# HG changeset patch
# User jfb
# Date 1517955127 18000
# Node ID c0de8ed09b7d95fd3ba6961c3004a539fd491880

Uploaded

diff -r 000000000000 -r c0de8ed09b7d kinatestid_r.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/kinatestid_r.xml	Tue Feb 06 17:12:07 2018 -0500
@@ -0,0 +1,46 @@
+<tool id="kinatestid_r" name="Kinatest-ID 7_to_7" version="0.1.0">
+    <description>calculate optimal substrates</description>
+    <requirements>
+       <requirement type="package">R</requirement>
+    </requirements>
+    <command><![CDATA[
+        ln -s '$__tool_directory__/screener7-7.csv' screener &&
+        ln -s '$substrates' input1 && 
+        ln -s '$negatives' input2 && 
+        ln -s '$SBF' input3 &&
+        Rscript '$__tool_directory__/Kinatest-R_part1.R' &&
+        Rscript '$__tool_directory__/Kinatest-R_part2.R' &&
+        mv output1 output1.csv &&
+        mv output2 output2.csv &&
+        mv output3 output3.csv
+    ]]></command>
+    <inputs>
+        <param format="csv" name="substrates" type="data" label="Positive/Phosphorylated Substrate List"/>
+        <param format="csv" name="negatives" type="data" label="Negative/unPhosphorylated Substrate List"/>
+        <param format="csv" name="SBF" type="data" label="Substrate Background Frequency List"/>
+    </inputs>      
+    <outputs>
+        <data format="csv" name="SDtable" from_work_dir="output1.csv" label="Standard Deviation Table"/>
+        <data format="csv" name="EPM" from_work_dir="output2.csv" label="Endogenous Probability Matrix"/>
+        <data format="csv" name="Characterization" from_work_dir="output3.csv" label="Characterization Table"/>
+    </outputs>
+    <tests>
+        <test>
+            <param name="substrates" ftype="tabular" value="substrates.tsv"/>
+            <param name="negatives" ftype="tabular" value="negatives.tsv"/>
+            <param name="SBF" ftype="tabular" value="SBF.tsv"/>
+            <output name="SDtable" file="SDtable.csv"/>
+            <output name="EPM" file="EPM.csv"/>
+            <output name="Characterization" file="Characterization.csv"/>
+        </test>
+    </tests>
+
+    
+    <help><![CDATA[
+This tool is intended for use in conjunction with KinaMine.jar and Negative Motif Finder.  Using the outputs from those two functions (The Positive and Negative substrates as well as the Substrate Background Frequency) this tool calculates optimal substrates
+    ]]></help>
+    <citations>
+        <citation type="doi">10.1021/ja507164a</citation>
+    </citations>
+</tool>
+