view emboss_trimest.xml @ 19:d0847fe9b443 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit 18de4aa9ba00124b1b3e3afe14219e46931e58a9"

<tool id="EMBOSS: trimest102" name="trimest" version="@VERSION@.1">
  <description>Trim poly-A tails off EST sequences</description>
  <macros>
    <import>macros.xml</import>
  </macros>
  <expand macro="requirements" />
  <code file="emboss_format_corrector.py" />
  <command>trimest -sequence '$input1' -outseq '$out_file1' -minlength $minlength -mismatches $mismatches -reverse $reverse -tolower $tolower -fiveprime $fiveprime -osformat2 $out_format1
  -auto</command>
  <inputs>
    <param name="input1" type="data" format="fasta" label="Sequences" />
    <param name="minlength" type="integer" value="4" label="Minimum length that a poly-A (or poly-T) tail must have before it is removed" />
    <param name="mismatches" type="integer" value="1" label="Number of fewer mismatched non-A bases in a poly-A tail" />
    <param name="reverse" type="select" label="Change the sequence to the forward sense when it is written out">
      <option value="yes">Yes</option>
      <option value="no">No</option>
    </param>
    <param name="tolower" type="select" label="Mask poly-A by converting to lowercase">
      <option value="no">No</option>
      <option value="yes">Yes</option>
    </param>
    <param name="fiveprime" type="select" label="Inspect 5' end of the sequence for poly-T tails">
      <option value="yes">Yes</option>
      <option value="no">No</option>
    </param>
    <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="input1" value="2.fasta"/>
      <param name="minlength" value="4"/>
      <param name="mismatches" value="1"/>
      <param name="reverse" value="yes"/>
      <param name="tolower" value="no"/>
      <param name="fiveprime" value="yes"/>
      <param name="out_format1" value="fasta"/>
      <output name="out_file1" file="emboss_trimest_out.fasta"/>
    </test>
  </tests>
  <help>
.. 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/trimest.html
  </help>
  <expand macro="citations" />
</tool>