# HG changeset patch
# User jfb
# Date 1517956003 18000
# Node ID 64c66b59d76913d1cd490f0d355832983a4eefe1
# Parent  72f4afa462657e6e79453b309f95ee8ecb774476
Uploaded

diff -r 72f4afa46265 -r 64c66b59d769 kinatestid_r.xml
--- a/kinatestid_r.xml	Tue Feb 06 17:25:40 2018 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,46 +0,0 @@
-<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="csv" value="substrates.csv"/>
-            <param name="negatives" ftype="csv" value="negatives.csv"/>
-            <param name="SBF" ftype="csv" value="SBF.csv"/>
-            <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>
-
diff -r 72f4afa46265 -r 64c66b59d769 kinatestid_r/kinatestid_r.xml
--- a/kinatestid_r/kinatestid_r.xml	Tue Feb 06 17:25:40 2018 -0500
+++ b/kinatestid_r/kinatestid_r.xml	Tue Feb 06 17:26:43 2018 -0500
@@ -26,9 +26,9 @@
     </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"/>
+            <param name="substrates" ftype="csv" value="substrates.csv"/>
+            <param name="negatives" ftype="csv" value="negatives.csv"/>
+            <param name="SBF" ftype="csv" value="SBF.csv"/>
             <output name="SDtable" file="SDtable.csv"/>
             <output name="EPM" file="EPM.csv"/>
             <output name="Characterization" file="Characterization.csv"/>