|
Commit message:
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidedb commit c8f0a6706869a8f2988a096c61d7de7de573434f" |
|
added:
proteomiqon_peptidedb.xml test-data/result_1.json test-data/result_2.json test-data/result_3.json test-data/sample.fasta |
| b |
| diff -r 000000000000 -r 1e5400393797 proteomiqon_peptidedb.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/proteomiqon_peptidedb.xml Sun Jul 04 21:26:08 2021 +0000 |
| [ |
| b'@@ -0,0 +1,210 @@\n+<tool id="proteomiqon_peptidedb" name="ProteomIQon PeptideDB" version="@VERSION@" profile="20.05">\n+ <description>\n+ creates a peptide database in the SQLite format.\n+ </description>\n+ <macros>\n+ <token name="@VERSION@">0.0.7</token>\n+ </macros>\n+ <requirements>\n+ <requirement type="package" version="@VERSION@">proteomiqon-peptidedb</requirement>\n+ </requirements>\n+ <command detect_errors="exit_code"><![CDATA[\n+ #if $outputParamfile:\n+ cat \'$paramfile\' >> \'$out_paramfile\' &&\n+ #end if\n+ proteomiqon-peptidedb -i \'$fasta\' -p \'$paramfile\' -o ./ &&\n+ cp \'./galaxy.db\' \'$out_db\'\n+ ]]>\n+ </command>\n+ <configfiles>\n+ <configfile name="paramfile">\n+ <![CDATA[\n+ {\n+ "Name": "galaxy",\n+ "ParseProteinIDRegexPattern": "${ParseProteinIDRegexPattern}",\n+ "Protease": { "Case": "${Protease}" },\n+ "MinMissedCleavages": ${MinMissedCleavages},\n+ "MaxMissedCleavages": ${MaxMissedCleavages},\n+ "MaxMass": ${MaxMass},\n+ "MinPepLength": ${MinPepLength},\n+ "MaxPepLength": ${MaxPepLength},\n+ "IsotopicMod": [\n+ #set isotopicModList = $list($IsotopicMod)\n+ #for $mod in $range($len($isotopicModList))\n+ #if $mod != $len($isotopicModList) -1\n+ {"Case":"${isotopicModList[$mod]}"},\n+ #else\n+ {"Case":"${isotopicModList[$mod]}"}\n+ #end if\n+ #end for\n+ ],\n+ "MassMode": {\n+ "Case": "${MassMode}"\n+ },\n+ "FixedMods": [\n+ #set fixedModList = $list($FixedMods)\n+ #for $mod in $range($len($fixedModList))\n+ #if $mod != $len($fixedModList) -1\n+ {"Case":"${fixedModList[$mod]}"},\n+ #else\n+ {"Case":"${fixedModList[$mod]}"}\n+ #end if\n+ #end for\n+ ],\n+ "VariableMods": [\n+ #set variableModList = $list($VariableMods)\n+ #for $mod in $range($len($variableModList))\n+ #if $mod != $len($variableModList) -1\n+ {"Case":"${variableModList[$mod]}"},\n+ #else\n+ {"Case":"${variableModList[$mod]}"}\n+ #end if\n+ #end for\n+ ],\n+ "VarModThreshold": ${VarModThreshold}\n+ }\n+ ]]>\n+ </configfile>\n+ </configfiles>\n+ <inputs>\n+ <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."/>\n+ <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.">\n+ <sanitizer sanitize="false" />\n+ </param>\n+ <param name="Protease" type="select" label="Protease" help="Select a protease the tool can use when performing in silico digestion.">\n+ <option selected="true" value="Trypsin">Trypsin</option>\n+ <option value="Trypsin_P">Trypsin_P</option>\n+ <option value="LysC">LysC</option>\n+ <option value="LysC_P">LysC_P</option>\n+ <option value="Chymotrypsin">Chymotrypsin</option>\n+ <option value="PepsinA">PepsinA</option>\n+ </param>\n+ <param name="MinMissedCleavages" type="integer" value="0" label="Min missed cleavages" help="Select the minimum amount of miss cleavages in a peptide sequence."/>\n'..b'<param name="VarModThreshold" value="4"/>\n+ <param name="outputParamfile" value="false"/>\n+ </test>\n+ <test expect_num_outputs="2">\n+ <param name="fasta" value="sample.fasta"/>\n+ <param name="ParseProteinIDRegexPattern" value="id"/>\n+ <param name="Protease" value="Trypsin"/>\n+ <param name="MinMissedCleavages" value="0"/>\n+ <param name="MaxMissedCleavages" value="2"/>\n+ <param name="MaxMass" value="15000.0"/>\n+ <param name="MinPepLength" value="4"/>\n+ <param name="MaxPepLength" value="65"/>\n+ <param name="IsotopicMod" value="N15"/>\n+ <param name="MassMode" value="Monoisotopic"/>\n+ <param name="FixedMods" value="Acetylation\'ProtNTerm\'"/>\n+ <param name="VariableMods" value="Acetylation\'ProtNTerm\'"/>\n+ <param name="VarModThreshold" value="4"/>\n+ <param name="outputParamfile" value="true"/>\n+ <output name="out_paramfile" file="result_1.json"/>\n+ </test>\n+ <test expect_num_outputs="2">\n+ <param name="fasta" value="sample.fasta"/>\n+ <param name="ParseProteinIDRegexPattern" value="id"/>\n+ <param name="Protease" value="Trypsin"/>\n+ <param name="MinMissedCleavages" value="0"/>\n+ <param name="MaxMissedCleavages" value="2"/>\n+ <param name="MaxMass" value="15000.0"/>\n+ <param name="MinPepLength" value="4"/>\n+ <param name="MaxPepLength" value="65"/>\n+ <param name="IsotopicMod" value="N15"/>\n+ <param name="MassMode" value="Monoisotopic"/>\n+ <param name="FixedMods" value="Acetylation\'ProtNTerm\',Carbamidomethyl\'Cys\',Oxidation\'Met\',Phosphorylation\'Ser\'Thr\'Tyr\',Pyro_Glu\'GluNterm\',Pyro_Glu\'GlnNterm\'"/>\n+ <param name="VariableMods" value="Acetylation\'ProtNTerm\',Carbamidomethyl\'Cys\',Oxidation\'Met\',Phosphorylation\'Ser\'Thr\'Tyr\',Pyro_Glu\'GluNterm\',Pyro_Glu\'GlnNterm\'"/>\n+ <param name="VarModThreshold" value="4"/>\n+ <param name="outputParamfile" value="true"/>\n+ <output name="out_paramfile" file="result_2.json"/>\n+ </test>\n+ <test expect_num_outputs="2">\n+ <param name="fasta" value="sample.fasta"/>\n+ <param name="ParseProteinIDRegexPattern" value="id"/>\n+ <param name="Protease" value="Trypsin"/>\n+ <param name="MinMissedCleavages" value="0"/>\n+ <param name="MaxMissedCleavages" value="2"/>\n+ <param name="MaxMass" value="15000.0"/>\n+ <param name="MinPepLength" value="4"/>\n+ <param name="MaxPepLength" value="65"/>\n+ <param name="IsotopicMod" value=""/>\n+ <param name="MassMode" value="Average"/>\n+ <param name="FixedMods" value=""/>\n+ <param name="VariableMods" value=""/>\n+ <param name="VarModThreshold" value="4"/>\n+ <param name="outputParamfile" value="true"/>\n+ <output name="out_paramfile" file="result_3.json"/>\n+ </test>\n+ </tests>\n+ <help>\n+ <![CDATA[\n+Introduction\n+------------\n+MS-based shotgun proteomics estimates protein abundances using a proxy: peptides. \n+An established method to identify acquired MS/MS spectra is the comparison of each spectrum with peptides in a reference database. \n+\n+What It Does\n+------------\n+The PeptideDB tool helps to create peptide databases by in silico digestion given proteome information in the FASTA format and a set of parameters \n+that allow the user to mimic conditions of their specific experiment. \n+The created database stores peptide protein relationships in a SQLite database which can then be supplied to other ProteomIQon tools.\n+\n+Further Reading\n+---------------\n+Additional information about the tool can be found in the `documentation <https://csbiology.github.io/ProteomIQon/tools/PeptideDB.html>`_.\n+ ]]>\n+ </help>\n+</tool>\n\\ No newline at end of file\n' |
| b |
| diff -r 000000000000 -r 1e5400393797 test-data/result_1.json --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/result_1.json Sun Jul 04 21:26:08 2021 +0000 |
| [ |
| @@ -0,0 +1,27 @@ + + + { + "Name": "galaxy", + "ParseProteinIDRegexPattern": "id", + "Protease": { "Case": "Trypsin" }, + "MinMissedCleavages": 0, + "MaxMissedCleavages": 2, + "MaxMass": 15000.0, + "MinPepLength": 4, + "MaxPepLength": 65, + "IsotopicMod": [ + {"Case":"N15"} + ], + "MassMode": { + "Case": "Monoisotopic" + }, + "FixedMods": [ + {"Case":"Acetylation'ProtNTerm'"} + ], + "VariableMods": [ + {"Case":"Acetylation'ProtNTerm'"} + ], + "VarModThreshold": 4 + } + + \ No newline at end of file |
| b |
| diff -r 000000000000 -r 1e5400393797 test-data/result_2.json --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/result_2.json Sun Jul 04 21:26:08 2021 +0000 |
| [ |
| @@ -0,0 +1,37 @@ + + + { + "Name": "galaxy", + "ParseProteinIDRegexPattern": "id", + "Protease": { "Case": "Trypsin" }, + "MinMissedCleavages": 0, + "MaxMissedCleavages": 2, + "MaxMass": 15000.0, + "MinPepLength": 4, + "MaxPepLength": 65, + "IsotopicMod": [ + {"Case":"N15"} + ], + "MassMode": { + "Case": "Monoisotopic" + }, + "FixedMods": [ + {"Case":"Acetylation'ProtNTerm'"}, + {"Case":"Carbamidomethyl'Cys'"}, + {"Case":"Oxidation'Met'"}, + {"Case":"Phosphorylation'Ser'Thr'Tyr'"}, + {"Case":"Pyro_Glu'GluNterm'"}, + {"Case":"Pyro_Glu'GlnNterm'"} + ], + "VariableMods": [ + {"Case":"Acetylation'ProtNTerm'"}, + {"Case":"Carbamidomethyl'Cys'"}, + {"Case":"Oxidation'Met'"}, + {"Case":"Phosphorylation'Ser'Thr'Tyr'"}, + {"Case":"Pyro_Glu'GluNterm'"}, + {"Case":"Pyro_Glu'GlnNterm'"} + ], + "VarModThreshold": 4 + } + + \ No newline at end of file |
| b |
| diff -r 000000000000 -r 1e5400393797 test-data/result_3.json --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/result_3.json Sun Jul 04 21:26:08 2021 +0000 |
| [ |
| @@ -0,0 +1,24 @@ + + + { + "Name": "galaxy", + "ParseProteinIDRegexPattern": "id", + "Protease": { "Case": "Trypsin" }, + "MinMissedCleavages": 0, + "MaxMissedCleavages": 2, + "MaxMass": 15000.0, + "MinPepLength": 4, + "MaxPepLength": 65, + "IsotopicMod": [ + ], + "MassMode": { + "Case": "Average" + }, + "FixedMods": [ + ], + "VariableMods": [ + ], + "VarModThreshold": 4 + } + + \ No newline at end of file |
| b |
| diff -r 000000000000 -r 1e5400393797 test-data/sample.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/sample.fasta Sun Jul 04 21:26:08 2021 +0000 |
| b |
| @@ -0,0 +1,5 @@ +>sp|A0A023PZB3|FMP49_YEAST Protein FMP49, mitochondrial OS=Saccharomyces cerevisiae (strain ATCC 204508 / S288c) OX=559292 GN=FMP49 PE=4 SV=1 +MYYFSRVAARTFCCCIFFCLATAYSRPDRNPRKIEKKDKKFFGASKNTNPANAMGNLFKA +PTIEYVVEEVTRTHQPEQYDIPTDMSPLMTIAASESADKFTDKFFVDQSSIMKEKTSSKG +NARTLL +>sp|P04050|RPB1_YEAST DNA-directed RNA polymerase II subunit RPB1 OS=Saccharomyces cerevisiae (strain ATCC 204508 / S288c) OX=559292 GN=RPO21 PE=1 SV=2 |