Mercurial > repos > iracooke > msgfplus

changeset 6:79ed4588f7ae draft

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Uploaded
author iracooke
date Tue, 18 Mar 2014 19:46:10 -0400
parents 233ce0ebad08
children 9ee2e20c6f1a
files msgfplus_search.xml
diffstat 1 files changed, 5 insertions(+), 2 deletions(-) [+]
line wrap: on
line diff
--- a/msgfplus_search.xml	Wed Mar 05 01:16:36 2014 -0500
+++ b/msgfplus_search.xml	Tue Mar 18 19:46:10 2014 -0400
@@ -1,4 +1,4 @@
-<tool id="proteomics_search_msgfplus_1" name="MSGF+ MSMS Search" version="1.0.1">
+<tool id="proteomics_search_msgfplus_1" name="MSGF+ MSMS Search" version="1.0.2">
     <description>Run an MSGF+ Search</description>
     <requirements>
         <requirement type="package" version="1.2.6">protk</requirement>
@@ -32,7 +32,8 @@
         -r 
         --enzyme=$enzyme 
         --precursor-ion-tol-units=$precursor_tolu 
-        -v $missed_cleavages 
+        -v $missed_cleavages
+        $cleavage_semi
         -f $fragment_ion_tol 
         -p $precursor_ion_tol 
         --instrument=$instrument
@@ -97,6 +98,8 @@
             <option value="2">2</option>
         </param>
         
+        <param name="cleavage_semi" type="boolean" label="Allow semi-cleaved peptides" help="This can increase search time dramatically" truevalue="" falsevalue="--no-cleavage-semi" />
+
         <param name="enzyme" type="select" format="text">
             <label>Enzyme</label>
             <option value="0">unspecific cleavage</option>