diff searchgui.xml @ 42:80ed6522192c draft

planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6e846f7195a9e939047ac975c6523e8cf99da6b4

--- a/searchgui.xml	Thu Sep 27 04:31:22 2018 -0400
+++ b/searchgui.xml	Fri Oct 12 08:55:43 2018 -0400
@@ -1,4 +1,4 @@
-<tool id="search_gui" name="Search GUI" version="@SEARCHGUI_VERSION@.1">
+<tool id="search_gui" name="Search GUI" version="@SEARCHGUI_VERSION@">
     <description>
         Perform protein identification using various search engines and prepare results for input to Peptide Shaker
     </description>
@@ -23,6 +23,8 @@
         cwd=`pwd`;
         export HOME=\$cwd;
 
+        echo "" > $temp_stderr && 
+
         ## echo the search engines to run (single quotes important because X!Tandem)
         echo '$search_engines_options.engines';
         echo 'DB: ${input_database.element_identifier} sequences: ${input_database.metadata.sequences}';
@@ -43,7 +45,7 @@
         ####       Set paths                   ####
         ###########################################
         echo 'Setting paths' &&
-        searchgui eu.isas.searchgui.cmd.PathSettingsCLI
+        searchgui -Djava.awt.headless=true eu.isas.searchgui.cmd.PathSettingsCLI
             --exec_dir="\$cwd/${bin_dir}" 
             -temp_folder \$cwd 
             -log \$cwd/searchgui.log  2>> $temp_stderr &&
@@ -53,7 +55,7 @@
         ###########################################
         #if $protein_database_options.create_decoy:
             echo 'Creating decoy database.' &&
-            searchgui eu.isas.searchgui.cmd.FastaCLI 
+            searchgui -Djava.awt.headless=true eu.isas.searchgui.cmd.FastaCLI 
                 --exec_dir="\$cwd/${bin_dir}" 
                 -in input_database.fasta
                 -decoy  2>> $temp_stderr &&
@@ -66,7 +68,7 @@
         ## generate IdentificationParameters for SearchGUI ##
         #####################################################
         echo 'setting identification parameters' &&
-        (searchgui eu.isas.searchgui.cmd.IdentificationParametersCLI
+        (searchgui -Djava.awt.headless=true eu.isas.searchgui.cmd.IdentificationParametersCLI
             --exec_dir="\$cwd/${bin_dir}"
             -out SEARCHGUI_IdentificationParameters.par
 
@@ -435,9 +437,7 @@
 
         (zip -u searchgui_out.zip searchgui.properties 2>> $temp_stderr);
 
-        exit_code_for_galaxy=\$?;
         cat $temp_stderr 2>&1;
-        (exit \$exit_code_for_galaxy)
 ]]>
     </command>
     <inputs>
@@ -1108,8 +1108,8 @@
             <param name="min_charge" value="1"/>
             <param name="max_charge" value="3"/>
             <param name="engines" value="X!Tandem,MSGF,MyriMatch,OMSSA,Comet"/>
-            <param name="xtandem.xtandem_advanced" value="yes"/>
-            <param name="xtandem_advanced.xtandem_refine_selector" value="yes"/>
+            <param name="xtandem|xtandem_advanced" value="yes"/>
+            <param name="xtandem|xtandem_advanced|xtandem_refine_selector" value="yes"/>
             <output name="searchgui_results" file="tiny_searchgui_result1.zip" ftype="searchgui_archive" compare="sim_size" delta="30000" />
         </test>
         <!-- Test that search works with MSAmanda -->
@@ -1124,7 +1124,6 @@
         </test>
 
         <!-- Test that specifying non-default search engines works using modifications -->
-        <!--
         <test>
             <param name="peak_lists" value="searchgui_tinyspectra1.mgf"/>
             <param name="input_database" value="searchgui_tinydb1.fasta" ftype="fasta"/>
@@ -1134,13 +1133,11 @@
             <param name="min_charge" value="1"/>
             <param name="max_charge" value="3"/>
             <param name="engines" value="X!Tandem,MSGF,MyriMatch,OMSSA,Comet"/>
-            <param name="xtandem.xtandem_advanced" value="yes"/>
-            <param name="xtandem_advanced.xtandem_refine_selector" value="yes"/>
-            <output name="output" file="tiny_searchgui_modifications_result1.zip" ftype="searchgui_archive" compare="sim_size" delta="30000" />
+            <param name="xtandem|xtandem_advanced" value="yes"/>
+            <param name="xtandem|xtandem_advanced|xtandem_refine_selector" value="yes"/>
+            <output name="searchgui_results" file="tiny_searchgui_modifications_result1.zip" ftype="searchgui_archive" compare="sim_size" delta="30000" />
         </test>
-        -->
         <!-- Test that search works with MSAmanda - with modifications -->
-        <!--
         <test>
             <param name="peak_lists" value="searchgui_tinyspectra1.mgf"/>
             <param name="input_database" value="searchgui_tinydb1.fasta" ftype="fasta"/>
@@ -1150,9 +1147,8 @@
             <param name="min_charge" value="1"/>
             <param name="max_charge" value="3"/>
             <param name="engines" value="MS_Amanda"/>
-            <output name="output" file="tiny_searchgui_modifications_result_amandaonly.zip" ftype="searchgui_archive" compare="sim_size" delta="5000" />
+            <output name="searchgui_results" file="tiny_searchgui_modifications_result_amandaonly.zip" ftype="searchgui_archive" compare="sim_size" delta="5000" />
         </test>
-        -->
     </tests>
     <help>
 **What it does**