diff reverse.xml @ 105:f258fbfead4b draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/reverse.xml	Fri Apr 11 16:32:28 2014 -0400
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+<tool id="compomics_reverse" name="Create Target-Decoy Database" version="0.1.0">
+    <description>Creates a target-decoy database for use with Peptide Shaker</description>
+    <requirements>
+        <requirement type="set_environment">PEPTIDESHAKER_SCRIPT_PATH</requirement>
+    </requirements>
+    <command interpreter="python">
+        reverse.py 
+            --input='$input'
+            --output='$output'
+            --script_path \$PEPTIDESHAKER_SCRIPT_PATH
+    </command>
+    <inputs>
+        <param format="fasta" name="input" type="data" label="FASTA Input" />
+    </inputs>
+    <outputs>
+        <data format="fasta" name="output" />
+    </outputs>
+    <help>
+**What it does**
+
+Given an input database, this tool will produce a target-decoy
+database in the format required by PeptideShaker using dbtoolkit.
+
+------
+
+**Citation**
+
+For the underlying tool, please cite `Martens et al. DBToolkit: processing protein databases for peptide-centric proteomics. Bioinformatics (2005) vol. 21 (17) pp. 3584-5`.
+
+If you use this tool in Galaxy, please cite Chilton J, et al. https://bitbucket.org/galaxyp/peptideshaker .
+
+    </help>
+</tool>