annotate emboss_extractfeat.xml @ 14:2e0fb4bc860e draft

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

<tool id="EMBOSS: extractfeat34" name="extractfeat" version="@VERSION@.1">
  <!-- tool tested with documentation, functional test not designed due to empty files resulting from test input sequences -->
  <description>Extract features from a sequence</description>
  <macros>
    <import>macros.xml</import>
  </macros>
  <expand macro="requirements" />
  <code file="emboss_format_corrector.py" />
  <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 name="input1" type="data" format="data" label="Sequences" />
    <param name="before" type="integer" value="0" label="Number of bases or residues before the feature to include in the extracted sequence" />
    <param name="after" type="integer" value="0" label="Number of bases or residues after the feature to include in the extracted sequence" />
    <param name="source" type="text" value="*" label="Feature source" />
    <param name="type" type="text" value="*" label="Feature type" />
    <param name="sense" type="select" label="Feature sense">
      <option value="0">Any sense</option>
      <option value="1">Forward sense</option>
      <option value="-1">Reverse sense</option>
    </param>
    <param name="minscore" type="float" value="0.0" label="Minimum score" />
    <param name="maxscore" type="float" value="0.0" label="Maximum score" />
    <param name="tag" type="text" value="*" label="Feature tags" />
    <param name="value" type="text" value="*" label="Tag values" />
    <param name="join" type="select" label="Join features">
      <option value="no">No</option>
      <option value="yes">Yes</option>
    </param>
    <param name="featinname" type="select" label="Put feature type in sequence name">
      <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" />
    <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>
  <help>
    You can view the original documentation here_.

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