annotate chimera.perseus.xml @ 0:35c11001da8b draft

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

<tool profile="16.07" id="mothur_chimera_perseus" name="Chimera.perseus" version="@WRAPPER_VERSION@.0">
    <description>Find putative chimeras using chimeraCheck</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 "$fasta" fasta.dat &&
        ln -s "$name" name.dat &&
        ln -s "$group" group.dat &&

        echo 'chimera.perseus(
            fasta=fasta.dat,
            #if $name.is_of_type("mothur.names"):
                name=name.dat,
            #elif $name.is_of_type("mothur.count_table"):
                count=name.dat,
            #end if
            #if $group:
                group=group.dat,
            #end if
            alpha=$alpha,
            beta=$beta,
            cutoff=$cutoff,
            dereplicate=$dereplicate,
            processors='\${GALAXY_SLOTS:-8}'
        )'
        | sed 's/ //g'  ## mothur trips over whitespace
        | mothur
        | tee mothur.out.log
    ]]></command>
    <inputs>
        <param name="fasta" type="data" format="mothur.align" label="fasta - Candiate Aligned Sequences"/>
        <param name="name" type="data" format="mothur.names,mothur.count_table" label="name - Names or count_table"/>
        <param name="group" type="data" format="mothur.groups" optional="true" label="group - Sequences Name reference"/>
        <param name="alpha" type="float" value="-5.54" label="alpha" help="The default is -5.54"/>
        <param name="beta" type="float" value="0.33" label="beta" help="The default is 0.33"/>
        <param name="cutoff" type="float" value="0.50" label="cutoff" help="The default is 0.50"/>
        <param name="dereplicate" type="boolean" falsevalue="false" truevalue="true" checked="false" label="dereplicate - remove chimeric sequences from all groups" help="If parameter is false, then if one group finds the seqeunce to be chimeric, then all groups find it to be chimeric. default=false"/>
    </inputs>
    <outputs>
        <expand macro="logfile-output"/>
        <data name="out_chimeras" format="tabular" from_work_dir="fasta.perseus.chimeras" label="${tool.name} on ${on_string}: perseus.chimeras"/>
        <data name="out_accnos" format="mothur.accnos" from_work_dir="fasta.perseus.accnos" label="${tool.name} on ${on_string}: perseus.accnos"/>
    </outputs>
    <tests>
        <test>
            <param name="fasta" value="amazon.fasta" ftype="fasta"/>
            <param name="name" value="amazon1.names" ftype="mothur.names"/>
            <output name="out_chimeras" md5="bcd513127321a32035764a2087c23528" ftype="tabular"/>
            <expand macro="logfile-test"/>
        </test>
        <!-- TODO: find/create test dataset with chimera present -->
    </tests>
    <help>
<![CDATA[

@MOTHUR_OVERVIEW@

**Command Documentation**

The chimera.perseus_ command reads a fasta and name file, and outputs potentially chimeric sequences.

.. _chimera.perseus: https://www.mothur.org/wiki/Chimera.perseus

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