annotate emboss_transeq.xml @ 14:2e0fb4bc860e draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit fed02ef07e0a45f0d5a89cdca364607ab8da6cf9

<tool id="EMBOSS: transeq101" name="transeq" version="@VERSION@">
    <description>Translate nucleic acid sequences</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements" />
    <code file="emboss_format_corrector.py" />
    <command detect_errors="aggressive"><![CDATA[
transeq
-sequence '$input1'
-outseq '$out_file1'
-frame $frame
-table $table
#if str($regions).strip():
    -regions '$regions'
#end if
-trim $trim
-clean $clean
-alternative $alternative
-osformat2 '$out_format1'
-auto
    ]]></command>
    <inputs>
        <param name="input1" argument="-sequence" type="data" format="fasta" label="Sequences" />
        <param argument="-frame" type="select" label="Frame(s) to translate">
            <option value="1">Frame 1</option>
            <option value="2">Frame 2</option>
            <option value="3">Frame 3</option>
            <option value="F">Forward three frames</option>
            <option value="-1">Frame -1</option>
            <option value="-2">Frame -2</option>
            <option value="-3">Frame -3</option>
            <option value="R">Reverse three frames</option>
            <option value="6">All six frames</option>
        </param>
        <param argument="-table" type="select" label="Code to use">
            <option value="0">Standard</option>
            <option value="1">Standard (with alternative initiation codons)</option>
            <option value="2">Vertebrate Mitochondrial</option>
            <option value="3">Yeast Mitochondrial</option>
            <option value="4">Mold, Protozoan, Coelenterate Mitochondrial and Mycoplasma/Spiroplasma</option>
            <option value="5">Invertebrate Mitochondrial</option>
            <option value="6">Ciliate Macronuclear and Dasycladacean</option>
            <option value="9">Echinoderm Mitochondrial</option>
            <option value="10">Euplotid Nuclear</option>
            <option value="11">Bacterial</option>
            <option value="12">Alternative Yeast Nuclear</option>
            <option value="13">Ascidian Mitochondrial</option>
            <option value="14">Flatworm Mitochondrial</option>
            <option value="15">Blepharisma Macronuclear</option>
            <option value="16">Chlorophycean Mitochondrial</option>
            <option value="21">Trematode Mitochondrial</option>
            <option value="22">Scenedesmus obliquus</option>
            <option value="23">Thraustochytrium Mitochondrial</option>
        </param>
        <param argument="-regions" type="text" value="" label="Regions to translate" />
        <param argument="-trim" type="select" label="Remove all 'X' and '*' characters from the right end of the translation">
            <option value="no">No</option>
            <option value="yes">Yes</option>
        </param>
        <param argument="-clean" type="select" label="Change all STOP codon positions from the '*' character to 'X'">
            <option value="no">No</option>
            <option value="yes">Yes</option>
        </param>
        <param argument="-alternative" type="select" label="Define frame '-1' as using the set of codons starting with the last codon of the sequence">
            <option value="no">No</option>
            <option value="yes">Yes</option>
        </param>
        <param name="out_format1" argument="-osformat2" type="select" label="Output sequence file format">
            <option value="fasta">FASTA (m)</option>
            <option value="acedb">ACeDB (m)</option>
            <option value="asn1">ASN.1 (m)</option>
            <option value="clustal">Clustal (m)</option>
            <option value="codata">CODATA (m)</option>
            <option value="embl">EMBL (m)</option>
            <option value="fitch">Fitch (m)</option>
            <option value="gcg">Wisconsin Package GCG 9.x and 10.x (s)</option>
            <option value="genbank">GENBANK (m)</option>
            <option value="gff">GFF (m)</option>
            <option value="hennig86">Hennig86 (m)</option>
            <option value="ig">Intelligenetics (m)</option>
            <option value="jackknifer">Jackknifer (m)</option>
            <option value="jackknifernon">Jackknifernon (m)</option>
            <option value="mega">Mega (m)</option>
            <option value="meganon">Meganon (m)</option>
            <option value="msf">Wisconsin Package GCG's MSF (m)</option>
            <option value="pir">NBRF (PIR) (m)</option>
            <option value="ncbi">NCBI style FASTA (m)</option>
            <option value="nexus">Nexus/PAUP (m)</option>
            <option value="nexusnon">Nexusnon/PAUPnon (m)</option>
            <option value="phylip">PHYLIP interleaved (m)</option>
            <option value="phylipnon">PHYLIP non-interleaved (m)</option>
            <option value="selex">SELEX (m)</option>
            <option value="staden">Staden (s)</option>
            <option value="strider">DNA strider (m)</option>
            <option value="swiss">SwisProt entry (m)</option>
            <option value="text">Plain sequence (s)</option>
            <option value="treecon">Treecon (m)</option>
        </param>
    </inputs>
    <outputs>
        <data name="out_file1" format="fasta" />
    </outputs>
    <tests>
        <test>
            <param name="input1" value="2.fasta"/>
            <param name="frame" value="1"/>
            <param name="table" value="0"/>
            <param name="regions" value=""/>
            <param name="trim" value="no"/>
            <param name="clean" value="no"/>
            <param name="alternative" value="no"/>
            <param name="out_format1" value="fasta"/>
            <output name="out_file1" file="emboss_transeq_out.fasta"/>
        </test>
    </tests>
    <help><![CDATA[
.. class:: warningmark

The input dataset needs to be sequences.

-----

You can view the original documentation here_.

.. _here: http://galaxy-iuc.github.io/emboss-5.0-docs/transeq.html
    ]]></help>
    <expand macro="citations" />
</tool>