Mercurial > repos > galaxyp > proteomiqon_peptidedb

annotate proteomiqon_peptidedb.xml @ 0:1e5400393797 draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidedb commit c8f0a6706869a8f2988a096c61d7de7de573434f"
author galaxyp
date Sun, 04 Jul 2021 21:26:08 +0000
parents
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
1e5400393797 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidedb commit c8f0a6706869a8f2988a096c61d7de7de573434f"
galaxyp
parents:
diff changeset
1 <tool id="proteomiqon_peptidedb" name="ProteomIQon PeptideDB" version="@VERSION@" profile="20.05">
1e5400393797 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidedb commit c8f0a6706869a8f2988a096c61d7de7de573434f"
galaxyp
parents:
diff changeset
2 <description>
1e5400393797 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidedb commit c8f0a6706869a8f2988a096c61d7de7de573434f"
galaxyp
parents:
diff changeset
3 creates a peptide database in the SQLite format.
1e5400393797 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidedb commit c8f0a6706869a8f2988a096c61d7de7de573434f"
galaxyp
parents:
diff changeset
4 </description>
1e5400393797 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidedb commit c8f0a6706869a8f2988a096c61d7de7de573434f"
galaxyp
parents:
diff changeset
5 <macros>
1e5400393797 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidedb commit c8f0a6706869a8f2988a096c61d7de7de573434f"
galaxyp
parents:
diff changeset
6 <token name="@VERSION@">0.0.7</token>
1e5400393797 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidedb commit c8f0a6706869a8f2988a096c61d7de7de573434f"
galaxyp
parents:
diff changeset
7 </macros>
1e5400393797 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidedb commit c8f0a6706869a8f2988a096c61d7de7de573434f"
galaxyp
parents:
diff changeset
8 <requirements>
1e5400393797 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidedb commit c8f0a6706869a8f2988a096c61d7de7de573434f"
galaxyp
parents:
diff changeset
9 <requirement type="package" version="@VERSION@">proteomiqon-peptidedb</requirement>
1e5400393797 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidedb commit c8f0a6706869a8f2988a096c61d7de7de573434f"
galaxyp
parents:
diff changeset
10 </requirements>
1e5400393797 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidedb commit c8f0a6706869a8f2988a096c61d7de7de573434f"
galaxyp
parents:
diff changeset
11 <command detect_errors="exit_code"><![CDATA[
1e5400393797 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidedb commit c8f0a6706869a8f2988a096c61d7de7de573434f"
galaxyp
parents:
diff changeset
12 #if $outputParamfile:
1e5400393797 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidedb commit c8f0a6706869a8f2988a096c61d7de7de573434f"
galaxyp
parents:
diff changeset
13 cat '$paramfile' >> '$out_paramfile' &&
1e5400393797 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidedb commit c8f0a6706869a8f2988a096c61d7de7de573434f"
galaxyp
parents:
diff changeset
14 #end if
1e5400393797 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidedb commit c8f0a6706869a8f2988a096c61d7de7de573434f"
galaxyp
parents:
diff changeset
15 proteomiqon-peptidedb -i '$fasta' -p '$paramfile' -o ./ &&
1e5400393797 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidedb commit c8f0a6706869a8f2988a096c61d7de7de573434f"
galaxyp
parents:
diff changeset
16 cp './galaxy.db' '$out_db'
1e5400393797 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidedb commit c8f0a6706869a8f2988a096c61d7de7de573434f"
galaxyp
parents:
diff changeset
17 ]]>
1e5400393797 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidedb commit c8f0a6706869a8f2988a096c61d7de7de573434f"
galaxyp
parents:
diff changeset
18 </command>
1e5400393797 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidedb commit c8f0a6706869a8f2988a096c61d7de7de573434f"
galaxyp
parents:
diff changeset
19 <configfiles>
1e5400393797 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidedb commit c8f0a6706869a8f2988a096c61d7de7de573434f"
galaxyp
parents:
diff changeset
20 <configfile name="paramfile">
1e5400393797 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidedb commit c8f0a6706869a8f2988a096c61d7de7de573434f"
galaxyp
parents:
diff changeset
21 <![CDATA[
1e5400393797 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidedb commit c8f0a6706869a8f2988a096c61d7de7de573434f"
galaxyp
parents:
diff changeset
22 {
1e5400393797 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidedb commit c8f0a6706869a8f2988a096c61d7de7de573434f"
galaxyp
parents:
diff changeset
23 "Name": "galaxy",
1e5400393797 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidedb commit c8f0a6706869a8f2988a096c61d7de7de573434f"
galaxyp
parents:
diff changeset
24 "ParseProteinIDRegexPattern": "${ParseProteinIDRegexPattern}",
1e5400393797 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidedb commit c8f0a6706869a8f2988a096c61d7de7de573434f"
galaxyp
parents:
diff changeset
25 "Protease": { "Case": "${Protease}" },
1e5400393797 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidedb commit c8f0a6706869a8f2988a096c61d7de7de573434f"
galaxyp
parents:
diff changeset
26 "MinMissedCleavages": ${MinMissedCleavages},
1e5400393797 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidedb commit c8f0a6706869a8f2988a096c61d7de7de573434f"
galaxyp
parents:
diff changeset
27 "MaxMissedCleavages": ${MaxMissedCleavages},
1e5400393797 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidedb commit c8f0a6706869a8f2988a096c61d7de7de573434f"
galaxyp
parents:
diff changeset
28 "MaxMass": ${MaxMass},
1e5400393797 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidedb commit c8f0a6706869a8f2988a096c61d7de7de573434f"
galaxyp
parents:
diff changeset
29 "MinPepLength": ${MinPepLength},
1e5400393797 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidedb commit c8f0a6706869a8f2988a096c61d7de7de573434f"
galaxyp
parents:
diff changeset
30 "MaxPepLength": ${MaxPepLength},
1e5400393797 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidedb commit c8f0a6706869a8f2988a096c61d7de7de573434f"
galaxyp
parents:
diff changeset
31 "IsotopicMod": [
1e5400393797 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidedb commit c8f0a6706869a8f2988a096c61d7de7de573434f"
galaxyp
parents:
diff changeset
32 #set isotopicModList = $list($IsotopicMod)
1e5400393797 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidedb commit c8f0a6706869a8f2988a096c61d7de7de573434f"
galaxyp
parents:
diff changeset
33 #for $mod in $range($len($isotopicModList))
1e5400393797 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidedb commit c8f0a6706869a8f2988a096c61d7de7de573434f"
galaxyp
parents:
diff changeset
34 #if $mod != $len($isotopicModList) -1
1e5400393797 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidedb commit c8f0a6706869a8f2988a096c61d7de7de573434f"
galaxyp
parents:
diff changeset
35 {"Case":"${isotopicModList[$mod]}"},
1e5400393797 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidedb commit c8f0a6706869a8f2988a096c61d7de7de573434f"
galaxyp
parents:
diff changeset
36 #else
1e5400393797 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidedb commit c8f0a6706869a8f2988a096c61d7de7de573434f"
galaxyp
parents:
diff changeset
37 {"Case":"${isotopicModList[$mod]}"}
1e5400393797 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidedb commit c8f0a6706869a8f2988a096c61d7de7de573434f"
galaxyp
parents:
diff changeset
38 #end if
1e5400393797 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidedb commit c8f0a6706869a8f2988a096c61d7de7de573434f"
galaxyp
parents:
diff changeset
39 #end for
1e5400393797 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidedb commit c8f0a6706869a8f2988a096c61d7de7de573434f"
galaxyp
parents:
diff changeset
40 ],
1e5400393797 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidedb commit c8f0a6706869a8f2988a096c61d7de7de573434f"
galaxyp
parents:
diff changeset
41 "MassMode": {
1e5400393797 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidedb commit c8f0a6706869a8f2988a096c61d7de7de573434f"
galaxyp
parents:
diff changeset
42 "Case": "${MassMode}"
1e5400393797 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidedb commit c8f0a6706869a8f2988a096c61d7de7de573434f"
galaxyp
parents:
diff changeset
43 },
1e5400393797 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidedb commit c8f0a6706869a8f2988a096c61d7de7de573434f"
galaxyp
parents:
diff changeset
44 "FixedMods": [
1e5400393797 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidedb commit c8f0a6706869a8f2988a096c61d7de7de573434f"
galaxyp
parents:
diff changeset
45 #set fixedModList = $list($FixedMods)
1e5400393797 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidedb commit c8f0a6706869a8f2988a096c61d7de7de573434f"
galaxyp
parents:
diff changeset
46 #for $mod in $range($len($fixedModList))
1e5400393797 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidedb commit c8f0a6706869a8f2988a096c61d7de7de573434f"
galaxyp
parents:
diff changeset
47 #if $mod != $len($fixedModList) -1
1e5400393797 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidedb commit c8f0a6706869a8f2988a096c61d7de7de573434f"
galaxyp
parents:
diff changeset
48 {"Case":"${fixedModList[$mod]}"},
1e5400393797 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidedb commit c8f0a6706869a8f2988a096c61d7de7de573434f"
galaxyp
parents:
diff changeset
49 #else
1e5400393797 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidedb commit c8f0a6706869a8f2988a096c61d7de7de573434f"
galaxyp
parents:
diff changeset
50 {"Case":"${fixedModList[$mod]}"}
1e5400393797 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidedb commit c8f0a6706869a8f2988a096c61d7de7de573434f"
galaxyp
parents:
diff changeset
51 #end if
1e5400393797 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidedb commit c8f0a6706869a8f2988a096c61d7de7de573434f"
galaxyp
parents:
diff changeset
52 #end for
1e5400393797 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidedb commit c8f0a6706869a8f2988a096c61d7de7de573434f"
galaxyp
parents:
diff changeset
53 ],
1e5400393797 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidedb commit c8f0a6706869a8f2988a096c61d7de7de573434f"
galaxyp
parents:
diff changeset
54 "VariableMods": [
1e5400393797 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidedb commit c8f0a6706869a8f2988a096c61d7de7de573434f"
galaxyp
parents:
diff changeset
55 #set variableModList = $list($VariableMods)
1e5400393797 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidedb commit c8f0a6706869a8f2988a096c61d7de7de573434f"
galaxyp
parents:
diff changeset
56 #for $mod in $range($len($variableModList))
1e5400393797 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidedb commit c8f0a6706869a8f2988a096c61d7de7de573434f"
galaxyp
parents:
diff changeset
57 #if $mod != $len($variableModList) -1
1e5400393797 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidedb commit c8f0a6706869a8f2988a096c61d7de7de573434f"
galaxyp
parents:
diff changeset
58 {"Case":"${variableModList[$mod]}"},
1e5400393797 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidedb commit c8f0a6706869a8f2988a096c61d7de7de573434f"
galaxyp
parents:
diff changeset
59 #else
1e5400393797 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidedb commit c8f0a6706869a8f2988a096c61d7de7de573434f"
galaxyp
parents:
diff changeset
60 {"Case":"${variableModList[$mod]}"}
1e5400393797 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidedb commit c8f0a6706869a8f2988a096c61d7de7de573434f"
galaxyp
parents:
diff changeset
61 #end if
1e5400393797 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidedb commit c8f0a6706869a8f2988a096c61d7de7de573434f"
galaxyp
parents:
diff changeset
62 #end for
1e5400393797 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidedb commit c8f0a6706869a8f2988a096c61d7de7de573434f"
galaxyp
parents:
diff changeset
63 ],
1e5400393797 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidedb commit c8f0a6706869a8f2988a096c61d7de7de573434f"
galaxyp
parents:
diff changeset
64 "VarModThreshold": ${VarModThreshold}
1e5400393797 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidedb commit c8f0a6706869a8f2988a096c61d7de7de573434f"
galaxyp
parents:
diff changeset
65 }
1e5400393797 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidedb commit c8f0a6706869a8f2988a096c61d7de7de573434f"
galaxyp
parents:
diff changeset
66 ]]>
1e5400393797 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidedb commit c8f0a6706869a8f2988a096c61d7de7de573434f"
galaxyp
parents:
diff changeset
67 </configfile>
1e5400393797 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidedb commit c8f0a6706869a8f2988a096c61d7de7de573434f"
galaxyp
parents:
diff changeset
68 </configfiles>
1e5400393797 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidedb commit c8f0a6706869a8f2988a096c61d7de7de573434f"
galaxyp
parents:
diff changeset
69 <inputs>
1e5400393797 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidedb commit c8f0a6706869a8f2988a096c61d7de7de573434f"
galaxyp
parents:
diff changeset
70 <param name="fasta" type="data" format="fasta" label="Fasta file" help="Please specify your protein sequences in the .fasta format. If you want to search for contaminants you have to include the sequences in your file. You do not have to supply decoy sequences, those are generated for you."/>
1e5400393797 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidedb commit c8f0a6706869a8f2988a096c61d7de7de573434f"
galaxyp
parents:
diff changeset
71 <param name="ParseProteinIDRegexPattern" type="text" value="id" label="Regex pattern to parse protein ID from .fasta header" help="Fasta headers do often contain additional information in addition to your protein identifier, by specifying a regex pattern the tool can extract the protein IDs. If you fasta headers are already cleaned you can leave this field empty.">
1e5400393797 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidedb commit c8f0a6706869a8f2988a096c61d7de7de573434f"
galaxyp
parents:
diff changeset
72 <sanitizer sanitize="false" />
1e5400393797 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidedb commit c8f0a6706869a8f2988a096c61d7de7de573434f"
galaxyp
parents:
diff changeset
73 </param>
1e5400393797 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidedb commit c8f0a6706869a8f2988a096c61d7de7de573434f"
galaxyp
parents:
diff changeset
74 <param name="Protease" type="select" label="Protease" help="Select a protease the tool can use when performing in silico digestion.">
1e5400393797 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidedb commit c8f0a6706869a8f2988a096c61d7de7de573434f"
galaxyp
parents:
diff changeset
75 <option selected="true" value="Trypsin">Trypsin</option>
1e5400393797 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidedb commit c8f0a6706869a8f2988a096c61d7de7de573434f"
galaxyp
parents:
diff changeset
76 <option value="Trypsin_P">Trypsin_P</option>
1e5400393797 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidedb commit c8f0a6706869a8f2988a096c61d7de7de573434f"
galaxyp
parents:
diff changeset
77 <option value="LysC">LysC</option>
1e5400393797 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidedb commit c8f0a6706869a8f2988a096c61d7de7de573434f"
galaxyp
parents:
diff changeset
78 <option value="LysC_P">LysC_P</option>
1e5400393797 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidedb commit c8f0a6706869a8f2988a096c61d7de7de573434f"
galaxyp
parents:
diff changeset
79 <option value="Chymotrypsin">Chymotrypsin</option>
1e5400393797 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidedb commit c8f0a6706869a8f2988a096c61d7de7de573434f"
galaxyp
parents:
diff changeset
80 <option value="PepsinA">PepsinA</option>
1e5400393797 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidedb commit c8f0a6706869a8f2988a096c61d7de7de573434f"
galaxyp
parents:
diff changeset
81 </param>
1e5400393797 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidedb commit c8f0a6706869a8f2988a096c61d7de7de573434f"
galaxyp
parents:
diff changeset
82 <param name="MinMissedCleavages" type="integer" value="0" label="Min missed cleavages" help="Select the minimum amount of miss cleavages in a peptide sequence."/>
1e5400393797 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidedb commit c8f0a6706869a8f2988a096c61d7de7de573434f"
galaxyp
parents:
diff changeset
83 <param name="MaxMissedCleavages" type="integer" value="2" label="Max missed cleavages" help="Select the maximum amount of miss cleavages in a peptide sequence."/>
1e5400393797 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidedb commit c8f0a6706869a8f2988a096c61d7de7de573434f"
galaxyp
parents:
diff changeset
84 <param name="MaxMass" type="float" value="15000.0" label="Max mass" help="Select the maximum mass of peptides included in the data base."/>
1e5400393797 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidedb commit c8f0a6706869a8f2988a096c61d7de7de573434f"
galaxyp
parents:
diff changeset
85 <param name="MinPepLength" type="integer" value="4" label="Min peptide length" help="Select the minimum amino acid length of peptides included in the data base."/>
1e5400393797 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidedb commit c8f0a6706869a8f2988a096c61d7de7de573434f"
galaxyp
parents:
diff changeset
86 <param name="MaxPepLength" type="integer" value="65" label="Max peptide length" help="Select the minimum amino acid length of peptides included in the data base."/>
1e5400393797 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidedb commit c8f0a6706869a8f2988a096c61d7de7de573434f"
galaxyp
parents:
diff changeset
87 <param name="IsotopicMod" type="select" label="Isotopic mod" help="Select isotopic amino acid modifications. These modifications change the natural abundance of isotopes of single elements. Each peptide sequence is duplicated and included in the data base at natural isotopic abundances and using the modified isotopic abundances." multiple="true">
1e5400393797 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidedb commit c8f0a6706869a8f2988a096c61d7de7de573434f"
galaxyp
parents:
diff changeset
88 <option value="N15" selected="true">N15</option>
1e5400393797 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidedb commit c8f0a6706869a8f2988a096c61d7de7de573434f"
galaxyp
parents:
diff changeset
89 <option value="C13">C13</option>
1e5400393797 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidedb commit c8f0a6706869a8f2988a096c61d7de7de573434f"
galaxyp
parents:
diff changeset
90 <option value="O17">O17</option>
1e5400393797 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidedb commit c8f0a6706869a8f2988a096c61d7de7de573434f"
galaxyp
parents:
diff changeset
91 <option value="O18">O18</option>
1e5400393797 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidedb commit c8f0a6706869a8f2988a096c61d7de7de573434f"
galaxyp
parents:
diff changeset
92 <option value="D">D</option>
1e5400393797 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidedb commit c8f0a6706869a8f2988a096c61d7de7de573434f"
galaxyp
parents:
diff changeset
93 </param>
1e5400393797 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidedb commit c8f0a6706869a8f2988a096c61d7de7de573434f"
galaxyp
parents:
diff changeset
94 <param name="MassMode" type="select" label="Mass mode" help="Specify how the peptide masses should be calculated.">
1e5400393797 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidedb commit c8f0a6706869a8f2988a096c61d7de7de573434f"
galaxyp
parents:
diff changeset
95 <option value="Monoisotopic" selected="true">Monoisotopic</option>
1e5400393797 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidedb commit c8f0a6706869a8f2988a096c61d7de7de573434f"
galaxyp
parents:
diff changeset
96 <option value="Average">Average</option>
1e5400393797 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidedb commit c8f0a6706869a8f2988a096c61d7de7de573434f"
galaxyp
parents:
diff changeset
97 </param>
1e5400393797 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidedb commit c8f0a6706869a8f2988a096c61d7de7de573434f"
galaxyp
parents:
diff changeset
98 <param name="FixedMods" type="select" label="Fixed mods" help="Select fixed amino acid modifications. These Modifications are applied whenever possible." multiple="true">
1e5400393797 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidedb commit c8f0a6706869a8f2988a096c61d7de7de573434f"
galaxyp
parents:
diff changeset
99 <option value="Acetylation'ProtNTerm'">Acetylation'ProtNTerm'</option>
1e5400393797 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidedb commit c8f0a6706869a8f2988a096c61d7de7de573434f"
galaxyp
parents:
diff changeset
100 <option value="Carbamidomethyl'Cys'">Carbamidomethyl'Cys'</option>
1e5400393797 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidedb commit c8f0a6706869a8f2988a096c61d7de7de573434f"
galaxyp
parents:
diff changeset
101 <option value="Oxidation'Met'">Oxidation'Met'</option>
1e5400393797 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidedb commit c8f0a6706869a8f2988a096c61d7de7de573434f"
galaxyp
parents:
diff changeset
102 <option value="Phosphorylation'Ser'Thr'Tyr'">Phosphorylation'Ser'Thr'Tyr'</option>
1e5400393797 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidedb commit c8f0a6706869a8f2988a096c61d7de7de573434f"
galaxyp
parents:
diff changeset
103 <option value="Pyro_Glu'GluNterm'">Pyro_Glu'GluNterm'</option>
1e5400393797 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidedb commit c8f0a6706869a8f2988a096c61d7de7de573434f"
galaxyp
parents:
diff changeset
104 <option value="Pyro_Glu'GlnNterm'">Pyro_Glu'GlnNterm'</option>
1e5400393797 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidedb commit c8f0a6706869a8f2988a096c61d7de7de573434f"
galaxyp
parents:
diff changeset
105 </param>
1e5400393797 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidedb commit c8f0a6706869a8f2988a096c61d7de7de573434f"
galaxyp
parents:
diff changeset
106 <param name="VariableMods" type="select" label="Variable mods" help="Select variable amino acid modifications. Whenever a this modification can be applied the peptide sequence is duplicated and included in the data base in a modified and unmodiefied version." multiple="true">
1e5400393797 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidedb commit c8f0a6706869a8f2988a096c61d7de7de573434f"
galaxyp
parents:
diff changeset
107 <option value="Acetylation'ProtNTerm'" selected="true">Acetylation'ProtNTerm'</option>
1e5400393797 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidedb commit c8f0a6706869a8f2988a096c61d7de7de573434f"
galaxyp
parents:
diff changeset
108 <option value="Carbamidomethyl'Cys'">Carbamidomethyl'Cys'</option>
1e5400393797 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidedb commit c8f0a6706869a8f2988a096c61d7de7de573434f"
galaxyp
parents:
diff changeset
109 <option value="Oxidation'Met'" selected="true">Oxidation'Met'</option>
1e5400393797 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidedb commit c8f0a6706869a8f2988a096c61d7de7de573434f"
galaxyp
parents:
diff changeset
110 <option value="Phosphorylation'Ser'Thr'Tyr'">Phosphorylation'Ser'Thr'Tyr'</option>
1e5400393797 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidedb commit c8f0a6706869a8f2988a096c61d7de7de573434f"
galaxyp
parents:
diff changeset
111 <option value="Pyro_Glu'GluNterm'">Pyro_Glu'GluNterm'</option>
1e5400393797 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidedb commit c8f0a6706869a8f2988a096c61d7de7de573434f"
galaxyp
parents:
diff changeset
112 <option value="Pyro_Glu'GlnNterm'">Pyro_Glu'GlnNterm'</option>
1e5400393797 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidedb commit c8f0a6706869a8f2988a096c61d7de7de573434f"
galaxyp
parents:
diff changeset
113 </param>
1e5400393797 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidedb commit c8f0a6706869a8f2988a096c61d7de7de573434f"
galaxyp
parents:
diff changeset
114 <param name="VarModThreshold" type="integer" value="4" label="Variable mod threshold" help="Select the maximum amount of variable amino acid modifications in one sequence. This parameter is needed to circumvent a combinatoric explosion."/>
1e5400393797 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidedb commit c8f0a6706869a8f2988a096c61d7de7de573434f"
galaxyp
parents:
diff changeset
115 <param name="outputParamfile" type="boolean" value="false" label="Output parameter file"/>
1e5400393797 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidedb commit c8f0a6706869a8f2988a096c61d7de7de573434f"
galaxyp
parents:
diff changeset
116 </inputs>
1e5400393797 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidedb commit c8f0a6706869a8f2988a096c61d7de7de573434f"
galaxyp
parents:
diff changeset
117 <outputs>
1e5400393797 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidedb commit c8f0a6706869a8f2988a096c61d7de7de573434f"
galaxyp
parents:
diff changeset
118 <data format="sqlite" name="out_db" />
1e5400393797 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidedb commit c8f0a6706869a8f2988a096c61d7de7de573434f"
galaxyp
parents:
diff changeset
119 <data format="json" name="out_paramfile">
1e5400393797 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidedb commit c8f0a6706869a8f2988a096c61d7de7de573434f"
galaxyp
parents:
diff changeset
120 <filter>outputParamfile</filter>
1e5400393797 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidedb commit c8f0a6706869a8f2988a096c61d7de7de573434f"
galaxyp
parents:
diff changeset
121 </data>
1e5400393797 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidedb commit c8f0a6706869a8f2988a096c61d7de7de573434f"
galaxyp
parents:
diff changeset
122 </outputs>
1e5400393797 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidedb commit c8f0a6706869a8f2988a096c61d7de7de573434f"
galaxyp
parents:
diff changeset
123 <tests>
1e5400393797 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidedb commit c8f0a6706869a8f2988a096c61d7de7de573434f"
galaxyp
parents:
diff changeset
124 <test expect_num_outputs="1">
1e5400393797 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidedb commit c8f0a6706869a8f2988a096c61d7de7de573434f"
galaxyp
parents:
diff changeset
125 <param name="fasta" value="sample.fasta"/>
1e5400393797 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidedb commit c8f0a6706869a8f2988a096c61d7de7de573434f"
galaxyp
parents:
diff changeset
126 <param name="ParseProteinIDRegexPattern" value="id"/>
1e5400393797 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidedb commit c8f0a6706869a8f2988a096c61d7de7de573434f"
galaxyp
parents:
diff changeset
127 <param name="Protease" value="Trypsin"/>
1e5400393797 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidedb commit c8f0a6706869a8f2988a096c61d7de7de573434f"
galaxyp
parents:
diff changeset
128 <param name="MinMissedCleavages" value="0"/>
1e5400393797 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidedb commit c8f0a6706869a8f2988a096c61d7de7de573434f"
galaxyp
parents:
diff changeset
129 <param name="MaxMissedCleavages" value="2"/>
1e5400393797 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidedb commit c8f0a6706869a8f2988a096c61d7de7de573434f"
galaxyp
parents:
diff changeset
130 <param name="MaxMass" value="15000.0"/>
1e5400393797 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidedb commit c8f0a6706869a8f2988a096c61d7de7de573434f"
galaxyp
parents:
diff changeset
131 <param name="MinPepLength" value="4"/>
1e5400393797 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidedb commit c8f0a6706869a8f2988a096c61d7de7de573434f"
galaxyp
parents:
diff changeset
132 <param name="MaxPepLength" value="65"/>
1e5400393797 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidedb commit c8f0a6706869a8f2988a096c61d7de7de573434f"
galaxyp
parents:
diff changeset
133 <param name="IsotopicMod" value="N15"/>
1e5400393797 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidedb commit c8f0a6706869a8f2988a096c61d7de7de573434f"
galaxyp
parents:
diff changeset
134 <param name="MassMode" value="Monoisotopic"/>
1e5400393797 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidedb commit c8f0a6706869a8f2988a096c61d7de7de573434f"
galaxyp
parents:
diff changeset
135 <param name="FixedMods" value="Acetylation'ProtNTerm'"/>
1e5400393797 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidedb commit c8f0a6706869a8f2988a096c61d7de7de573434f"
galaxyp
parents:
diff changeset
136 <param name="VariableMods" value="Acetylation'ProtNTerm'"/>
1e5400393797 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidedb commit c8f0a6706869a8f2988a096c61d7de7de573434f"
galaxyp
parents:
diff changeset
137 <param name="VarModThreshold" value="4"/>
1e5400393797 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidedb commit c8f0a6706869a8f2988a096c61d7de7de573434f"
galaxyp
parents:
diff changeset
138 <param name="outputParamfile" value="false"/>
1e5400393797 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidedb commit c8f0a6706869a8f2988a096c61d7de7de573434f"
galaxyp
parents:
diff changeset
139 </test>
1e5400393797 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidedb commit c8f0a6706869a8f2988a096c61d7de7de573434f"
galaxyp
parents:
diff changeset
140 <test expect_num_outputs="2">
1e5400393797 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidedb commit c8f0a6706869a8f2988a096c61d7de7de573434f"
galaxyp
parents:
diff changeset
141 <param name="fasta" value="sample.fasta"/>
1e5400393797 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidedb commit c8f0a6706869a8f2988a096c61d7de7de573434f"
galaxyp
parents:
diff changeset
142 <param name="ParseProteinIDRegexPattern" value="id"/>
1e5400393797 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidedb commit c8f0a6706869a8f2988a096c61d7de7de573434f"
galaxyp
parents:
diff changeset
143 <param name="Protease" value="Trypsin"/>
1e5400393797 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidedb commit c8f0a6706869a8f2988a096c61d7de7de573434f"
galaxyp
parents:
diff changeset
144 <param name="MinMissedCleavages" value="0"/>
1e5400393797 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidedb commit c8f0a6706869a8f2988a096c61d7de7de573434f"
galaxyp
parents:
diff changeset
145 <param name="MaxMissedCleavages" value="2"/>
1e5400393797 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidedb commit c8f0a6706869a8f2988a096c61d7de7de573434f"
galaxyp
parents:
diff changeset
146 <param name="MaxMass" value="15000.0"/>
1e5400393797 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidedb commit c8f0a6706869a8f2988a096c61d7de7de573434f"
galaxyp
parents:
diff changeset
147 <param name="MinPepLength" value="4"/>
1e5400393797 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidedb commit c8f0a6706869a8f2988a096c61d7de7de573434f"
galaxyp
parents:
diff changeset
148 <param name="MaxPepLength" value="65"/>
1e5400393797 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidedb commit c8f0a6706869a8f2988a096c61d7de7de573434f"
galaxyp
parents:
diff changeset
149 <param name="IsotopicMod" value="N15"/>
1e5400393797 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidedb commit c8f0a6706869a8f2988a096c61d7de7de573434f"
galaxyp
parents:
diff changeset
150 <param name="MassMode" value="Monoisotopic"/>
1e5400393797 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidedb commit c8f0a6706869a8f2988a096c61d7de7de573434f"
galaxyp
parents:
diff changeset
151 <param name="FixedMods" value="Acetylation'ProtNTerm'"/>
1e5400393797 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidedb commit c8f0a6706869a8f2988a096c61d7de7de573434f"
galaxyp
parents:
diff changeset
152 <param name="VariableMods" value="Acetylation'ProtNTerm'"/>
1e5400393797 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidedb commit c8f0a6706869a8f2988a096c61d7de7de573434f"
galaxyp
parents:
diff changeset
153 <param name="VarModThreshold" value="4"/>
1e5400393797 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidedb commit c8f0a6706869a8f2988a096c61d7de7de573434f"
galaxyp
parents:
diff changeset
154 <param name="outputParamfile" value="true"/>
1e5400393797 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidedb commit c8f0a6706869a8f2988a096c61d7de7de573434f"
galaxyp
parents:
diff changeset
155 <output name="out_paramfile" file="result_1.json"/>
1e5400393797 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidedb commit c8f0a6706869a8f2988a096c61d7de7de573434f"
galaxyp
parents:
diff changeset
156 </test>
1e5400393797 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidedb commit c8f0a6706869a8f2988a096c61d7de7de573434f"
galaxyp
parents:
diff changeset
157 <test expect_num_outputs="2">
1e5400393797 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidedb commit c8f0a6706869a8f2988a096c61d7de7de573434f"
galaxyp
parents:
diff changeset
158 <param name="fasta" value="sample.fasta"/>
1e5400393797 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidedb commit c8f0a6706869a8f2988a096c61d7de7de573434f"
galaxyp
parents:
diff changeset
159 <param name="ParseProteinIDRegexPattern" value="id"/>
1e5400393797 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidedb commit c8f0a6706869a8f2988a096c61d7de7de573434f"
galaxyp
parents:
diff changeset
160 <param name="Protease" value="Trypsin"/>
1e5400393797 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidedb commit c8f0a6706869a8f2988a096c61d7de7de573434f"
galaxyp
parents:
diff changeset
161 <param name="MinMissedCleavages" value="0"/>
1e5400393797 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidedb commit c8f0a6706869a8f2988a096c61d7de7de573434f"
galaxyp
parents:
diff changeset
162 <param name="MaxMissedCleavages" value="2"/>
1e5400393797 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidedb commit c8f0a6706869a8f2988a096c61d7de7de573434f"
galaxyp
parents:
diff changeset
163 <param name="MaxMass" value="15000.0"/>
1e5400393797 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidedb commit c8f0a6706869a8f2988a096c61d7de7de573434f"
galaxyp
parents:
diff changeset
164 <param name="MinPepLength" value="4"/>
1e5400393797 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidedb commit c8f0a6706869a8f2988a096c61d7de7de573434f"
galaxyp
parents:
diff changeset
165 <param name="MaxPepLength" value="65"/>
1e5400393797 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidedb commit c8f0a6706869a8f2988a096c61d7de7de573434f"
galaxyp
parents:
diff changeset
166 <param name="IsotopicMod" value="N15"/>
1e5400393797 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidedb commit c8f0a6706869a8f2988a096c61d7de7de573434f"
galaxyp
parents:
diff changeset
167 <param name="MassMode" value="Monoisotopic"/>
1e5400393797 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidedb commit c8f0a6706869a8f2988a096c61d7de7de573434f"
galaxyp
parents:
diff changeset
168 <param name="FixedMods" value="Acetylation'ProtNTerm',Carbamidomethyl'Cys',Oxidation'Met',Phosphorylation'Ser'Thr'Tyr',Pyro_Glu'GluNterm',Pyro_Glu'GlnNterm'"/>
1e5400393797 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidedb commit c8f0a6706869a8f2988a096c61d7de7de573434f"
galaxyp
parents:
diff changeset
169 <param name="VariableMods" value="Acetylation'ProtNTerm',Carbamidomethyl'Cys',Oxidation'Met',Phosphorylation'Ser'Thr'Tyr',Pyro_Glu'GluNterm',Pyro_Glu'GlnNterm'"/>
1e5400393797 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidedb commit c8f0a6706869a8f2988a096c61d7de7de573434f"
galaxyp
parents:
diff changeset
170 <param name="VarModThreshold" value="4"/>
1e5400393797 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidedb commit c8f0a6706869a8f2988a096c61d7de7de573434f"
galaxyp
parents:
diff changeset
171 <param name="outputParamfile" value="true"/>
1e5400393797 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidedb commit c8f0a6706869a8f2988a096c61d7de7de573434f"
galaxyp
parents:
diff changeset
172 <output name="out_paramfile" file="result_2.json"/>
1e5400393797 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidedb commit c8f0a6706869a8f2988a096c61d7de7de573434f"
galaxyp
parents:
diff changeset
173 </test>
1e5400393797 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidedb commit c8f0a6706869a8f2988a096c61d7de7de573434f"
galaxyp
parents:
diff changeset
174 <test expect_num_outputs="2">
1e5400393797 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidedb commit c8f0a6706869a8f2988a096c61d7de7de573434f"
galaxyp
parents:
diff changeset
175 <param name="fasta" value="sample.fasta"/>
1e5400393797 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidedb commit c8f0a6706869a8f2988a096c61d7de7de573434f"
galaxyp
parents:
diff changeset
176 <param name="ParseProteinIDRegexPattern" value="id"/>
1e5400393797 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidedb commit c8f0a6706869a8f2988a096c61d7de7de573434f"
galaxyp
parents:
diff changeset
177 <param name="Protease" value="Trypsin"/>
1e5400393797 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidedb commit c8f0a6706869a8f2988a096c61d7de7de573434f"
galaxyp
parents:
diff changeset
178 <param name="MinMissedCleavages" value="0"/>
1e5400393797 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidedb commit c8f0a6706869a8f2988a096c61d7de7de573434f"
galaxyp
parents:
diff changeset
179 <param name="MaxMissedCleavages" value="2"/>
1e5400393797 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidedb commit c8f0a6706869a8f2988a096c61d7de7de573434f"
galaxyp
parents:
diff changeset
180 <param name="MaxMass" value="15000.0"/>
1e5400393797 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidedb commit c8f0a6706869a8f2988a096c61d7de7de573434f"
galaxyp
parents:
diff changeset
181 <param name="MinPepLength" value="4"/>
1e5400393797 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidedb commit c8f0a6706869a8f2988a096c61d7de7de573434f"
galaxyp
parents:
diff changeset
182 <param name="MaxPepLength" value="65"/>
1e5400393797 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidedb commit c8f0a6706869a8f2988a096c61d7de7de573434f"
galaxyp
parents:
diff changeset
183 <param name="IsotopicMod" value=""/>
1e5400393797 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidedb commit c8f0a6706869a8f2988a096c61d7de7de573434f"
galaxyp
parents:
diff changeset
184 <param name="MassMode" value="Average"/>
1e5400393797 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidedb commit c8f0a6706869a8f2988a096c61d7de7de573434f"
galaxyp
parents:
diff changeset
185 <param name="FixedMods" value=""/>
1e5400393797 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidedb commit c8f0a6706869a8f2988a096c61d7de7de573434f"
galaxyp
parents:
diff changeset
186 <param name="VariableMods" value=""/>
1e5400393797 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidedb commit c8f0a6706869a8f2988a096c61d7de7de573434f"
galaxyp
parents:
diff changeset
187 <param name="VarModThreshold" value="4"/>
1e5400393797 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidedb commit c8f0a6706869a8f2988a096c61d7de7de573434f"
galaxyp
parents:
diff changeset
188 <param name="outputParamfile" value="true"/>
1e5400393797 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidedb commit c8f0a6706869a8f2988a096c61d7de7de573434f"
galaxyp
parents:
diff changeset
189 <output name="out_paramfile" file="result_3.json"/>
1e5400393797 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidedb commit c8f0a6706869a8f2988a096c61d7de7de573434f"
galaxyp
parents:
diff changeset
190 </test>
1e5400393797 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidedb commit c8f0a6706869a8f2988a096c61d7de7de573434f"
galaxyp
parents:
diff changeset
191 </tests>
1e5400393797 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidedb commit c8f0a6706869a8f2988a096c61d7de7de573434f"
galaxyp
parents:
diff changeset
192 <help>
1e5400393797 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidedb commit c8f0a6706869a8f2988a096c61d7de7de573434f"
galaxyp
parents:
diff changeset
193 <![CDATA[
1e5400393797 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidedb commit c8f0a6706869a8f2988a096c61d7de7de573434f"
galaxyp
parents:
diff changeset
194 Introduction
1e5400393797 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidedb commit c8f0a6706869a8f2988a096c61d7de7de573434f"
galaxyp
parents:
diff changeset
195 ------------
1e5400393797 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidedb commit c8f0a6706869a8f2988a096c61d7de7de573434f"
galaxyp
parents:
diff changeset
196 MS-based shotgun proteomics estimates protein abundances using a proxy: peptides.
1e5400393797 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidedb commit c8f0a6706869a8f2988a096c61d7de7de573434f"
galaxyp
parents:
diff changeset
197 An established method to identify acquired MS/MS spectra is the comparison of each spectrum with peptides in a reference database.
1e5400393797 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidedb commit c8f0a6706869a8f2988a096c61d7de7de573434f"
galaxyp
parents:
diff changeset
198
1e5400393797 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidedb commit c8f0a6706869a8f2988a096c61d7de7de573434f"
galaxyp
parents:
diff changeset
199 What It Does
1e5400393797 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidedb commit c8f0a6706869a8f2988a096c61d7de7de573434f"
galaxyp
parents:
diff changeset
200 ------------
1e5400393797 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidedb commit c8f0a6706869a8f2988a096c61d7de7de573434f"
galaxyp
parents:
diff changeset
201 The PeptideDB tool helps to create peptide databases by in silico digestion given proteome information in the FASTA format and a set of parameters
1e5400393797 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidedb commit c8f0a6706869a8f2988a096c61d7de7de573434f"
galaxyp
parents:
diff changeset
202 that allow the user to mimic conditions of their specific experiment.
1e5400393797 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidedb commit c8f0a6706869a8f2988a096c61d7de7de573434f"
galaxyp
parents:
diff changeset
203 The created database stores peptide protein relationships in a SQLite database which can then be supplied to other ProteomIQon tools.
1e5400393797 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidedb commit c8f0a6706869a8f2988a096c61d7de7de573434f"
galaxyp
parents:
diff changeset
204
1e5400393797 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidedb commit c8f0a6706869a8f2988a096c61d7de7de573434f"
galaxyp
parents:
diff changeset
205 Further Reading
1e5400393797 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidedb commit c8f0a6706869a8f2988a096c61d7de7de573434f"
galaxyp
parents:
diff changeset
206 ---------------
1e5400393797 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidedb commit c8f0a6706869a8f2988a096c61d7de7de573434f"
galaxyp
parents:
diff changeset
207 Additional information about the tool can be found in the `documentation <https://csbiology.github.io/ProteomIQon/tools/PeptideDB.html>`_.
1e5400393797 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidedb commit c8f0a6706869a8f2988a096c61d7de7de573434f"
galaxyp
parents:
diff changeset
208 ]]>
1e5400393797 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidedb commit c8f0a6706869a8f2988a096c61d7de7de573434f"
galaxyp
parents:
diff changeset
209 </help>
1e5400393797 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidedb commit c8f0a6706869a8f2988a096c61d7de7de573434f"
galaxyp
parents:
diff changeset
210 </tool>