comparison emboss_digest.xml @ 11:0e2484b6829b draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit b583bbeb8fc90cd4b1e987a56982e7cf4aed1a68
author iuc
date Mon, 30 Jan 2017 13:27:40 -0500
parents 9b98d3d903c6
children 27c43fb015f0
comparison
equal deleted inserted replaced
10:9b98d3d903c6 11:0e2484b6829b
1 <tool id="EMBOSS: digest23" name="digest" version="5.0.0"> 1 <tool id="EMBOSS: digest23" name="digest" version="5.0.0">
2 <description>Protein proteolytic enzyme or reagent cleavage digest</description> 2 <description>Protein proteolytic enzyme or reagent cleavage digest</description>
3 <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements> 3 <macros>
4 <command>digest -seqall $input1 -outfile $out_file1 -menu $menu -unfavoured $unfavoured -overlap $overlap -allpartials $allpartials -rformat2 $out_format1 -auto</command> 4 <import>macros.xml</import>
5 </macros>
6 <expand macro="requirements" />
7 <code file="emboss_format_corrector.py" />
8 <command>digest -seqall '$input1' -outfile '$out_file1' -menu $menu -unfavoured $unfavoured -overlap $overlap -allpartials $allpartials -rformat2 $out_format1 -auto</command>
5 <inputs> 9 <inputs>
6 <param format="data" name="input1" type="data"> 10 <param name="input1" type="data" format="data" label="Sequence" />
7 <label>Sequence</label> 11 <param name="menu" type="select" label="Enzyme/Reagent">
8 </param>
9 <param name="menu" type="select">
10 <label>Enzyme/Reagent</label>
11 <option value="1">Trypsin</option> 12 <option value="1">Trypsin</option>
12 <option value="2">Lys-C</option> 13 <option value="2">Lys-C</option>
13 <option value="3">Arg-C</option> 14 <option value="3">Arg-C</option>
14 <option value="4">Asp-N</option> 15 <option value="4">Asp-N</option>
15 <option value="5">V8-bicarb</option> 16 <option value="5">V8-bicarb</option>
16 <option value="6">V8-phosph</option> 17 <option value="6">V8-phosph</option>
17 <option value="7">Chymotrypsin</option> 18 <option value="7">Chymotrypsin</option>
18 <option value="8">CNBr</option> 19 <option value="8">CNBr</option>
19 </param> 20 </param>
20 <param name="unfavoured" type="select"> 21 <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">
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> 22 <option value="no">No</option>
23 <option value="yes">Yes</option> 23 <option value="yes">Yes</option>
24 </param> 24 </param>
25 <param name="overlap" type="select"> 25 <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">
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> 26 <option value="no">No</option>
29 <option value="yes">Yes</option> 27 <option value="yes">Yes</option>
30 </param> 28 </param>
31 <param name="allpartials" type="select"> 29 <param name="allpartials" type="select" label="As for overlap but fragments containing more than one potential cut site are included">
32 <label>As for overlap but fragments containing more than one potential cut site are included.</label>
33 <option value="no">No</option> 30 <option value="no">No</option>
34 <option value="yes">Yes</option> 31 <option value="yes">Yes</option>
35 </param> 32 </param>
36 <param name="out_format1" type="select"> 33 <param name="out_format1" type="select" label="Output report file format">
37 <label>Output Report File Format</label>
38 <option value="seqtable">SeqTable</option> 34 <option value="seqtable">SeqTable</option>
39 <option value="embl">EMBL</option> 35 <option value="embl">EMBL</option>
40 <option value="genbank">GENBANK</option> 36 <option value="genbank">GENBANK</option>
41 <option value="gff">GFF</option> 37 <option value="gff">GFF</option>
42 <option value="pir">PIR</option> 38 <option value="pir">PIR</option>
52 <option value="table">Table</option> 48 <option value="table">Table</option>
53 <option value="tagseq">TagSeq</option> 49 <option value="tagseq">TagSeq</option>
54 </param> 50 </param>
55 </inputs> 51 </inputs>
56 <outputs> 52 <outputs>
57 <data format="digest" name="out_file1" /> 53 <data name="out_file1" format="digest" />
58 </outputs> 54 </outputs>
59 <code file="emboss_format_corrector.py" />
60 <help> 55 <help>
61 You can view the original documentation here_. 56 You can view the original documentation here_.
62
63 .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/digest.html
64 57
65 ------ 58 .. _here: http://galaxy-iuc.github.io/emboss-5.0-docs/digest.html
66
67 **Citation**
68
69 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;`_
70
71 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;`_
72 </help> 59 </help>
60 <expand macro="citations" />
73 </tool> 61 </tool>