# HG changeset patch
# User jfb
# Date 1529946805 14400
# Node ID ca6ead0ba4ed2dd5335f4a2807a17fc65cf21861
# Parent  e2fc6666ce139dbdf5514d7b980f2bb77adaffaa
Uploaded

diff -r e2fc6666ce13 -r ca6ead0ba4ed ST Kinamine/STKinamine.xml
--- a/ST Kinamine/STKinamine.xml	Mon Jun 25 13:04:10 2018 -0400
+++ b/ST Kinamine/STKinamine.xml	Mon Jun 25 13:13:25 2018 -0400
@@ -33,12 +33,11 @@
     <help><![CDATA[
 	
 	THIS TOOL IS INTENDED TO USE ONLY WITH SERINE-THREONINE KALIP OUTPUTS!  IF YOURS IS A TYROSINE KINASE, TURN BACK AND DO NOT USE THIS TOOL!
+	
 Kinamine takes a Distinct Peptide Report and extracts from it all peptides containing a phospho(Y), along with the 7 amino acids N- and C- terminal to the pY in that peptide (assuming they were discovered at a threshold above the given FDR value).  This file is the *Substrates* file
 Additionally, all discovered peptides are assumed to have come from a protein.  For every phospho(Y) peptide, KinaMine takes the associated protein accession number, searches the FASTA file for that accession number and returns the amino acid percent composition of the protein(s) which that peptide came from.  This file is the *Substrate Background Frequency* file
 This tool is intended to be used in conjunction with Negative Motif Finder and Kinatest, the three together creating a GalaxyP version of the KINATEST-ID workbook.
 
-java -Djava.awt.headless=true -jar ST_KinaMine.jar FDRreport.txt reference.fasta outputs 3 output
-
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 Inputs
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