# HG changeset patch
# User jfb
# Date 1519751517 18000
# Node ID c2c215a5dea0d47eb16a5ac243f0586cbc65fda3
# Parent  eac197ac2fb22e9681a83194d81b2f263fa1e896
Uploaded

diff -r eac197ac2fb2 -r c2c215a5dea0 transposy/._NMF.xml
Binary file transposy/._NMF.xml has changed
diff -r eac197ac2fb2 -r c2c215a5dea0 transposy/._transposy.xml
Binary file transposy/._transposy.xml has changed
diff -r eac197ac2fb2 -r c2c215a5dea0 transposy/NMF.xml
--- a/transposy/NMF.xml	Tue Feb 27 11:29:18 2018 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,47 +0,0 @@
-<tool id="kinamine_java" name="Negative-Motif-Finder 7_to_7" version="1.0.0">
-    <description>discover unphosphorylated substrates</description>
-    <requirements>
-       <requirement type="package">R</requirement>
-    </requirements>
-    <command><![CDATA[
-		ln -s '$FASTA' input1.tabular && 
-        ln -s '$positives' input2.csv &&
-		ln -s '$SBF' input3.csv &&
-        Rscript '$__tool_directory__/NMF.R'
-    ]]></command>
-    <inputs>
-		<param format="csv" name="SBF" type="data" label="Substrate Background Frequency"/>
-        <param format="tabular" name="FASTA" type="data" label="Human Proteome Reference"/>
-        <param format="csv" name="positives" type="data" label="Positive/Phosphorylated Substrate List"/>
-    </inputs>      
-    <outputs>
-        <data format="csv" name="Negatives" from_work_dir="output1.csv" label="Negative Motifs.csv"/>
-    </outputs>
-    <tests>
-        <test>
-            <param name="FASTA" ftype="csv" value="reference.csv"/>
-            <param name="positives" ftype="csv" value="substrates.csv"/>
-            <param name="SBF" ftype="csv" value="SBF.csv"/>
-			<output name="Negatives" file="negatives.csv"/>
-        </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
-
-    ]]></help>
-    <citations>
-        <citation type="doi">10.1021/ja507164a</citation>
-    </citations>
-</tool>
-
diff -r eac197ac2fb2 -r c2c215a5dea0 transposy/transposy.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/transposy/transposy.xml	Tue Feb 27 12:11:57 2018 -0500
@@ -0,0 +1,29 @@
+<tool id="transposy" name="Transposing_Data_Cleanup_For_Kinamine" version="1.0.0">
+    <description>data cleanup for Kinamine</description>
+    <requirements>
+       <requirement type="package">R</requirement>
+    </requirements>
+    <command><![CDATA[
+		ln -s '$transposy' transposy.csv && 
+        Rscript '$__tool_directory__/transposy.R'
+    ]]></command>
+    <inputs>
+		<param format="csv" name="transposy" type="data" label="Transpose_Data"/>
+    </inputs>      
+    <outputs>
+        <data format="csv" name="output" from_work_dir="outputy.csv" label="output.csv"/>
+    </outputs>
+    <tests>
+        <test>
+            <param name="transposy" ftype="csv" value="transposy.csv"/>
+			<output name="output" file="output.csv"/>
+        </test>
+    </tests>
+    <help><![CDATA[	This simply tool is only intended for a specific step in the kinatest pathway wherein it performs some data cleanup.
+
+    ]]></help>
+    <citations>
+        <citation type="doi">10.1021/ja507164a</citation>
+    </citations>
+</tool>
+