view daa2rma.xml @ 2:102d29c7c5a7 draft default tip

planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/megan commit 20ad8976adec9d011d21484859258bf1ad22f42e-dirty

<tool id="daa2rma" name="daa2rma" version="@TOOL_VERSION@" profile="19.01">
    <description>Compute a MEGAN rma6 file from a DIAMOND daa file</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements"/>
    <expand macro="stdio"/>
    <expand macro="version_command"/>
    <command detect_errors="aggressive"><![CDATA[
@CLASSIFICATION_UTILS@

#set CATEGORIES=['gi2', 'acc2', 'syn2', 'tags4']
#set TARGETS=['taxa', 'eggnog', 'interpro2go', 'seed', 'kegg']

ln -s $in input.daa &&
daa2rma
-i input.daa
-o '$rma'

@MDF_CLI@
@READS_CLI@
--pairedReadsInOneFile $reads.pairedReadsInOneFile
@PARAMETERS_CLI@
--maxMatchesPerRead $params.maxMatchesPerRead
@CLASSIFICATION_CLI@
@OTHER_CLI@
    ]]></command>
    <inputs>
        <param argument="--in" type="data" format="daa" label="Input DAA file"/>
        <expand macro="mdf_macro"/>
        <expand macro="reads_macro">
            <param argument="--pairedReadsInOneFile" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Paired reads in one file" help="usually they are in two" />
        </expand>
        <expand macro="params_macro">
            <param argument="--maxMatchesPerRead" type="integer" value="100" label="Max matches per read" />
        </expand>
        <expand macro="classification_macro"/>
        <expand macro="other_macro"/>
    </inputs>
    <outputs>
        <data name="rma" format="rma6" label="${tool.name} on ${on_string}"/>
    </outputs>
    <tests>
        <test>
            <param name="in" ftype="daa" value="diamond_results.daa"/>
            <output name="rma" ftype="rma6" value="diamond_results.rma" compare="sim_size" />
       </test>
    </tests>
    <help><![CDATA[
Compute a MEGAN RMA6 file from a DIAMOND DAA file

**Input**

- DAA file
- metadata mapping file (as defined in http://qiime.org/documentation/file_formats.html
- BIOM 1 format (see http://biom-format.org/documentation/format-versions/biom-1.0.html

**Output**

- RMA6 file

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