diff peptide_shaker.xml @ 29:78fad25eff17 draft

planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 4256c7c6fde06722b66f433f5913c2e707bc930f-dirty

--- a/peptide_shaker.xml	Wed Jun 08 13:05:47 2016 -0400
+++ b/peptide_shaker.xml	Fri Jun 10 09:58:03 2016 -0400
@@ -1,4 +1,4 @@
-<tool id="peptide_shaker" name="Peptide Shaker" version="1.10.0">
+<tool id="peptide_shaker" name="Peptide Shaker" version="1.11.0">
     <description>
         Perform protein identification using various search engines based on results from SearchGUI
     </description>
@@ -6,7 +6,7 @@
         <import>macros.xml</import>
     </macros>
     <requirements>
-        <requirement type="package" version="1.10">peptide_shaker</requirement>
+        <requirement type="package" version="1.11">peptide_shaker</requirement>
     </requirements>
     <expand macro="stdio" />
     <command>
@@ -58,6 +58,7 @@
                     #end if
                 #end if
                 -protein_fraction_mw_confidence "${processing_options.protein_fraction_mw_confidence}"
+                -ptm_alignment "${processing_options.ptm_alignment}"
             #end if
 
            ##Optional filtering parameters:
@@ -476,6 +477,7 @@
                             help="Automatic mode will be used if not set" />
                     </when>
                 </conditional>
+                <param name="ptm_alignment" label="Align peptide ambiguously localized PTMs on confident sites" type="boolean" truevalue="1" falsevalue="0" checked="true"/>
                 <!-- SKIPPING -protein_fraction_mw_confidence ${processing_options.protein_fraction_mw_confidence} -->
             </when>
         </conditional>