annotate tools/emboss_5/emboss_trimseq.xml @ 1:cdcb0ce84a1b

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<tool id="EMBOSS: trimseq103" name="trimseq" version="5.0.0">
  <description>Trim ambiguous bits off the ends of sequences</description>
  <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
  <command>trimseq -sequence $input1 -outseq $out_file1 -window "$window" -percent "$percent" -strict $strict -star $star -left $left -right $right -osformat2 $out_format1 -auto</command>
  <inputs>
    <param format="fasta" name="input1" type="data">
      <label>Sequences</label>
    </param>
    <param name="window" size="4" type="text" value="1">
      <label>Window size</label>
    </param>
    <param name="percent" size="5" type="text" value="100.0">
      <label>Threshold of the percentage ambiguity</label>
    </param>
    <param name="strict" type="select">
      <label>Trim all ambiguity codes</label>
      <option value="no">No</option>
      <option value="yes">Yes</option>
    </param>
    <param name="star" type="select">
      <label>In protein sequences, trim off not only X's, but also the *'s</label>
      <option value="no">No</option>
      <option value="yes">Yes</option>
    </param>
    <param name="left" type="select">
      <label>Trim at the start</label>
      <option value="yes">Yes</option>
      <option value="no">No</option>
    </param>
    <param name="right" type="select">
      <label>Trim at the end</label>
      <option value="yes">Yes</option>
      <option value="no">No</option>
    </param>
    <param name="out_format1" type="select">
      <label>Output Sequence File Format</label>
      <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 format="fasta" name="out_file1" />
  </outputs>
  <tests>
    <test>
      <param name="input1" value="2.fasta"/>
      <param name="window" value="1"/>
      <param name="percent" value="100.0"/>
      <param name="strict" value="no"/>
      <param name="star" value="no"/>
      <param name="left" value="yes"/>
      <param name="right" value="yes"/>
      <param name="out_format1" value="fasta"/>
      <output name="out_file1" file="emboss_trimseq_out.fasta"/>
    </test>
  </tests>
  <code file="emboss_format_corrector.py" />
  <help>

.. class:: warningmark 

The input dataset needs to be sequences. 

----- 

    You can view the original documentation here_.
    
    .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/trimseq.html
  </help>
</tool>