# HG changeset patch
# User galaxyp
# Date 1611149314 0
# Node ID 560a08e0de13c9f2c01e817f808de35562e88b24
# Parent  b72821cab1d7873833971534e669c6365db5a696
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f2f9adb0e2389a95599d651b4eecab6b10244c75"

diff -r b72821cab1d7 -r 560a08e0de13 README.rst
--- a/README.rst	Fri Jan 15 14:05:46 2021 +0000
+++ b/README.rst	Wed Jan 20 13:28:34 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 b72821cab1d7 -r 560a08e0de13 macros_basic.xml
--- a/macros_basic.xml	Fri Jan 15 14:05:46 2021 +0000
+++ b/macros_basic.xml	Wed Jan 20 13:28:34 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 b72821cab1d7 -r 560a08e0de13 searchgui.xml
--- a/searchgui.xml	Fri Jan 15 14:05:46 2021 +0000
+++ b/searchgui.xml	Wed Jan 20 13:28:34 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'