diff digestdb.xml @ 0:e27d4f0f4b01 draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/digestdb.xml	Wed Dec 19 00:30:14 2012 -0500
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+<tool id="digestdb" version="0.1.0" name="Digest Database">
+  <description>Perform a theoretical digest of a protein database.</description>
+  <requirements>
+    <requirement type="package">transproteomic_pipeline</requirement>    
+  </requirements>  
+  <command>
+    digestdb -m$missed_cleavages -l$min_mass -h$max_mass -r${str($enzyme).split(":")[0]} -n${str($enzyme).split(":")[1]} $sequences > $output
+  </command>
+  <inputs>
+    <param format="fasta" name="sequences" type="data" label="Input FASTA Database"/>
+    <param name="missed_cleavages" type="integer" label="Missed Cleavages" value="1"/>
+    <param name="min_mass" type="float" label="Minimum Peptide Mass" value="800.0"/>
+    <param name="max_mass" type="float" label="Maximum Peptide Mass" value="3000.0"/>
+    <param name="enzyme" type="select">
+      <option value="KR:P" selected="true">Trypsin</option>
+      <option value="KR:-">Trypsin/P</option>
+      <option value="FLWY:P">Chymotrypsin</option>
+      <option value="FLWY:-">Chymotrypsin/P</option>
+      <option value="EZ:P">V8_E</option>
+      <option value="EDBZ:P">V8_DE</option>
+      <option value="K:P">LysC</option>
+      <option value="K:-">LysC/P</option>
+    </param>
+  </inputs>
+  <outputs>
+    <data format="tabular" name="output" label="Digest of database ${sequences.name}"/>
+  </outputs>
+  <help>
+**What it does**
+
+Produces a tabular description of peptides resulting from theoretical
+digest of a given protein database by the selected enzyme agent using
+the digestdb program distributed with the Transproteomic Pipeline.
+
+** Output **
+
+ Results are spit out to stdout in a tab-delimited format.
+
+ Asterisks (*) in sequence are treated as proper break points
+
+ Output columns:
+ - peptide length
+ - protein reference
+ - peptide mass
+ - previous amino acid before peptide
+ - peptide sequence
+ - next amino acid after peptide
+ - peptide start location
+ - peptide end location
+ - pI
+
+------
+
+**Citation**
+
+For the underlying tool, please cite `Proteomics. 2010 Mar;10(6):1150-9. A guided tour of the Trans-Proteomic Pipeline. Deutsch EW, Mendoza L, Shteynberg D, Farrah T, Lam H, Tasman N, Sun Z, Nilsson E, Pratt B, Prazen B, Eng JK, Martin DB, Nesvizhskii AI, Aebersold R. PMID 20101611`
+
+If you use this tool in Galaxy, please cite Chilton J, et al. https://bitbucket.org/galaxyp/galaxyp-toolshed-digestdb
+
+  </help>
+</tool>