annotate reverse.seqs.xml @ 0:a8a1a7c5ab14 draft

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

<tool profile="16.07" id="mothur_reverse_seqs" name="Reverse.seqs" version="@WRAPPER_VERSION@.0">
    <description>Reverse complement the sequences</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 &&

        echo 'reverse.seqs(
            fasta=fasta.dat
        )'
        | sed 's/ //g'  ## mothur trips over whitespace
        | mothur
        | tee mothur.out.log
    ]]></command>
    <inputs>
        <param name="fasta" type="data" format="fasta,mothur.align" label="fasta - Sequences to reverse complement"/>
    </inputs>
    <outputs>
        <expand macro="logfile-output"/>
        <data name="out_fasta" format_source="fasta" from_work_dir="fasta*.rc.*" label="${tool.name} on ${on_string}: rc.fasta"/>
    </outputs>
    <tests>
        <test>
            <param name="fasta" value="Mock_S280_L001_R1_001_small.trim.contigs.good.align_head"/>
            <output name="out_fasta" file="Mock_S280_L001_R1_001_small.trim.contigs.good.rc.align_head"/>
            <expand macro="logfile-test"/>
        </test>
    </tests>
    <help>
<![CDATA[

@MOTHUR_OVERVIEW@

**Command Documentation**

The reverse.seqs_ command will generate a fasta containing the reverse complement of each sequence in the input fasta.

.. _reverse.seqs: https://www.mothur.org/wiki/Reverse.seqs
]]>
    </help>
    <expand macro="citations"/>
</tool>