--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/zippable Kinamine/Kinamine.xml	Tue Feb 20 14:41:44 2018 -0500
@@ -0,0 +1,49 @@
+<tool id="kinamine_java" name="Kinamine_7_to_7" version="0.5.0">
+    <description>Extracts phosphorylated motifs</description>
+    <requirements>
+       <requirement type="package" version="8.0.1440.1">Java</requirement>
+    </requirements>
+    <command><![CDATA[
+        mkdir -p output &&
+        java -Djava.awt.headless=true -cp '$__tool_directory__/Kinamine.jar' kinamine.KinaMine $FDRreport $reference output $fdr
+    ]]></command>
+    <inputs>
+        <param format="txt" name="FDRreport" type="data" label="Distinct Peptide Report"/>
+        <param format="fasta" name="reference" type="data" label="FASTA reference genome"/>
+        <param name="fdr" type="integer" value"1" min="1"  max="100"  label="FDR"/>
+        <param name="outGroup" type="text" value"kinase" label="Kinase Name"/>
+    </inputs>      
+    <outputs>
+        <data format="csv" name="Substrates" from_work_dir="output_Substrates.csv" label="${outGroup}_Substrates.csv"/>
+        <data format="csv" name="SBF" from_work_dir="output2_Substrate Background Frequency.csv" label="$[outGroup]_Substrate Background Frequency"/>
+    </outputs>
+    <tests>
+        <test>
+            <param name="FDRreport" ftype="txt" value="FDRreport.csv"/>
+            <param name="reference" ftype="fasta" value="reference.fasta"/>
+            <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 takes a Distinct Peptide Report and extracts from it all phospho-motifs that were discovered at a threshold above a given FDR value.  This tool is intended to be used in conjunction with Negative Motif Finder and Kinatest.R, the three together creating a GalaxyP version of the KINATEST-ID workbook.
+
+===========
+Inputs
+===========
+**Distinct Peptide Report**
+This is... ask Minervo
+
+**FASTA reference**
+This should be a FASTA taken from the Reviewed Human Uniprot database, consisting of all human proteins plus a list of common Mass Spectrometry contaminants
+
+    ]]></help>
+    <citations>
+        <citation type="doi">10.1021/ja507164a</citation>
+    </citations>
+</tool>
+