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comparison ProteinDigestor.xml @ 0:163892325845 draft default tip

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author galaxyp
date Fri, 10 May 2013 17:15:08 -0400
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1 <!--
2 # =====================================================
3 # $Id: ProteinDigestor.xml 90 2011-01-19 13:20:31Z pieter.neerincx@gmail.com $
4 # $URL: https://trac.nbic.nl/svn/galaxytools/trunk/tools/general/FastaTools/ProteinDigestor.xml $
5 # $LastChangedDate: 2011-01-19 07:20:31 -0600 (Wed, 19 Jan 2011) $
6 # $LastChangedRevision: 90 $
7 # $LastChangedBy: pieter.neerincx@gmail.com $
8 # =====================================================
9 -->
10 <tool id="ProteinDigestor1" name="ProteinDigestor" version="2.0">
11 <description>In silico digestion of proteins into peptides</description>
12 <command interpreter="perl">ProteinDigestor.pl -i $input -o $output -r '$rule' -l ERROR</command>
13 <inputs>
14 <param format="fasta" name="input" type="data" label="Proteins to digest" help="in FASTA format."/>
15 <param name="rule" type="select" label="Protease">
16 <!--<label>Protease</label>-->
17 <option value="c:K,R:P=1">Trypsin</option>
18 <option value="c:K,R">Trypsin/P</option>
19 <option value="c:F,L,W,Y:P=1">Chymotrypsin</option>
20 <option value="c:F,L,W,Y">Chymotrypsin/P</option>
21 <option value="c:E,Z:P=1">V8_E</option>
22 <option value="c:E,D,B,Z:P=1">V8_DE</option>
23 <option value="c:K:P=1">LysC</option>
24 <option value="c:K">LysC/P</option>
25 <option value="n:K">LysN/P</option>
26 </param>
27 </inputs>
28 <outputs>
29 <data format="tabular" name="output" label="${rule.value_label} digest on ${input.name}"/>
30 </outputs>
31 <!--
32 <tests>
33 <test>
34 <param name="input" value="" />
35 <output name="output" file="" />
36 </test>
37 </tests>
38 -->
39 <help>
40
41 .. class:: infomark
42
43 **What it does**
44
45 This tool digests protein sequences from a FASTA file.\
46 In addition some statistics are calculated for each peptide:
47
48 * Molecular weight in Da (MW).
49 * Isoelectric point (pI)
50 * Net charge assuming K, R and H add +1 and D and E add -1 to the net charge of the peptide.
51 * The mount of potential phosphorilation sites (S, T or Y amino acids).
52
53 **Getting input data**
54
55 This tool requires protein sequences in FASTA format. \
56 If your protein sequences are not in FASTA format, you'll have to convert it first.\
57 For sequences in tab delimited files for example you can use the *FASTA manipulation* -> *Tabular-to-FASTA* tool.
58
59 -----
60
61 **Example**
62
63 If for example the protein sequences in FASTA format would be this::
64
65 >FamousDatabase:Q42593Z L-ascorbate peroxidase T, chloroplastic;
66 MSVSLSAKASHLLCSSTRVSLSPAVTSSSSSPVVRPALSSSTS*
67 >FamousDatabase:A0MQ79Z Ascorbate peroxidase;
68 MVKPNYPVVSEEYLIAVDKAKKKLRGFIAEKNCAPLMLRL*
69
70 and you would perform an *in silico* digest with Trypsin, the result will look like this::
71
72 Protein ID Peptide MW pI Charge number S number T number Y
73 FamousDatabase:Q42593Z ASHLLCSSTR 1074.225 8.30219268798828 2 3 1 0
74 FamousDatabase:Q42593Z VSLSPAVTSSSSSPVVRPALSSSTS 2390.61 9.72000885009766 1 11 2 0
75 FamousDatabase:Q42593Z MSVSLSAK 821.995 8.50011444091797 1 3 0 0
76 FamousDatabase:A0MQ79Z NCAPLMLR 917.175 8.24974822998047 1 0 0 0
77 FamousDatabase:A0MQ79Z K 146.19 8.75005340576172 1 0 0 0
78 FamousDatabase:A0MQ79Z K 146.19 8.75005340576172 1 0 0 0
79 FamousDatabase:A0MQ79Z LR 287.375 9.75002288818359 1 0 0 0
80 FamousDatabase:A0MQ79Z GFIAEK 663.775 6.00136566162109 0 0 0 0
81 FamousDatabase:A0MQ79Z L 131.18 5.52498626708984 0 0 0 0
82 FamousDatabase:A0MQ79Z AK 217.265 8.79502105712891 1 0 0 0
83 FamousDatabase:A0MQ79Z MVKPNYPVVSEEYLIAVDK 2194.59 4.67711639404297 -1 1 0 2
84
85
86 ========================================================
87 *Need to digest with another protease?*
88 ========================================================
89
90 Contact your local bioinformaticians to add other proteases...
91
92 </help>
93 </tool>