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/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
 1<tool id="EMBOSS: digest23" name="digest" version="5.0.0">
 2  <description>Protein proteolytic enzyme or reagent cleavage digest</description>
 3  <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
 4  <command>digest -seqall $input1 -outfile $out_file1 -menu $menu -unfavoured $unfavoured -overlap $overlap -allpartials $allpartials -rformat2 $out_format1 -auto</command>
 5  <inputs>
 6    <param format="data" name="input1" type="data">
 7      <label>Sequence</label>
 8    </param>
 9    <param name="menu" type="select">
10      <label>Enzyme/Reagent</label>
11      <option value="1">Trypsin</option>
12      <option value="2">Lys-C</option>
13      <option value="3">Arg-C</option>
14      <option value="4">Asp-N</option>
15      <option value="5">V8-bicarb</option>
16      <option value="6">V8-phosph</option>
17      <option value="7">Chymotrypsin</option>
18      <option value="8">CNBr</option>
19    </param>
20    <param name="unfavoured" type="select">
21      <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>
22      <option value="no">No</option>
23      <option value="yes">Yes</option>
24    </param>
25    <param name="overlap" type="select">
26      <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
27      within it.</label>
28      <option value="no">No</option>
29      <option value="yes">Yes</option>
30    </param>
31    <param name="allpartials" type="select">
32      <label>As for overlap but fragments containing more than one potential cut site are included.</label>
33      <option value="no">No</option>
34      <option value="yes">Yes</option>
35    </param>
36    <param name="out_format1" type="select">
37      <label>Output Report File Format</label>
38      <option value="seqtable">SeqTable</option>
39      <option value="embl">EMBL</option>
40      <option value="genbank">GENBANK</option>
41      <option value="gff">GFF</option>
42      <option value="pir">PIR</option>
43      <option value="swiss">SwissProt</option>
44      <option value="dbmotif">DbMotif</option>
45      <option value="diffseq">Diffseq</option>
46      <option value="excel">Excel (tab delimited)</option>
47      <option value="feattable">FeatTable</option>
48      <option value="motif">Motif</option>
49      <option value="regions">Regions</option>
50      <option value="simple">SRS Simple</option>
51      <option value="srs">SRS</option>
52      <option value="table">Table</option>
53      <option value="tagseq">TagSeq</option>
54    </param>
55  </inputs>
56  <outputs>
57    <data format="digest" name="out_file1" />
58  </outputs>
59  <code file="emboss_format_corrector.py" />
60  <help>
61    You can view the original documentation here_.
62    
63    .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/digest.html
64
65------
66
67**Citation**
68
69If 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;`_
70  </help>
71</tool>