diff macros.xml @ 47:44ca2967218c draft

planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 69b2ae0ff05482e85ee086005462e7859b383064

--- a/macros.xml	Wed Jul 11 08:14:23 2018 -0400
+++ b/macros.xml	Sat Sep 15 08:51:12 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."/>