# HG changeset patch
# User galaxyp
# Date 1537015855 14400
# Node ID fec15a483a5c86eda143404713a4413eec708120
# Parent  f63401dd6cbb53f73b27c488636d5876051932fe
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 69b2ae0ff05482e85ee086005462e7859b383064

diff -r f63401dd6cbb -r fec15a483a5c macros.xml
--- a/macros.xml	Wed Jul 11 08:14:05 2018 -0400
+++ b/macros.xml	Sat Sep 15 08:50:55 2018 -0400
@@ -2,7 +2,10 @@
     <xml name="stdio">
         <stdio>
             <exit_code range="1:" level="fatal" description="Job Failed" />
-            <regex match="java.*Exception" level="fatal" description="Java Exception"/>
+	    <regex match="java.lang.OutOfMemoryError" level="fatal_oom" description="Java memory Exception"/>
+	    <regex match="Could not allocate metaspace" level="fatal_oom" description="Java memory Exception"/>
+	    <regex match="Cannot create VM thread" level="fatal_oom" description="Java memory Exception"/>
+	    <regex match="java.*Exception" level="fatal" description="Java Exception"/>
             <regex match="Could not create the Java virtual machine" level="fatal" description="JVM Error"/>
             <regex match="CompomicsError" level="fatal" description="Compomics Error"/>
         </stdio>
@@ -55,51 +58,31 @@
         <section name="protein_digest_options" expanded="false" title="Protein Digestion Options">
             <conditional name="digestion">
                 <param name="cleavage" type="select" label="Digestion">
-                    <option value="default" selected="true">Trypsin</option>
                     <option value="0">Select Enzymes</option>
                     <option value="1">Unspecific Cleavage</option>
                     <option value="2">Whole Protein</option>
                 </param>
-                <when value="default">
-                    <param name="missed_cleavages" type="integer" value="2" label="Maximum Missed Cleavages"
-                        help="Allow peptides to contain up to this many missed enzyme cleavage sites."/>
-                </when>
                 <when value="0">
                     <repeat name="digests" min="1" title="Enzymes">
                         <param name="enzyme" type="select" label="Enzyme"
                             help="Which enzyme was used for protein digest in experiment? In most cases, trypsin is used">
                             <option value="Trypsin">Trypsin</option>
+                            <option value="Trypsin (no P rule)">Trypsin (no P rule)</option>
                             <option value="Arg-C">Arg-C</option>
-                            <option value="CNBr">CNBr</option>
-                            <option value="Chymotrypsin (FYWL)">Chymotrypsin (FYWL)</option>
-                            <option value="Formic Acid">Formic Acid</option>
-                            <option value="Lys-C">Lys-C</option>
-                            <option value="Lys-C, no P rule">Lys-C, no P rule</option>
-                            <option value="Pepsin A">Pepsin A</option>
-                            <option value="Trypsin + CNBr">Trypsin + CNBr</option>
-                            <option value="Trypsin + Chymotrypsin (FYWLKR)">Trypsin + Chymotrypsin (FYWLKR)</option>
-                            <option value="Trypsin, no P rule">Trypsin, no P rule</option>
-                            <option value="Whole Protein">Whole Protein</option>
-                            <option value="Asp-N">Asp-N</option>
+                            <option value="Arg-C (no P rule)">Arg-C</option>
+                            <option value="Arg-N">Arg-N</option>
                             <option value="Glu-C">Glu-C</option>
-                            <option value="Asp-N + Glu-C">Asp-N + Glu-C</option>
-                            <option value="Top-Down">Top-Down</option>
-                            <option value="Semi-Tryptic">Semi-Tryptic</option>
-                            <option value="Unspecific">Unspecific (No enzyme)</option> <!-- note: cleaves at every residue! -->
-                            <option value="Chymotrypsin, no P rule (FYWL)">Chymotrypsin, no P rule (FYWL)</option>
-                            <option value="Asp-N (DE)">Asp-N (DE)</option>
-                            <option value="Glu-C (DE)">Glu-C (DE)</option>
-                            <option value="Lys-N (K)">Lys-N (K)</option>
-                            <option value="Thermolysin, no P rule">Thermolysin, no P rule</option>
-                            <option value="Semi-Chymotrypsin (FYWL)">Semi-Chymotrypsin (FYWL)</option>
-                            <option value="Semi-Glu-C">Semi-Glu-C</option>
+                            <option value="Lys-C">Lys-C</option>
+                            <option value="Lys-C (no P rule)">Lys-C (no P rule)</option>
+                            <option value="Lys-N">Lys-N</option>
+                            <option value="Asp-N">Asp-N</option>
+                            <option value="Asp-N (ambic)">Asp-N (ambic)</option>
+                            <option value="Chymotrypsin">Chymotrypsin</option>
+                            <option value="Chymotrypsin (no P rule)">Chymotrypsin (no P rule)</option>
+                            <option value="Pepsin A">Pepsin A</option>
+                            <option value="CNBr">CNBr</option>
+                            <option value="Thermolysin">Thermolysin</option>
                             <option value="LysargiNase">LysargiNase</option>
-                            <option value="Semi-LysargiNase">Semi-LysargiNase</option>
-                            <option value="Trypsin + Glu-C">Trypsin + Glu-C</option>
-                            <option value="Semi-Arg-C">Semi-Arg-C</option>
-                            <option value="Semi-Glu-C (DE)">Semi-Glu-C (DE)</option>
-                            <option value="Arg-N">Arg-N</option>
-                            <option value="Semi-Arg-N">Semi-Arg-N</option>
                         </param>
                         <param name="missed_cleavages" type="integer" value="2" label="Maximum Missed Cleavages"
                             help="Allow peptides to contain up to this many missed enzyme cleavage sites."/>
diff -r f63401dd6cbb -r fec15a483a5c searchgui.xml
--- a/searchgui.xml	Wed Jul 11 08:14:05 2018 -0400
+++ b/searchgui.xml	Sat Sep 15 08:50:55 2018 -0400
@@ -6,11 +6,11 @@
         <import>macros.xml</import>
     </macros>
     <requirements>
-	<requirement type="package" version="@SEARCHGUI_VERSION@">searchgui</requirement>
-	<requirement type="package" version="3.0">zip</requirement>
+        <requirement type="package" version="@SEARCHGUI_VERSION@">searchgui</requirement>
+        <requirement type="package" version="3.0">zip</requirement>
     </requirements>
     <expand macro="stdio" />
-    <command>
+    <command use_shared_home="false">
 <![CDATA[
         #from datetime import datetime
         #set $exp_str = "Galaxy_Experiment_%s" % datetime.now().strftime("%Y%m%d%H%M%s")
@@ -23,28 +23,40 @@
         cwd=`pwd`;
         export HOME=\$cwd;
 
-        ## echo the search engines to run
-        echo "$search_engines_options.engines";
-        echo "DB: ${input_database.display_name} sequences: ${input_database.metadata.sequences}";
+        ## echo the search engines to run (single quotes important because X!Tandem)
+        echo '$search_engines_options.engines';
+        echo 'DB: ${input_database.display_name} sequences: ${input_database.metadata.sequences}';
 
         ##Create a searchgui.properties file for the version, which will be added to the searchgui_results if not already present
-        echo "searchgui.version=@SEARCHGUI_VERSION@" >> searchgui.properties;
+        echo 'searchgui.version=@SEARCHGUI_VERSION@' >> searchgui.properties;
 
         #for $mgf in $peak_lists:
             #set $input_name = $mgf.display_name.split('/')[-1].replace(".mgf", "") + ".mgf"
             ln -s -f '${mgf}' '${input_name}';
             #set $encoded_id = $__app__.security.encode_id($mgf.id)
-            echo "Spectrums:${mgf.display_name}(API:${encoded_id}) ";
+            echo 'Spectrums:${mgf.display_name}(API:${encoded_id})';
         #end for
         ##ln -s "${input_database}" input_database.fasta;
         cp "${input_database}" input_database.fasta;
 
         ###########################################
+        ####       Set paths                   ####
+        ###########################################
+        echo 'Setting paths' &&
+        searchgui eu.isas.searchgui.cmd.PathSettingsCLI
+            --exec_dir="\$cwd/${bin_dir}" 
+            -temp_folder \$cwd 
+            -log \$cwd/searchgui.log  2>> $temp_stderr &&
+
+        ###########################################
         ####       Creating decoy database     ####
         ###########################################
         #if $protein_database_options.create_decoy:
-            echo "Creating decoy database.";
-            searchgui eu.isas.searchgui.cmd.FastaCLI --exec_dir="\$cwd/${bin_dir}" -in input_database.fasta -decoy &&
+            echo 'Creating decoy database.' &&
+            searchgui eu.isas.searchgui.cmd.FastaCLI 
+                --exec_dir="\$cwd/${bin_dir}" 
+                -in input_database.fasta
+                -decoy  2>> $temp_stderr &&
             rm input_database.fasta &&
             cp input_database_concatenated_target_decoy.fasta input_database.fasta &&
             ## ln -sf input_database_concatenated_target_decoy.fasta input_database.fasta;
@@ -53,6 +65,7 @@
         #####################################################
         ## generate IdentificationParameters for SearchGUI ##
         #####################################################
+        echo 'setting identification parameters' &&
         (searchgui eu.isas.searchgui.cmd.IdentificationParametersCLI
             --exec_dir="\$cwd/${bin_dir}"
             -out SEARCHGUI_IdentificationParameters.par
@@ -323,9 +336,9 @@
         ################
         ## Search CLI ##
         ################
+        echo 'running search gui' &&
         (searchgui -Djava.awt.headless=true eu.isas.searchgui.cmd.SearchCLI
             --exec_dir="\$cwd/${bin_dir}"
-            -temp_folder `pwd`
             -spectrum_files \$cwd
             -output_folder \$cwd/output
             -id_params SEARCHGUI_IdentificationParameters.par
@@ -1097,7 +1110,7 @@
             <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_result1.zip" ftype="searchgui_archive" compare="sim_size" delta="30000" />
+            <output name="searchgui_results" file="tiny_searchgui_result1.zip" ftype="searchgui_archive" compare="sim_size" delta="30000" />
         </test>
         <!-- Test that search works with MSAmanda -->
         <test>
@@ -1107,7 +1120,7 @@
             <param name="min_charge" value="1"/>
             <param name="max_charge" value="3"/>
             <param name="engines" value="MS_Amanda"/>
-            <output name="output" file="tiny_searchgui_result_amandaonly.zip" ftype="searchgui_archive" compare="sim_size" delta="5000" />
+            <output name="searchgui_results" file="tiny_searchgui_result_amandaonly.zip" ftype="searchgui_archive" compare="sim_size" delta="5000" />
         </test>
 
         <!-- Test that specifying non-default search engines works using modifications -->