view emboss_extractfeat.xml @ 10:9b98d3d903c6 draft

planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/emboss_5 commit fc158bfe5f5927dc199321a2cf43310373cbc8ba

<tool id="EMBOSS: extractfeat34" name="extractfeat" version="5.0.0">
  <!-- tool tested with documentation, functional test not designed due to empty files resulting from test input sequences -->  
  <description>Extract features from a sequence</description>
  <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
  <command>extractfeat -sequence $input1 -outseq $out_file1 -before $before -after $after -source "$source" -type "$type" -sense $sense -minscore $minscore -maxscore $maxscore -tag "$tag" -value
  "$value" -join $join -featinname $featinname -describe "$describe" -osformat2 $out_format1 -auto</command>
  <inputs>
    <param format="data" name="input1" type="data">
      <label>Sequences</label>
    </param>
    <param name="before" type="text" value="0">
      <label>Number of bases or residues before the feature to include in the extracted sequence</label>
    </param>
    <param name="after" type="text" value="0">
      <label>Number of bases or residues after the feature to include in the extracted sequence</label>
    </param>
    <param name="source" type="text" value="*">
      <label>Feature source</label>
    </param>
    <param name="type" type="text" value="*">
      <label>Feature type</label>
    </param>
    <param name="sense" type="select">
      <label>Feature sense</label>
      <option value="0">Any sense</option>
      <option value="1">Forward sense</option>
      <option value="-1">Reverse sense</option>
    </param>
    <param name="minscore" type="text" value="0.0">
      <label>Minimum score</label>
    </param>
    <param name="maxscore" type="text" value="0.0">
      <label>Maximum score</label>
    </param>
    <param name="tag" type="text" value="*">
      <label>Feature tags</label>
    </param>
    <param name="value" type="text" value="*">
      <label>Tag values</label>
    </param>
    <param name="join" type="select">
      <label>Join features</label>
      <option value="no">No</option>
      <option value="yes">Yes</option>
    </param>
    <param name="featinname" type="select">
      <label>Put feature type in sequence name</label>
      <option value="no">No</option>
      <option value="yes">Yes</option>
    </param>
    <param name="describe" type="text" value="">
      <label>Specify one or more tag names that should be added to the output sequence Description text</label>
    </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>
  <code file="emboss_format_corrector.py" />
  <help>
    You can view the original documentation here_.
    
    .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/extractfeat.html

------

**Citation**

For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. &lt;http://www.ncbi.nlm.nih.gov/pubmed/10827456&gt;`_

If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. &lt;http://www.ncbi.nlm.nih.gov/pubmed/17568012&gt;`_
  </help>
</tool>