diff peptide_shaker.xml @ 2:fb591fc7241c draft

Improved some datatype handling

--- a/peptide_shaker.xml	Thu Jun 20 10:53:16 2013 -0400
+++ b/peptide_shaker.xml	Thu Jun 20 11:02:36 2013 -0400
@@ -4,6 +4,9 @@
     Peform protein identification combining X! Tandem and OMSSA (using SearchGUI) and PeptideShaker pipeline.
   </description>
   <command>
+    #from datetime import datetime
+    #set $exp_str = "Galaxy Experiment %s" % datetime.now().strftime("%Y%m%d%H%M%s")              
+    #set $samp_str = "Sample %s" % datetime.now().strftime("%Y%m%d%H%M%s")
     mkdir spectra;
     mkdir output;
     mkdir output_reports;
@@ -45,8 +48,8 @@
     #end if
     -db $input_database;
     PeptideShakerCLI \
-    -experiment 'Galaxy Experiment' \
-    -sample 'Sample' \ 
+    -experiment '$exp_str' \
+    -sample '$samp_str' \ 
     -replicate 1 \
     -spectrum_files \$cwd/spectra \
     -identification_files \$cwd/output \ 
@@ -210,12 +213,14 @@
   <help>
 **What it does**
 
+Runs multiple search engines (X! Tandem and OMSSA) on any number of MGF peak lists using the SearchGUI application and combines the result via PeptideShaker.
+
 ------
 
 **Citation**
 
 For the underlying tool, please cite `TODO`
 
-If you use this tool in Galaxy, please cite TODO
+If you use this tool in Galaxy, please cite Chilton J, et al. https://bitbucket.org/galaxyp/galaxyp-toolshed-peptideshaker
   </help>
 </tool>