| Next changeset 1:a79a24eb9e76 (2021-07-24) |
|
Commit message:
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidespectrummatching commit 2ae9320c0e55f3a2a7d5b6121002722e59b42ab4" |
|
added:
proteomiqon_peptidespectrummatching.xml static/images/PSM.png test-data/result_1.json test-data/result_2.json test-data/result_3.json test-data/sample.db test-data/sample.mzlite |
| b |
| diff -r 000000000000 -r db6faafbf75b proteomiqon_peptidespectrummatching.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/proteomiqon_peptidespectrummatching.xml Thu Jul 15 07:11:01 2021 +0000 |
| [ |
| b'@@ -0,0 +1,195 @@\n+<tool id="proteomiqon_peptidespectrummatching" name="ProteomIQon PeptideSpectrumMatching" version="@VERSION@" profile="20.05">\n+ <description>\n+ iterates across all MS/MS scans in an MS run, determines precursor charge states and possible peptide spectrum matches.\n+ </description>\n+ <macros>\n+ <token name="@VERSION@">0.0.7</token>\n+ </macros>\n+ <requirements>\n+ <requirement type="package" version="@VERSION@">proteomiqon-peptidespectrummatching</requirement>\n+ </requirements>\n+ <command detect_errors="exit_code"><![CDATA[\n+ #import re\n+ #set basename = $re.sub(r\'[^\\w ,.\\-+]\',\'_\',$instrumentOutput.element_identifier)\n+ #if $outputParamfile:\n+ cat \'$paramfile\' >> \'$out_paramfile\' &&\n+ #end if\n+ ln -s \'$instrumentOutput\' \'${basename}.mzlite\' &&\n+ ln -s \'$out_psm\' \'${basename}.psm\' &&\n+ proteomiqon-peptidespectrummatching -i \'./${basename}.mzlite\' -d \'$peptideDB\' -p \'$paramfile\' -o ./\n+ ]]>\n+ </command>\n+ <configfiles>\n+ <configfile name="paramfile">\n+ <![CDATA[\n+ {\n+ "ChargeStateDeterminationParams": {\n+ "ExpectedMinimalCharge": ${ChargeStateDeterminationParams.ExpectedMinimalCharge},\n+ "ExpectedMaximumCharge": ${ChargeStateDeterminationParams.ExpectedMaximumCharge},\n+ "Width": ${ChargeStateDeterminationParams.Width},\n+ "MinIntensity": ${ChargeStateDeterminationParams.MinIntensity},\n+ "DeltaMinIntensity": ${ChargeStateDeterminationParams.DeltaMinIntensity},\n+ "NrOfRndSpectra": ${ChargeStateDeterminationParams.NrOfRndSpectra}\n+ },\n+ "LookUpPPM": ${LookUpPPM},\n+ "nTerminalSeries": { "Case": "${nTerminalSeries}" },\n+ "cTerminalSeries": { "Case": "${cTerminalSeries}" },\n+ "Andromeda": {\n+ "PMinPMax": {\n+ "Item1": ${Andromeda.PMin},\n+ "Item2": ${Andromeda.PMax}\n+ },\n+ "MatchingIonTolerancePPM": ${Andromeda.MatchingIonTolerancePPM}\n+ }\n+ }\n+ ]]>\n+ </configfile>\n+ </configfiles>\n+ <inputs>\n+ <param name="instrumentOutput" type="data" format="sqlite" label="Instrument output" help="Specify mass spectrometry data you want to analyze."/>\n+ <param name="peptideDB" type="data" format="sqlite" label="Peptide database" help="Specify the peptide data base."/>\n+ <section name="ChargeStateDeterminationParams" title="Charge state determination parameters" >\n+ <param name="ExpectedMinimalCharge" type="integer" min="1" max="8" value="2" label="Expected minimal charge" help="Specify the minimum peptide ion charge state to consider."/>\n+ <param name="ExpectedMaximumCharge" type="integer" min="1" max="8" value="5" label="Expected maximum charge" help="Specify the maximum peptide ion charge state to consider."/>\n+ <param name="Width" type="float" value="1.1" label="Width" help="Specify the width around the picked precursor ion used in charge state determination."/>\n+ <param name="MinIntensity" type="float" value="0.15" label="Min intensity" help="Specify minimum relative intensity within an putative isotopic envelope to be included when performing charge state determination."/>\n+ <param name="DeltaMinIntensity" type="float" value="0.3" label="Delta min intensity" help="Specify minimum relative intensity to the prior peak when iterating through peak lists while performing charge state determination."/>\n+ <param name="NrOfRndSpectra" type="integer" value="10000" label="Number of random spectra" help="When performing charge state determination we compared measured envelopes to the distribution of randomly generated spectra. This parameter tunes the size of the generated data set."/>\n+ </section> \n+ <param name="LookUpPPM" type="float" value="30" label="Lookup PPM" help="Specify the width '..b' </section>\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="instrumentOutput" value="sample.mzlite"/>\n+ <param name="peptideDB" value="sample.db"/>\n+ <param name="LookUpPPM" value="30"/>\n+ <param name="nTerminalSeries" value="A"/>\n+ <param name="cTerminalSeries" value="Z"/>\n+ <section name="ChargeStateDeterminationParams">\n+ <param name="ExpectedMinimalCharge" value="2"/>\n+ <param name="ExpectedMaximumCharge" value="5"/>\n+ <param name="Width" value="1.1"/>\n+ <param name="MinIntensity" value="0.15"/>\n+ <param name="DeltaMinIntensity" value="0.3"/>\n+ <param name="NrOfRndSpectra" value="10000"/>\n+ </section>\n+ <section name="Andromeda">\n+ <param name="PMin" value="4"/>\n+ <param name="PMax" value="10"/>\n+ <param name="MatchingIonTolerancePPM" value="100.0"/>\n+ </section>\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="instrumentOutput" value="sample.mzlite"/>\n+ <param name="peptideDB" value="sample.db"/>\n+ <param name="LookUpPPM" value="30"/>\n+ <param name="nTerminalSeries" value="C"/>\n+ <param name="cTerminalSeries" value="X"/>\n+ <section name="ChargeStateDeterminationParams">\n+ <param name="ExpectedMinimalCharge" value="2"/>\n+ <param name="ExpectedMaximumCharge" value="5"/>\n+ <param name="Width" value="1.1"/>\n+ <param name="MinIntensity" value="0.15"/>\n+ <param name="DeltaMinIntensity" value="0.3"/>\n+ <param name="NrOfRndSpectra" value="10000"/>\n+ </section>\n+ <section name="Andromeda">\n+ <param name="PMin" value="4"/>\n+ <param name="PMax" value="10"/>\n+ <param name="MatchingIonTolerancePPM" value="100.0"/>\n+ </section>\n+ <param name="outputParamfile" value="true"/>\n+ <output name="out_paramfile" file="result_3.json"/>\n+ </test>\n+ </tests>\n+ <help>\n+ <![CDATA[\n+What It Does\n+------------\n+**Disclaimer** this tool needs a peptide database to query against, if you did not create one yet you can do so by using the `PeptideDB <https://csbiology.github.io/ProteomIQon/tools/PeptideDB.html>`_ tool.\n+\n+Given raw a MS run in the mzite format, this tool iterates accross all recorded MS/MS scans and determines the charge state of precursor ions which were selected for fragmentation. \n+With this it is possible to query the peptide data base for every precursor ion mass +/- a tolerance (which defines the so called \'search space\') and retrieve peptides that are \n+theoretical candidates for a match. For each of the peptide candidates we create an theoretical spectrum in silico and compare it to the measured MS/MS scan.\n+\n+.. image:: PSM.png\n+ :width: 768pt\n+ :height: 563pt\n+\n+To measure similarity we use our own implementations of three established search enginge scores: SEQUEST, Andromeda and XTandem. \n+The search space is extended by so called decoys. Decoys are reversed counterparts of peptides within the search space and allow \n+us to assign a false discovery rate to each scored peptide using the `PSMStatistics <https://csbiology.github.io/ProteomIQon/tools/PSMStatistics.html>`_ tool.\n+\n+Further Reading\n+---------------\n+Additional information about the tool can be found in the `documentation <https://csbiology.github.io/ProteomIQon/tools/PeptideSpectrumMatching.html>`_. \n+ ]]>\n+ </help>\n+</tool>\n\\ No newline at end of file\n' |
| b |
| diff -r 000000000000 -r db6faafbf75b static/images/PSM.png |
| b |
| Binary file static/images/PSM.png has changed |
| b |
| diff -r 000000000000 -r db6faafbf75b test-data/result_1.json --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/result_1.json Thu Jul 15 07:11:01 2021 +0000 |
| b |
| @@ -0,0 +1,24 @@ + + + { + "ChargeStateDeterminationParams": { + "ExpectedMinimalCharge": 2, + "ExpectedMaximumCharge": 5, + "Width": 1.1, + "MinIntensity": 0.15, + "DeltaMinIntensity": 0.3, + "NrOfRndSpectra": 10000 + }, + "LookUpPPM": 30.0, + "nTerminalSeries": { "Case": "B" }, + "cTerminalSeries": { "Case": "Y" }, + "Andromeda": { + "PMinPMax": { + "Item1": 4, + "Item2": 10 + }, + "MatchingIonTolerancePPM": 100.0 + } + } + + \ No newline at end of file |
| b |
| diff -r 000000000000 -r db6faafbf75b test-data/result_2.json --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/result_2.json Thu Jul 15 07:11:01 2021 +0000 |
| b |
| @@ -0,0 +1,24 @@ + + + { + "ChargeStateDeterminationParams": { + "ExpectedMinimalCharge": 2, + "ExpectedMaximumCharge": 5, + "Width": 1.1, + "MinIntensity": 0.15, + "DeltaMinIntensity": 0.3, + "NrOfRndSpectra": 10000 + }, + "LookUpPPM": 30.0, + "nTerminalSeries": { "Case": "A" }, + "cTerminalSeries": { "Case": "Z" }, + "Andromeda": { + "PMinPMax": { + "Item1": 4, + "Item2": 10 + }, + "MatchingIonTolerancePPM": 100.0 + } + } + + \ No newline at end of file |
| b |
| diff -r 000000000000 -r db6faafbf75b test-data/result_3.json --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/result_3.json Thu Jul 15 07:11:01 2021 +0000 |
| b |
| @@ -0,0 +1,24 @@ + + + { + "ChargeStateDeterminationParams": { + "ExpectedMinimalCharge": 2, + "ExpectedMaximumCharge": 5, + "Width": 1.1, + "MinIntensity": 0.15, + "DeltaMinIntensity": 0.3, + "NrOfRndSpectra": 10000 + }, + "LookUpPPM": 30.0, + "nTerminalSeries": { "Case": "C" }, + "cTerminalSeries": { "Case": "X" }, + "Andromeda": { + "PMinPMax": { + "Item1": 4, + "Item2": 10 + }, + "MatchingIonTolerancePPM": 100.0 + } + } + + \ No newline at end of file |
| b |
| diff -r 000000000000 -r db6faafbf75b test-data/sample.db |
| b |
| Binary file test-data/sample.db has changed |
| b |
| diff -r 000000000000 -r db6faafbf75b test-data/sample.mzlite |
| b |
| Binary file test-data/sample.mzlite has changed |
