annotate chimera.perseus.xml @ 6:0f3baac24045 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit debdcdbb89f9bf3e2c3eed05cb078eddb27d4684"

<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=$dereplicate,
    processors='\${GALAXY_SLOTS:-8}'
)'
| sed 's/ //g'  ## mothur trips over whitespace
| mothur
| tee mothur.out.log
    ]]></command>
    <inputs>
        <param argument="fasta" type="data" format="mothur.align" label="fasta - Candiate Aligned Sequences"/>
        <param argument="name" type="data" format="mothur.names,mothur.count_table" label="name - Names or count_table"/>
        <param argument="group" type="data" format="mothur.groups" optional="true" label="group - Sequences Name reference"/>
        <param argument="alpha" type="float" value="-5.54" label="alpha" help="The default is -5.54"/>
        <param argument="beta" type="float" value="0.33" label="beta" help="The default is 0.33"/>
        <param argument="cutoff" type="float" value="0.50" label="cutoff" help="The default is 0.50"/>
        <param argument="dereplicate" type="boolean" falsevalue="false" truevalue="true" checked="false" label="dereplicate - remove chimeric sequences from all groups"
            help="If parameter is false, then if one group finds the seqeunce to be chimeric, then all groups find it to be chimeric. default=false"/>
        <expand macro="param-savelog"/>
    </inputs>
    <outputs>
        <expand macro="logfile-output"/>
        <data name="out_chimeras" format="tabular" from_work_dir="fasta.perseus.chimeras" label="${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"/>
            <param name="savelog" value="true"/>
            <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">
        <citation type="doi">10.1186/1471-2105-12-38</citation>
    </expand>
</tool>