$probs,
    persample=$persample,
    cutoff=$cutoff,
    relabund=$relabund,
    output=$output,
    printlevel=$printlevel
)'
| sed 's/ //g'  ## mothur trips over whitespace
| mothur
| tee mothur.out.log
    ]]></command>
    <inputs>
        <param argument="list" name="otu" type="data" format="mothur.list" label="list - OTU List "/>
        <param argument="name" type="data" format="mothur.names" optional="true" label="name - taxonomy sequence names"/>
        <param argument="count" type="data" format="mothur.count_table" optional="true" label="count - used to represent the number of duplicate sequences for a given representative sequence"/>
        <conditional name="tax">
            <param name="source" type="select" label="Select Taxonomy from" help="">
                <option value="hist">History</option>
                <option value="ref">Cached Reference</option>
            </param>
            <when value="ref">
                <param argument="taxonomy" type="select" format="mothur.seq.taxonomy" label="taxonomy - Taxonomy Reference">
                    <options from_data_table="mothur_taxonomy"/>
                </param>
            </when>
            <when value="hist">
                <param argument="taxonomy" type="data" format="mothur.seq.taxonomy" label="taxonomy - Taxonomy Reference"/>
            </when>
        </conditional>
        <param argument="label" type="select" label="label - OTU Labels" multiple="true">
            <expand macro="labeloptions"/>
        </param>
        <param argument="cutoff" type="integer" value="60" min="0" max="100" label="cutoff - Confindence percentage cutoff between 1 and 100"/>
        <param argument="probs" type="boolean" falsevalue="false" truevalue="true" checked="true" label="probs - Show probabilities"/>
        <param argument="basis" type="select" label="basis - Summary file gives numbers of" help="">
            <option value="otu">OTU</option>
            <option value="sequence">sequence</option>
        </param>
        <param argument="group" type="data" format="mothur.groups" optional="true" label="group - Groups for summary file"/>
        <param argument="persample" type="boolean" falsevalue="false" truevalue="true" checked="false"
            label="persample - allows you to find a consensus taxonomy for each group"
            help="default false"/>
        <param argument="relabund" type="boolean" checked="false" truevalue="T" falsevalue="F" label="Relative abundance values?"
            help="use relative abundances rather than raw abundances for the tax.summary file"/>
        <expand macro="param-output"/>
        <expand macro="param-printlevel"/>
        <expand macro="param-savelog"/>
    </inputs>
    <outputs>
        <expand macro="logfile-output"/>
        <collection name="taxsummaries" type="list" label="${tool.name} on ${on_string}: tax.summary">
            <discover_datasets pattern=".*?\.(?P&lt;designation&gt;.*)\.cons\.tax\.summary" format="mothur.tax.summary"/>
        </collection>
        <collection name="taxonomies" type="list" label="${tool.name} on ${on_string}: taxonomy">
            <discover_datasets pattern=".*?\.(?P&lt;designation&gt;.*)\.cons\.taxonomy" format="mothur.cons.taxonomy"/>
        </collection>
    </outputs>
    <tests>
        <test><!-- test with defaults -->
            <param name="otu" value="amazon.an.list" ftype="mothur.list"/>
            <param name="source" value="hist"/>
            <param name="taxonomy" value="abrecovery.pds.wang.taxonomy" ftype="mothur.seq.taxonomy"/>
            <output_collection name="taxonomies" count="36">
                <element name="0.18" ftype="mothur.cons.taxonomy">
                    <assert_contents>
                        <expand macro="test-taxonomy-format"/>
                        <has_text text="Otu01"/>
                    </assert_contents>
                </element>
            </output_collection>
            <output_collection name="taxsummaries" count="36">
                <element name="0.18" ftype="mothur.tax.summary">
                    <assert_contents>
                        <expand macro="test-taxsummary-format"/>
                        <has_text text="Root"/>
                    </assert_contents>
                </element>
            </output_collection>
            <param name="savelog" value="true"/>
            <expand macro="logfile-test"/>
        </test>
        <test><!-- test with names file and label select -->
            <param name="otu" value="amazon.an.list" ftype="mothur.list"/>
            <param name="name" value="amazon1.names" ftype="mothur.names"/>
            <param name="source" value="hist"/>
            <param name="taxonomy" value="abrecovery.pds.wang.taxonomy" ftype="mothur.seq.taxonomy"/>
            <param name="sum" value="abrecovery.pds.wang.tree.sum"/>
            <param name="label" value="unique,0.05,0.18"/>
            <output_collection name="taxonomies" count="3">
                <element name="0.18" ftype="mothur.cons.taxonomy">
                    <assert_contents>
                        <expand macro="test-taxonomy-format"/>
                        <has_text text="Otu01"/>
                    </assert_contents>
                </element>
            </output_collection>
            <output_collection name="taxsummaries" count="3">
                <element name="0.18" ftype="mothur.tax.summary">
                    <assert_contents>
                        <expand macro="test-taxsummary-format"/>
                        <has_text text="Root"/>
                    </assert_contents>
                </element>
            </output_collection>
            <param name="savelog" value="true"/>
            <expand macro="logfile-test"/>
        </test>
        <test><!-- test with count table -->
            <param name="otu" value="amazon.an.list" ftype="mothur.list"/>
            <param name="count" value="amazon1.count_table" ftype="mothur.count_table"/>
            <param name="source" value="hist"/>
            <param name="label" value="unique,0.05,0.18"/>
            <param name="taxonomy" value="abrecovery.pds.wang.taxonomy" ftype="mothur.seq.taxonomy"/>
            <output_collection name="taxonomies" count="3">
                <element name="0.18" ftype="mothur.cons.taxonomy">
                    <assert_contents>
                        <expand macro="test-taxonomy-format"/>
                        <has_text text="Otu01"/>
                    </assert_contents>
                </element>
            </output_collection>
            <output_collection name="taxsummaries" count="3">
                <element name="0.18" ftype="mothur.tax.summary">
                    <assert_contents>
                        <expand macro="test-taxsummary-format"/>
                        <has_text text="Root"/>
                    </assert_contents>
                </element>
            </output_collection>
            <param name="savelog" value="true"/>
            <expand macro="logfile-test"/>
        </test>
        <test><!-- test with group file -->
            <param name="otu" value="amazon.an.list" ftype="mothur.list"/>
            <param name="group" value="amazon.groups" ftype="mothur.groups"/>
            <param name="source" value="hist"/>
            <param name="label" value="unique,0.05,0.18"/>
            <param name="taxonomy" value="abrecovery.pds.wang.taxonomy" ftype="mothur.seq.taxonomy"/>
            <output_collection name="taxonomies" count="3">
                <element name="0.18" ftype="mothur.cons.taxonomy">
                    <assert_contents>
                        <expand macro="test-taxonomy-format"/>
                        <has_text text="Otu01"/>
                    </assert_contents>
                </element>
            </output_collection>
            <output_collection name="taxsummaries" count="3">
                <element name="0.18" ftype="mothur.tax.summary">
                    <assert_contents>
                        <expand macro="test-taxsummary-format"/>
                        <has_text text="Root"/>
                    </assert_contents>
                </element>
            </output_collection>
            <param name="savelog" value="true"/>
            <expand macro="logfile-test"/>
        </test>
    </tests>
    <help><![CDATA[

@MOTHUR_OVERVIEW@

**Command Documentation**

The classify.otu_ command assigns sequences to chosen taxonomy outline.

The basis parameter allows you indicate what you want the summary file to represent, options are otu and sequence. Default is otu. For example consider the following basis=sequence could give Clostridiales 3 105 16 43 46, where 105 is the total number of sequences whose otu classified to Clostridiales. 16 is the number of sequences in the otus from groupA, 43 is the number of sequences in the otus from groupB, and 46 is the number of sequences in the otus from groupC. Now for basis=otu could give Clostridiales 3 7 6 1 2, where 7 is the number of otus that classified to Clostridiales. 6 is the number of otus containing sequences from groupA, 1 is the number of otus containing sequences from groupB, and 2 is the number of otus containing sequences from groupC.

.. _classify.otu: https://www.mothur.org/wiki/Classify.otu

v1.21.0: Updated to use Mothur 1.33. Added count parameter (1.28.0) and persample parameter (1.29.0)

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