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comparison macros.xml @ 47:44ca2967218c draft

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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
comparison
equal deleted inserted replaced
46:baeced706dbc 47:44ca2967218c
1 <macros> 1 <macros>
2 <xml name="stdio"> 2 <xml name="stdio">
3 <stdio> 3 <stdio>
4 <exit_code range="1:" level="fatal" description="Job Failed" /> 4 <exit_code range="1:" level="fatal" description="Job Failed" />
5 <regex match="java.*Exception" level="fatal" description="Java Exception"/> 5 <regex match="java.lang.OutOfMemoryError" level="fatal_oom" description="Java memory Exception"/>
6 <regex match="Could not allocate metaspace" level="fatal_oom" description="Java memory Exception"/>
7 <regex match="Cannot create VM thread" level="fatal_oom" description="Java memory Exception"/>
8 <regex match="java.*Exception" level="fatal" description="Java Exception"/>
6 <regex match="Could not create the Java virtual machine" level="fatal" description="JVM Error"/> 9 <regex match="Could not create the Java virtual machine" level="fatal" description="JVM Error"/>
7 <regex match="CompomicsError" level="fatal" description="Compomics Error"/> 10 <regex match="CompomicsError" level="fatal" description="Compomics Error"/>
8 </stdio> 11 </stdio>
9 </xml> 12 </xml>
10 <token name="@GENERAL_PARAMETERS@"> 13 <token name="@GENERAL_PARAMETERS@">
53 <xml name="general_options"> 56 <xml name="general_options">
54 57
55 <section name="protein_digest_options" expanded="false" title="Protein Digestion Options"> 58 <section name="protein_digest_options" expanded="false" title="Protein Digestion Options">
56 <conditional name="digestion"> 59 <conditional name="digestion">
57 <param name="cleavage" type="select" label="Digestion"> 60 <param name="cleavage" type="select" label="Digestion">
58 <option value="default" selected="true">Trypsin</option>
59 <option value="0">Select Enzymes</option> 61 <option value="0">Select Enzymes</option>
60 <option value="1">Unspecific Cleavage</option> 62 <option value="1">Unspecific Cleavage</option>
61 <option value="2">Whole Protein</option> 63 <option value="2">Whole Protein</option>
62 </param> 64 </param>
63 <when value="default">
64 <param name="missed_cleavages" type="integer" value="2" label="Maximum Missed Cleavages"
65 help="Allow peptides to contain up to this many missed enzyme cleavage sites."/>
66 </when>
67 <when value="0"> 65 <when value="0">
68 <repeat name="digests" min="1" title="Enzymes"> 66 <repeat name="digests" min="1" title="Enzymes">
69 <param name="enzyme" type="select" label="Enzyme" 67 <param name="enzyme" type="select" label="Enzyme"
70 help="Which enzyme was used for protein digest in experiment? In most cases, trypsin is used"> 68 help="Which enzyme was used for protein digest in experiment? In most cases, trypsin is used">
71 <option value="Trypsin">Trypsin</option> 69 <option value="Trypsin">Trypsin</option>
70 <option value="Trypsin (no P rule)">Trypsin (no P rule)</option>
72 <option value="Arg-C">Arg-C</option> 71 <option value="Arg-C">Arg-C</option>
72 <option value="Arg-C (no P rule)">Arg-C</option>
73 <option value="Arg-N">Arg-N</option>
74 <option value="Glu-C">Glu-C</option>
75 <option value="Lys-C">Lys-C</option>
76 <option value="Lys-C (no P rule)">Lys-C (no P rule)</option>
77 <option value="Lys-N">Lys-N</option>
78 <option value="Asp-N">Asp-N</option>
79 <option value="Asp-N (ambic)">Asp-N (ambic)</option>
80 <option value="Chymotrypsin">Chymotrypsin</option>
81 <option value="Chymotrypsin (no P rule)">Chymotrypsin (no P rule)</option>
82 <option value="Pepsin A">Pepsin A</option>
73 <option value="CNBr">CNBr</option> 83 <option value="CNBr">CNBr</option>
74 <option value="Chymotrypsin (FYWL)">Chymotrypsin (FYWL)</option> 84 <option value="Thermolysin">Thermolysin</option>
75 <option value="Formic Acid">Formic Acid</option>
76 <option value="Lys-C">Lys-C</option>
77 <option value="Lys-C, no P rule">Lys-C, no P rule</option>
78 <option value="Pepsin A">Pepsin A</option>
79 <option value="Trypsin + CNBr">Trypsin + CNBr</option>
80 <option value="Trypsin + Chymotrypsin (FYWLKR)">Trypsin + Chymotrypsin (FYWLKR)</option>
81 <option value="Trypsin, no P rule">Trypsin, no P rule</option>
82 <option value="Whole Protein">Whole Protein</option>
83 <option value="Asp-N">Asp-N</option>
84 <option value="Glu-C">Glu-C</option>
85 <option value="Asp-N + Glu-C">Asp-N + Glu-C</option>
86 <option value="Top-Down">Top-Down</option>
87 <option value="Semi-Tryptic">Semi-Tryptic</option>
88 <option value="Unspecific">Unspecific (No enzyme)</option> <!-- note: cleaves at every residue! -->
89 <option value="Chymotrypsin, no P rule (FYWL)">Chymotrypsin, no P rule (FYWL)</option>
90 <option value="Asp-N (DE)">Asp-N (DE)</option>
91 <option value="Glu-C (DE)">Glu-C (DE)</option>
92 <option value="Lys-N (K)">Lys-N (K)</option>
93 <option value="Thermolysin, no P rule">Thermolysin, no P rule</option>
94 <option value="Semi-Chymotrypsin (FYWL)">Semi-Chymotrypsin (FYWL)</option>
95 <option value="Semi-Glu-C">Semi-Glu-C</option>
96 <option value="LysargiNase">LysargiNase</option> 85 <option value="LysargiNase">LysargiNase</option>
97 <option value="Semi-LysargiNase">Semi-LysargiNase</option>
98 <option value="Trypsin + Glu-C">Trypsin + Glu-C</option>
99 <option value="Semi-Arg-C">Semi-Arg-C</option>
100 <option value="Semi-Glu-C (DE)">Semi-Glu-C (DE)</option>
101 <option value="Arg-N">Arg-N</option>
102 <option value="Semi-Arg-N">Semi-Arg-N</option>
103 </param> 86 </param>
104 <param name="missed_cleavages" type="integer" value="2" label="Maximum Missed Cleavages" 87 <param name="missed_cleavages" type="integer" value="2" label="Maximum Missed Cleavages"
105 help="Allow peptides to contain up to this many missed enzyme cleavage sites."/> 88 help="Allow peptides to contain up to this many missed enzyme cleavage sites."/>
106 <!-- 89 <!--
107 <param name="specificity" type="select" label="Specificity"> 90 <param name="specificity" type="select" label="Specificity">