/tools/emboss_5/emboss_digest.xml
https://bitbucket.org/cistrome/cistrome-harvard/ · XML · 71 lines · 67 code · 4 blank · 0 comment · 0 complexity · 37d7adbe0e3a676cd4504e07a9e43c16 MD5 · raw file
- <tool id="EMBOSS: digest23" name="digest" version="5.0.0">
- <description>Protein proteolytic enzyme or reagent cleavage digest</description>
- <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
- <command>digest -seqall $input1 -outfile $out_file1 -menu $menu -unfavoured $unfavoured -overlap $overlap -allpartials $allpartials -rformat2 $out_format1 -auto</command>
- <inputs>
- <param format="data" name="input1" type="data">
- <label>Sequence</label>
- </param>
- <param name="menu" type="select">
- <label>Enzyme/Reagent</label>
- <option value="1">Trypsin</option>
- <option value="2">Lys-C</option>
- <option value="3">Arg-C</option>
- <option value="4">Asp-N</option>
- <option value="5">V8-bicarb</option>
- <option value="6">V8-phosph</option>
- <option value="7">Chymotrypsin</option>
- <option value="8">CNBr</option>
- </param>
- <param name="unfavoured" type="select">
- <label>Trypsin will not normally cut after a K if it is followed by (e.g.) another K or a P. Specifying this shows those cuts, as well as the favoured ones.</label>
- <option value="no">No</option>
- <option value="yes">Yes</option>
- </param>
- <param name="overlap" type="select">
- <label>Used for partial digestion. Shows all cuts from favoured cut sites plus 1..3, 2..4, 3..5 etc but not (e.g.) 2..5. Overlaps are therefore fragments with exactly one potential cut site
- within it.</label>
- <option value="no">No</option>
- <option value="yes">Yes</option>
- </param>
- <param name="allpartials" type="select">
- <label>As for overlap but fragments containing more than one potential cut site are included.</label>
- <option value="no">No</option>
- <option value="yes">Yes</option>
- </param>
- <param name="out_format1" type="select">
- <label>Output Report File Format</label>
- <option value="seqtable">SeqTable</option>
- <option value="embl">EMBL</option>
- <option value="genbank">GENBANK</option>
- <option value="gff">GFF</option>
- <option value="pir">PIR</option>
- <option value="swiss">SwissProt</option>
- <option value="dbmotif">DbMotif</option>
- <option value="diffseq">Diffseq</option>
- <option value="excel">Excel (tab delimited)</option>
- <option value="feattable">FeatTable</option>
- <option value="motif">Motif</option>
- <option value="regions">Regions</option>
- <option value="simple">SRS Simple</option>
- <option value="srs">SRS</option>
- <option value="table">Table</option>
- <option value="tagseq">TagSeq</option>
- </param>
- </inputs>
- <outputs>
- <data format="digest" 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/digest.html
-
- ------
-
- **Citation**
-
- 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. <http://www.ncbi.nlm.nih.gov/pubmed/17568012>`_
- </help>
- </tool>