Mercurial > repos > galaxyp > peptideshaker
diff macros.xml @ 47:44ca2967218c draft
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 69b2ae0ff05482e85ee086005462e7859b383064
| author | galaxyp |
|---|---|
| date | Sat, 15 Sep 2018 08:51:12 -0400 |
| parents | baeced706dbc |
| children | 58a3e6cb2598 |
line wrap: on
line diff
--- 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."/>