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