diff NMF/NMF.xml @ 0:dd301fc4b54e draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/NMF/NMF.xml	Fri Feb 23 16:37:29 2018 -0500
@@ -0,0 +1,47 @@
+<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>
+