comparison emboss_extractfeat.xml @ 11:0e2484b6829b draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit b583bbeb8fc90cd4b1e987a56982e7cf4aed1a68

10:9b98d3d903c6

<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="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>

11:0e2484b6829b

<tool id="EMBOSS: extractfeat34" name="extractfeat" version="5.0.0.1">
  <!-- 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="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>