# HG changeset patch
# User jfb
# Date 1527101956 14400
# Node ID 9610fd10d9413dc5273e9f3d325ed35e5859d0d9
# Parent  6e3a0489af444b56c88d5375ff9c09fc08b53161
Uploaded

diff -r 6e3a0489af44 -r 9610fd10d941 C and D finder/CandD.xml
--- a/C and D finder/CandD.xml	Tue May 22 18:49:28 2018 -0400
+++ b/C and D finder/CandD.xml	Wed May 23 14:59:16 2018 -0400
@@ -1,5 +1,5 @@
 <tool id="commonality_r" name="commonality_finder" version="1.0.0">
-    <description>discover unphosphorylated substrates</description>
+    <description>finds commonality</description>
     <requirements>
        <requirement type="package">R</requirement>
     </requirements>
@@ -11,17 +11,17 @@
         <param format="csv" name="input2.csv" type="data" label="First Substrate Background Frequency"/>
 		<param format="csv" name="input3.csv" type="data" label="Second Substrate Set"/>
 		<param format="csv" name="input4.csv" type="data" label="Second Substrate Background Frequency"/>
-		<param format="csv" name="input5.csv" type="data" label="Substrate Background Frequency"/>
-		<param format="csv" name="input6.csv" type="data" label="Substrate Background Frequency"/>
+		<param format="csv" name="input5.csv" type="data" label="Third Substrate Set"/>
+		<param format="csv" name="input6.csv" type="data" label="Third Substrate Background Frequency"/>
 		<param name="outGroup" type="text" value="kinase" label="Kinase Name"/>
     </inputs>      
     <outputs>
-        <data format="csv" name="Negatives" from_work_dir="output1.csv" label="${outGroup}_Negative Motifs.csv"/>
-		<data format="csv" name="Negatives" from_work_dir="output1.csv" label="${outGroup}_Negative Motifs.csv"/>
-		<data format="csv" name="Negatives" from_work_dir="output1.csv" label="${outGroup}_Negative Motifs.csv"/>
-		<data format="csv" name="Negatives" from_work_dir="output1.csv" label="${outGroup}_Negative Motifs.csv"/>
-		<data format="csv" name="Negatives" from_work_dir="output1.csv" label="${outGroup}_Negative Motifs.csv"/>
-		<data format="csv" name="Negatives" from_work_dir="output1.csv" label="${outGroup}_Negative Motifs.csv"/>
+        <data format="csv" name="Negatives" from_work_dir="output1.csv" label="${outGroup}_First Unshared Substrates.csv"/>
+		<data format="csv" name="Negatives" from_work_dir="output1.csv" label="${outGroup}_First Unshared SBF.csv"/>
+		<data format="csv" name="Negatives" from_work_dir="output1.csv" label="${outGroup}_Second Unshared Substrates.csv"/>
+		<data format="csv" name="Negatives" from_work_dir="output1.csv" label="${outGroup}_Second Unshared SBF.csv"/>
+		<data format="csv" name="Negatives" from_work_dir="output1.csv" label="${outGroup}_Third Unshared Substrates.csv"/>
+		<data format="csv" name="Negatives" from_work_dir="output1.csv" label="${outGroup}_Third Unshared SBF.csv"/>
     </outputs>
     <tests>
         <test>
@@ -32,20 +32,7 @@
         </test>
     </tests>
     <help><![CDATA[
-Using the output from KinaMine, plus the Uniprot file that was used with KinaMine, this program finds all Y-centered motifs which *could* have been present as positive motifs but were not seen by the Mass Spec
-This tool is intended to be used in conjunction with KinaMine 7-7 and Kinatest.R, the three together creating a GalaxyP version of the KINATEST-ID workbook.
-
-
-Inputs
-
-**Substrate Background Frequency**
-**Positive/Phosphorylated Substrate List**
-These two come directly from the KinaMine output
-
-**Human Proteome Reference**
-This should be a tabularized version of a FASTA taken from the Reviewed Human Uniprot database, consisting of all human proteins plus a list of common Mass Spectrometry contaminants.
-This file should be created by using the same FASTA file used for KinaMine and running FASTA to Tabular on it using GalaxyP
-
+	This tool uses the output from 3 Kinamine runs to determine what motifs are shared between the three runs
     ]]></help>
     <citations>
         <citation type="doi">10.1021/ja507164a</citation>