# HG changeset patch
# User galaxyp
# Date 1626771311 0
# Node ID a6ff76e057fdc9d353f356fa7a748a1aa0112b93
# Parent  943a34df6047c9eb0660615982ce16a436195032
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 62d0c9c13383dc58cc75cd273e0395e53a42b003"

diff -r 943a34df6047 -r a6ff76e057fd macros_basic.xml
--- a/macros_basic.xml	Fri May 21 19:13:14 2021 +0000
+++ b/macros_basic.xml	Tue Jul 20 08:55:11 2021 +0000
@@ -11,10 +11,10 @@
         </stdio>
     </xml>
     <token name="@SEARCHGUI_MAJOR_VERSION@">4</token>
-    <token name="@SEARCHGUI_VERSION@">4.0.33</token>
+    <token name="@SEARCHGUI_VERSION@">4.0.41</token>
     <token name="@SEARCHGUI_VERSION_SUFFIX@">0</token>
-    <token name="@PEPTIDESHAKER_VERSION@">2.0.25</token>
-    <token name="@PEPTIDESHAKER_VERSION_SUFFIX@">0</token>
+    <token name="@PEPTIDESHAKER_VERSION@">2.0.33</token>
+    <token name="@PEPTIDESHAKER_VERSION_SUFFIX@">1</token>
     <xml name="citations">
         <citations>
             <citation type="doi">10.1186/1471-2105-12-70</citation>
diff -r 943a34df6047 -r a6ff76e057fd peptide_shaker.xml
--- a/peptide_shaker.xml	Fri May 21 19:13:14 2021 +0000
+++ b/peptide_shaker.xml	Tue Jul 20 08:55:11 2021 +0000
@@ -38,7 +38,9 @@
         #if $optional_main_parameters.input_optional_identification_parameters:
             cp '${optional_main_parameters.input_optional_identification_parameters}' SEARCHGUI_IdentificationParameters.par &&
         #else:
-            jar xvf searchgui_input.zip SEARCHGUI_IdentificationParameters.par &&
+            ## Note that there will be just one .par file, the one (with unkown name) used thorought SG execution. We will rename it to a "standard" name
+            unzip -o searchgui_input.zip *.par &&
+            mv *.par SEARCHGUI_IdentificationParameters.par &&
         #end if
         ## Optional Fasta file
         #if $optional_main_parameters.input_fasta_file:
@@ -68,7 +70,7 @@
         ######################
         ## PeptideShakerCLI ##
         ######################
-        
+
         ## TODO: --exec_dir may not be needed anymore. To be tested further (and maybe removed from the Conda package).
 
         peptide-shaker -Djava.awt.headless=true eu.isas.peptideshaker.cmd.PeptideShakerCLI
@@ -188,12 +190,12 @@
                 #end if
             #end if
         #end if
-        
+
         ## Whilst non-blocking exception " /usr/local/share/peptide-shaker-2.0.25-0/resources/conf/paths.txt (Permission denied)"
         ## is fixed , we can avoid the process to be stopped by removing that message from the output
-        
+
         |   grep -v "resources/conf/paths.txt (Permission denied)"
-        
+
         ## If the user chose to zip the results but also export reports out of the zip, we have to unzip them
         #if $exporting_options.zip_conditional.zip_output_boolean == 'zip' and $exporting_options.zip_conditional.export_reports_when_zip and (len(output_reports_list)>0 or $exporting_followup_boolean):
             ## This unzipping command creates a reports folder into the current folder!
diff -r 943a34df6047 -r a6ff76e057fd searchgui.xml
--- a/searchgui.xml	Fri May 21 19:13:14 2021 +0000
+++ b/searchgui.xml	Tue Jul 20 08:55:11 2021 +0000
@@ -180,7 +180,7 @@
         <!-- Search Engine Selection -->
         <section name="search_engines_options" expanded="true" title="Search Engine Options">
             <param name="engines" type="select" display="checkboxes" multiple="True" label="DB-Search Engines">
-                <help>Comet and Tide shouldn't both be selected since they use a similar algoritm. OMSSA may not work into isolated environments like containers. 
+                <help>Comet and Tide shouldn't both be selected since they use a similar algoritm. OMSSA might not work into isolated environments like containers. Ms Amanda may not work either when executed into isolated environments based on MacOS X.
                     MetaMorpheus only produce results when using mzML format.</help>
                 <option value="X!Tandem" selected="True">X!Tandem</option>
                 <option value="MSGF" selected="True">MS-GF+</option>
@@ -241,8 +241,8 @@
             <param name="engines" value="X!Tandem,MSGF,MyriMatch,Comet"/>
             <output name="searchgui_results" file="searchgui_tiny_result_default_4engines.zip" ftype="searchgui_archive" compare="sim_size" delta="30000" />
         </test>
-        
-        
+
+
         <!-- Test that search works with MetaMorpheus with default parameters works-->
         <!-- Test data has been taken from metamorpheus galaxy tool -->
         <test>
@@ -350,7 +350,7 @@
 
     >generic[your tag]|[protein accession]|[protein description]
 
-    or 
+    or
 
     >generic[your tag]|[protein accession]