Mercurial > repos > jfb > kinatest_r_7_7testing

changeset 12:cf93d3535a31 draft

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Uploaded
author jfb
date Thu, 08 Feb 2018 14:51:27 -0500
parents a36f9cce16a3
children d71eb1d66a88
files kinatestid_r/Kinatest-R_part1.R kinatestid_r/kinatestid_r.xml
diffstat 2 files changed, 49 insertions(+), 49 deletions(-) [+]
line wrap: on
line diff
--- a/kinatestid_r/Kinatest-R_part1.R	Thu Feb 08 14:51:12 2018 -0500
+++ b/kinatestid_r/Kinatest-R_part1.R	Thu Feb 08 14:51:27 2018 -0500
@@ -7,9 +7,9 @@
 
 
 
-FILENAME<-"output1"
-FILENAME2<-"output2"
-FILENAME3<-"output3"
+FILENAME<-"output1.csv"
+FILENAME2<-"output2.csv"
+FILENAME3<-"output3.csv"
 
 
 
--- a/kinatestid_r/kinatestid_r.xml	Thu Feb 08 14:51:12 2018 -0500
+++ b/kinatestid_r/kinatestid_r.xml	Thu Feb 08 14:51:27 2018 -0500
@@ -1,46 +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="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>
-
+<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>
+