--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/ProteinDigestor.xml	Fri May 10 17:15:08 2013 -0400
@@ -0,0 +1,93 @@
+<!-- 
+# =====================================================
+# $Id: ProteinDigestor.xml 90 2011-01-19 13:20:31Z pieter.neerincx@gmail.com $
+# $URL: https://trac.nbic.nl/svn/galaxytools/trunk/tools/general/FastaTools/ProteinDigestor.xml $
+# $LastChangedDate: 2011-01-19 07:20:31 -0600 (Wed, 19 Jan 2011) $ 
+# $LastChangedRevision: 90 $
+# $LastChangedBy: pieter.neerincx@gmail.com $
+# =====================================================
+-->
+<tool id="ProteinDigestor1" name="ProteinDigestor" version="2.0">
+  <description>In silico digestion of proteins into peptides</description>
+  <command interpreter="perl">ProteinDigestor.pl -i $input -o $output -r '$rule' -l ERROR</command>
+  <inputs>
+    <param format="fasta" name="input" type="data" label="Proteins to digest" help="in FASTA format."/>
+    <param name="rule" type="select" label="Protease">
+      <!--<label>Protease</label>-->
+      <option value="c:K,R:P=1">Trypsin</option>
+      <option value="c:K,R">Trypsin/P</option>
+      <option value="c:F,L,W,Y:P=1">Chymotrypsin</option>
+      <option value="c:F,L,W,Y">Chymotrypsin/P</option>
+      <option value="c:E,Z:P=1">V8_E</option>
+      <option value="c:E,D,B,Z:P=1">V8_DE</option>
+      <option value="c:K:P=1">LysC</option>
+      <option value="c:K">LysC/P</option>
+      <option value="n:K">LysN/P</option>
+    </param>
+  </inputs>
+  <outputs>
+    <data format="tabular" name="output" label="${rule.value_label} digest on ${input.name}"/>
+  </outputs>
+  <!--
+  <tests>
+    <test>
+      <param name="input"       value="" />
+      <output name="output"     file="" />
+    </test>
+  </tests>
+  -->
+  <help>
+
+.. class:: infomark
+
+**What it does**
+
+This tool digests protein sequences from a FASTA file.\
+In addition some statistics are calculated for each peptide:
+
+ * Molecular weight in Da (MW).
+ * Isoelectric point (pI)
+ * Net charge assuming K, R and H add +1 and D and E add -1 to the net charge of the peptide.
+ * The mount of potential phosphorilation sites (S, T or Y amino acids).
+
+**Getting input data** 
+
+This tool requires protein sequences in FASTA format. \
+If your protein sequences are not in FASTA format, you'll have to convert it first.\
+For sequences in tab delimited files for example you can use the *FASTA manipulation* -> *Tabular-to-FASTA* tool.
+
+-----
+
+**Example**
+
+If for example the protein sequences in FASTA format would be this::
+
+   >FamousDatabase:Q42593Z L-ascorbate peroxidase T, chloroplastic;
+   MSVSLSAKASHLLCSSTRVSLSPAVTSSSSSPVVRPALSSSTS*
+   >FamousDatabase:A0MQ79Z Ascorbate peroxidase;
+   MVKPNYPVVSEEYLIAVDKAKKKLRGFIAEKNCAPLMLRL*
+
+and you would perform an *in silico* digest with Trypsin, the result will look like this::
+   
+   Protein ID               Peptide                     MW         pI                  Charge   number S   number T   number Y
+   FamousDatabase:Q42593Z   ASHLLCSSTR                  1074.225   8.30219268798828    2        3          1          0
+   FamousDatabase:Q42593Z   VSLSPAVTSSSSSPVVRPALSSSTS   2390.61    9.72000885009766    1        11         2          0
+   FamousDatabase:Q42593Z   MSVSLSAK                    821.995    8.50011444091797    1        3          0          0
+   FamousDatabase:A0MQ79Z   NCAPLMLR                    917.175    8.24974822998047    1        0          0          0
+   FamousDatabase:A0MQ79Z   K                           146.19     8.75005340576172    1        0          0          0
+   FamousDatabase:A0MQ79Z   K                           146.19     8.75005340576172    1        0          0          0
+   FamousDatabase:A0MQ79Z   LR                          287.375    9.75002288818359    1        0          0          0
+   FamousDatabase:A0MQ79Z   GFIAEK                      663.775    6.00136566162109    0        0          0          0
+   FamousDatabase:A0MQ79Z   L                           131.18     5.52498626708984    0        0          0          0
+   FamousDatabase:A0MQ79Z   AK                          217.265    8.79502105712891    1        0          0          0
+   FamousDatabase:A0MQ79Z   MVKPNYPVVSEEYLIAVDK         2194.59    4.67711639404297   -1        1          0          2
+
+
+========================================================
+*Need to digest with another protease?*
+========================================================
+
+Contact your local bioinformaticians to add other proteases...
+
+  </help>
+</tool>