# HG changeset patch
# User galaxyp
# Date 1465567083 14400
# Node ID 78fad25eff17aa848bde6be1806d38d449b31ffb
# Parent  432140bcc7fe09353425c5959a89a0cd1de2b6f5
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 4256c7c6fde06722b66f433f5913c2e707bc930f-dirty

diff -r 432140bcc7fe -r 78fad25eff17 macros.xml
--- a/macros.xml	Wed Jun 08 13:05:47 2016 -0400
+++ b/macros.xml	Fri Jun 10 09:58:03 2016 -0400
@@ -26,7 +26,7 @@
             -ri $reverse_ion
     </token>
     <token name="@SEARCHGUI_MAJOR_VERSION@">2</token>
-    <token name="@SEARCHGUI_VERSION@">2.8</token>
+    <token name="@SEARCHGUI_VERSION@">2.9</token>
     <xml name="general_options">
         <param name="precursor_ion_tol_units" type="select" label="Precursor Ion Tolerance Units"
             help="Select based on instrument used, as different machines provide different quality of spectra. ppm is a standard for most precursor ions">
diff -r 432140bcc7fe -r 78fad25eff17 peptide_shaker.xml
--- a/peptide_shaker.xml	Wed Jun 08 13:05:47 2016 -0400
+++ b/peptide_shaker.xml	Fri Jun 10 09:58:03 2016 -0400
@@ -1,4 +1,4 @@
-<tool id="peptide_shaker" name="Peptide Shaker" version="1.10.0">
+<tool id="peptide_shaker" name="Peptide Shaker" version="1.11.0">
     <description>
         Perform protein identification using various search engines based on results from SearchGUI
     </description>
@@ -6,7 +6,7 @@
         <import>macros.xml</import>
     </macros>
     <requirements>
-        <requirement type="package" version="1.10">peptide_shaker</requirement>
+        <requirement type="package" version="1.11">peptide_shaker</requirement>
     </requirements>
     <expand macro="stdio" />
     <command>
@@ -58,6 +58,7 @@
                     #end if
                 #end if
                 -protein_fraction_mw_confidence "${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>
diff -r 432140bcc7fe -r 78fad25eff17 tool_dependencies.xml
--- a/tool_dependencies.xml	Wed Jun 08 13:05:47 2016 -0400
+++ b/tool_dependencies.xml	Fri Jun 10 09:58:03 2016 -0400
@@ -1,9 +1,9 @@
 <?xml version="1.0"?>
 <tool_dependency>
-    <package name="searchgui" version="2.8">
-        <repository changeset_revision="33a7c9c42472" name="package_searchgui_2_8" owner="galaxyp" toolshed="https://toolshed.g2.bx.psu.edu" />
+    <package name="searchgui" version="2.9">
+        <repository changeset_revision="a04e562f2ff0" name="package_searchgui_2_9" owner="galaxyp" toolshed="https://toolshed.g2.bx.psu.edu" />
     </package>
-    <package name="peptide_shaker" version="1.10">
-        <repository changeset_revision="63441af662c0" name="package_peptideshaker_1_10" owner="galaxyp" toolshed="https://toolshed.g2.bx.psu.edu" />
+    <package name="peptide_shaker" version="1.11">
+        <repository changeset_revision="bd41b685f845" name="package_peptideshaker_1_11" owner="galaxyp" toolshed="https://toolshed.g2.bx.psu.edu" />
     </package>
 </tool_dependency>