SG 4.0.33 & PS 2.0.25

tools/peptideshaker/fasta_cli.xml

@@ -28,7 +28,15 @@
         ###########################################
 
         echo 'Creating decoy database.' &&
-        searchgui -Djava.awt.headless=true eu.isas.searchgui.cmd.FastaCLI --exec_dir="./bin/" -temp_folder `pwd` -in '${input_database.display_name}' -decoy -decoy_flag $database_processing_options.decoy_tag -suffix $database_processing_options.decoy_type -decoy_suffix $database_processing_options.decoy_file_tag &&
+        searchgui -Djava.awt.headless=true eu.isas.searchgui.cmd.FastaCLI
+            --exec_dir="./bin/"
+            -use_log_folder 0
+            -temp_folder `pwd`
+            -in '${input_database.display_name}'
+            -decoy
+            -decoy_flag $database_processing_options.decoy_tag
+            -suffix $database_processing_options.decoy_type
+            -decoy_suffix $database_processing_options.decoy_file_tag &&
         mv '${output_db_name}' output
 ]]>
     </command>

tools/peptideshaker/ident_params.xml

@@ -30,8 +30,8 @@
         #####################################################
         searchgui eu.isas.searchgui.cmd.IdentificationParametersCLI
             --exec_dir="./bin/"
+            -use_log_folder 0
             -out './IdentificationParametersOutput.par'
-
             ## SPECTRUM MATCHING PARAMETERS
 
             -frag_tol '${spectrum_matching_options.fragment_tol}'

tools/peptideshaker/macros_basic.xml

@@ -11,9 +11,9 @@
         </stdio>
     </xml>
     <token name="@SEARCHGUI_MAJOR_VERSION@">4</token>
-    <token name="@SEARCHGUI_VERSION@">4.0.25</token>
+    <token name="@SEARCHGUI_VERSION@">4.0.33</token>
     <token name="@SEARCHGUI_VERSION_SUFFIX@">0</token>
-    <token name="@PEPTIDESHAKER_VERSION@">2.0.18</token>
+    <token name="@PEPTIDESHAKER_VERSION@">2.0.25</token>
     <token name="@PEPTIDESHAKER_VERSION_SUFFIX@">0</token>
     <xml name="citations">
         <citations>

tools/peptideshaker/peptide_shaker.xml

@@ -26,8 +26,6 @@
         #set $samp_str = "Sample_%s" % datetime.now().strftime("%Y%m%d%H%M%s")
         #set $bin_dir = "bin"
         #set $exporting_followup_boolean = False
-        ## TODO: Re-enable again when solving writing paths.txt to user-related folders and non-existing exportFactory.json file.
-        ## trap ">&2 cat resources/*.log" EXIT;
 
         mkdir output_reports &&
         cwd=`pwd` &&
@@ -70,10 +68,13 @@
         ######################
         ## 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
             -gui 0
             -temp_folder \$cwd/PeptideShakerCLI
-            -log \$cwd/resources
+            -use_log_folder 0
             -reference '$exp_str'
             -identification_files \$cwd/searchgui_input.zip
             -id_params \$cwd/SEARCHGUI_IdentificationParameters.par
@@ -187,7 +188,12 @@
                 #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!

tools/peptideshaker/searchgui.xml

@@ -65,6 +65,7 @@
         echo 'running search gui' &&
         searchgui -Djava.awt.headless=true eu.isas.searchgui.cmd.SearchCLI
             --exec_dir="\$cwd/${bin_dir}"
+            -use_log_folder 0
             -spectrum_files \$cwd
             -fasta_file "\$cwd/input_fasta_file.fasta"
             -output_folder \$cwd/output
@@ -173,21 +174,22 @@
         <param format="fasta" name="input_fasta_file" type="data" label="Fasta file" help="For postprocessing with PeptideShaker the sequences must have UniProt style headers and contain decoy sequences (see help)."/>
 
         <param name="peak_lists_files" format="mgf,mzml" type="data" multiple="true" label="Input Peak Lists"
-            help="Select appropriate MGF/MZML dataset(s) from history" />
+            help="Select appropriate MGF/MZML dataset(s) from history.
+               Remember to choose only .mzML files when using MetaMorpheus." />
 
         <!-- 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>
+                <help>Comet and Tide shouldn't both be selected since they use a similar algoritm. OMSSA may not work into isolated environments like containers. 
+                    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>
                 <option value="OMSSA">OMSSA</option>
                 <option value="Comet">Comet</option>
                 <option value="Tide">Tide</option>
                 <option value="MyriMatch">MyriMatch</option>
                 <option value="MS_Amanda">MS_Amanda</option>
-                <!-- TODO: MetaMorpheus Waiting for support for dotnet in bioconda package -->
-                <!-- <option value="MetaMorpheus">MetaMorpheus</option> -->
+                <option value="MetaMorpheus">MetaMorpheus</option>
                 <!-- Windows only
                 <option value="Andromeda">Andromeda</option>
                 -->
@@ -239,6 +241,21 @@
             <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>
+            <param name="peak_lists_files" value="searchgui_smallCalibratible_Yeast.mzML"/>
+            <param name="input_parameters_file" value="Identification_Parameters_default.par"/>
+            <param name="input_fasta_file" value="searchgui_smallYeast.fasta" ftype="fasta" />
+            <param name="engines" value="MetaMorpheus"/>
+            <output name="searchgui_results" ftype="searchgui_archive">
+                <assert_contents>
+                    <has_size value="798597" delta="10000"/>
+                </assert_contents>
+            </output>
+        </test>
 
         <!-- Test that search works with MSAmanda with default parameters works-->
         <test>
@@ -324,7 +341,7 @@ Runs multiple search engines on any number of MGF peak lists using SearchGUI.
 
 Default:     X! Tandem and MS-GF+ are executed.
 
-Optional:     MyriMatch, MS-Amanda, OMSSA (it may not work into isolated environments like containers), Comet, Tide, DirecTag and Novor can be executed.
+Optional:     MyriMatch, MS-Amanda, MetaMorpheus, OMSSA (it may not work into isolated environments like containers), Comet, Tide, DirecTag and Novor can be executed.
 
 **Input FASTA**