annotate emboss_newseq.xml @ 13:8992d258e42f draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit 9844cae766e7471d9fa6b2e8356e5194e77f6753

<tool id="EMBOSS: newseq59" name="newseq" version="@VERSION@">
  <description>Type in a short new sequence</description>
  <macros>
    <import>macros.xml</import>
  </macros>
  <expand macro="requirements" />
  <code file="emboss_format_corrector.py" />
  <command>
  <![CDATA[
    newseq
      -outseq '$out_file1'
      -name '$seqname'
      -description '$description'
      -type $type
      -sequence '$sequence'
      -osformat5 $out_format1
      -auto
  ]]>
  </command>
  <inputs>
    <param name="seqname" type="text" value="" label="Name of of the sequence" />
    <param name="description" type="text" value="" label="Description of the sequence" />
    <param name="type" type="select" label="Type of sequence">
      <option value="N">Nucleic</option>
      <option value="P">Protein</option>
    </param>
    <param name="sequence" type="text" value="" label="The sequence itself" />
    <param name="out_format1" 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="seqname" value="cytoc"/>
      <param name="description" value="fragment_of_cytochrome_c"/>
      <param name="type" value="N"/>
      <param name="sequence" value="KKKEERADLIAY"/>
      <param name="out_format1" value="fasta"/>
      <output name="out_file1" file="emboss_newseq_out.fasta"/>
    </test>
  </tests>
  <help>
    You can view the original documentation here_.

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