# HG changeset patch
# User galaxyp
# Date 1611149347 0
# Node ID 1beff3ddce588dd7a39f5afc193c0740c32b4fb3
# Parent  bb0130ff73cef6d27cfbd835e9514c0a9a48673c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f2f9adb0e2389a95599d651b4eecab6b10244c75"

diff -r bb0130ff73ce -r 1beff3ddce58 README.rst
--- a/README.rst	Fri Jan 15 14:06:27 2021 +0000
+++ b/README.rst	Wed Jan 20 13:29:07 2021 +0000
@@ -27,13 +27,14 @@
 General Requirements
 --------------------
 
-To avoid out of memory errors you should set the maximum heapspace for java processes as the default is most likely too small. For example, to set this in your shell:
+To avoid out of memory errors you may need to set the maximum heapspace for java processes if the default is too small for the data you are going to process (4gb for SearchGUI, 1GB for PeptideShaker).
+For example, to set this in your shell:
 
-    export _JAVA_OPTIONS='-Xmx1500M'
+    export _JAVA_OPTIONS='-Xmx8192m'
 
 On some systems you may also need to adjust the amount of memory available for class definitions in addition to the maximum heapspace. For example:
 
-	export _JAVA_OPTIONS='-Xmx1500M -XX:MaxPermSize=256M'
+	export _JAVA_OPTIONS='-Xmx8192m -XX:MaxPermSize=1024m'
 
 It is also possible to set this on a per tool basis using advanced features of the galaxy job config system.
 
@@ -52,7 +53,7 @@
 Note
 ----
 
-- Requires Galaxy release v16.01 or later.
+- Requires Galaxy release v20.01 or later.
 
 See:
 
diff -r bb0130ff73ce -r 1beff3ddce58 macros_basic.xml
--- a/macros_basic.xml	Fri Jan 15 14:06:27 2021 +0000
+++ b/macros_basic.xml	Wed Jan 20 13:29:07 2021 +0000
@@ -10,10 +10,10 @@
         </stdio>
     </xml>
     <token name="@SEARCHGUI_MAJOR_VERSION@">4</token>
-    <token name="@SEARCHGUI_VERSION@">4.0.7</token>
+    <token name="@SEARCHGUI_VERSION@">4.0.12</token>
     <token name="@SEARCHGUI_VERSION_SUFFIX@">0</token>
-    <token name="@PEPTIDESHAKER_VERSION@">2.0.5</token>
-    <token name="@PEPTIDESHAKER_VERSION_SUFFIX@">3</token>
+    <token name="@PEPTIDESHAKER_VERSION@">2.0.9</token>
+    <token name="@PEPTIDESHAKER_VERSION_SUFFIX@">0</token>
     <xml name="citations">
         <citations>
             <citation type="doi">10.1186/1471-2105-12-70</citation>
diff -r bb0130ff73ce -r 1beff3ddce58 searchgui.xml
--- a/searchgui.xml	Fri Jan 15 14:06:27 2021 +0000
+++ b/searchgui.xml	Wed Jan 20 13:29:07 2021 +0000
@@ -22,6 +22,8 @@
 
         mkdir output;
         mkdir output_reports;
+        mkdir temp_folder;
+        mkdir log_folder;
         cwd=`pwd`;
         export HOME=\$cwd;
 
@@ -63,7 +65,8 @@
             -fasta_file "\$cwd/input_fasta_file.fasta"
             -output_folder \$cwd/output
             -id_params ./SEARCHGUI_IdentificationParameters.par
-
+            -temp_folder \$cwd/temp_folder
+            -log \$cwd/log_folder
             -threads "\${GALAXY_SLOTS:-12}"
 
             #if $searchgui_advanced.searchgui_advanced_selector == 'advanced'