changeset 0:fada7c90fb64 draft

First upload, I don't expect this to work

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/zippable Kinamine/.shed.yml	Thu Feb 15 13:03:45 2018 -0500
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+categories: [Computational chemistry]
+description: Kinamine 7_to_7 extract substrates
+homepage_url: https://pubs.acs.org/doi/abs/10.1021/ja507164a
+long_description: This tool is intended for use with a mass spec file.name: kinamine
+owner: blank121
+remote_repository_url: https://github.umn.edu/blank121/KinaMine/tree/Galaxy-7-7

Binary file zippable Kinamine/KinaMine 7 to 7.jar has changed

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/zippable Kinamine/Kinamine.xml	Thu Feb 15 13:03:45 2018 -0500
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+<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[
+        ln -s 'FDR report' input1 && 
+        ln -s 'reference' input2 &&
+        java -jar '$__tool_directory__/Kinamine 7 to 7.jar' &&
+        mv output1 output1.csv &&
+        mv output2 output2.csv &&
+    ]]></command>
+    <inputs>
+        <param format="txt" name="FDR report" type="data" label="Distinct Peptide Report"/>
+        <param format="fasta" name="reference" type="data" label="FASTA reference"/>
+    </inputs>      
+    <outputs>
+        <data format="csv" name="Substrates" from_work_dir="output1.csv" label="Substrates"/>
+        <data format="csv" name="SBF" from_work_dir="output2.csv" label="Substrate Background Frequency"/>
+    </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 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>
+