Mercurial > repos > jjohnson > spectrast
changeset 4:c9bfe6adb7cd draft
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 592d86797e58318bad77de7c7de253056218cd1e-dirty
| author | jjohnson |
|---|---|
| date | Wed, 25 Jul 2018 14:41:20 -0400 |
| parents | 7f02fc51bddf |
| children | 274fdc50169b |
| files | macros.xml spectrast_create.xml spectrast_filter.xml spectrast_import.xml spectrast_params.py |
| diffstat | 5 files changed, 70 insertions(+), 72 deletions(-) [+] |
line wrap: on
line diff
--- a/macros.xml Wed Jul 25 10:58:17 2018 -0400 +++ b/macros.xml Wed Jul 25 14:41:20 2018 -0400 @@ -8,7 +8,7 @@ </xml> <token name="@LIBRARY_CREATE_OPTIONS@"> outputFileName = ${output.extra_files_path}/library.splib -#if $library_create.removeDecoyProteins is not None: +#if str($library_create.removeDecoyProteins) != '': removeDecoyProteins = $library_create.removeDecoyProteins #end if #if str($library_create.useProbTable) != 'None': @@ -17,21 +17,21 @@ #if str($library_create.useProteinList) != 'None': useProteinList = $library_create.useProteinList #end if -#if str($library_create.printMRMTable) != 'None': -printMRMTable = +#if str($library_create.printMRMTable) in ['true']: +printMRMTable = DEFAULT #end if -#if str($library_create.writeMgfFile) != 'None': +#if str($library_create.writeMgfFile) in ['true','false']: writeMgfFile = $library_create.writeMgfFile #end if -## #if str($library_create.writeDtaFiles) != 'None': +## #if str($library_create.writeDtaFiles) in ['true','false']: ## writeDtaFiles = $library_create.writeDtaFiles ## #end if -#if str($library_create.writePAIdent) != 'None': +#if str($library_create.writePAIdent) in ['true','false']: writePAIdent = $library_create.writePAIdent #end if </token> <xml name="library_create_outputs"> - <data name="library_pai" format="tabular" label="library.pai" from_work_dir="outdir/library.pai"> + <data name="library_pai" format="tabular" label="library.PAIdent" from_work_dir="outdir/library.PAIdent"> <filter>library_create['writePAIdent'] == 'true'</filter> </data> <data name="library_mrm" format="tabular" label="library.mrm" from_work_dir="outdir/library.mrm"> @@ -97,55 +97,55 @@ </section> </xml> <token name="@LIBRARY_IMPORT_OPTIONS@"> -#if $library_import.minimumProbabilityToInclude is not None: +#if str($library_import.minimumProbabilityToInclude) != '': minimumProbabilityToInclude = $library_import.minimumProbabilityToInclude #end if -#if $library_import.maximumFDRToInclude is not None: +#if str($library_import.maximumFDRToInclude) != '': maximumFDRToInclude = $library_import.maximumFDRToInclude #end if -#if $library_import.setFragmentation is not None: +#if str($library_import.setFragmentation) != 'None': setFragmentation = $library_import.setFragmentation #end if -#if $library_import.setDeamidatedNXST is not None: +#if str($library_import.setDeamidatedNXST) != 'None': setDeamidatedNXST = $library_import.setDeamidatedNXST #end if -#if $library_import.addMzXMLFileToDatasetName is not None: +#if str($library_import.addMzXMLFileToDatasetName) != 'None': addMzXMLFileToDatasetName = $library_import.addMzXMLFileToDatasetName #end if -#if $library_import.centroidPeaks is not None: +#if str($library_import.centroidPeaks) != 'None': centroidPeaks = $library_import.centroidPeaks #end if -#if $library_import.rawSpectraNoiseThreshold is not None: +#if str($library_import.rawSpectraNoiseThreshold) != '': rawSpectraNoiseThreshold = $library_import.rawSpectraNoiseThreshold #end if -#if $library_import.rawSpectraMaxDynamicRange is not None: +#if str($library_import.rawSpectraMaxDynamicRange) != '': rawSpectraMaxDynamicRange = $library_import.rawSpectraMaxDynamicRange #end if -#if $library_import.minimumNumAAToInclude is not None: +#if str($library_import.minimumNumAAToInclude) != '': minimumNumAAToInclude = $library_import.minimumNumAAToInclude #end if -#if $library_import.minimumNumPeaksToInclude is not None: +#if str($library_import.minimumNumPeaksToInclude) != '': minimumNumPeaksToInclude = $library_import.minimumNumPeaksToInclude #end if -#if $library_import.skipRawAnnotation is not None: +#if str($library_import.skipRawAnnotation) != 'None': skipRawAnnotation = $library_import.skipRawAnnotation #end if -#if $library_import.minimumDeltaCnToInclude is not None: +#if str($library_import.minimumDeltaCnToInclude) != '': minimumDeltaCnToInclude = $library_import.minimumDeltaCnToInclude #end if -#if $library_import.maximumMassDiffToInclude is not None: +#if str($library_import.maximumMassDiffToInclude) != '': maximumMassDiffToInclude = $library_import.maximumMassDiffToInclude #end if -#if $library_import.bracketSpectra is not None: +#if str($library_import.bracketSpectra) != 'None': bracketSpectra = $library_import.bracketSpectra #end if -#if $library_import.mergeBracket is not None: +#if str($library_import.mergeBracket) != 'None': mergeBracket = $library_import.mergeBracket #end if #if str($library_import.normalizeRTWithLandmarks) != 'None': normalizeRTWithLandmarks = $library_import.normalizeRTWithLandmarks #end if -#if $library_import.normalizeRTLinearRegression is not None: +#if str($library_import.normalizeRTLinearRegression) != 'None': normalizeRTLinearRegression = $library_import.normalizeRTLinearRegression #end if </token> @@ -157,10 +157,6 @@ <param name="maximumFDRToInclude" type="float" value="" min="0.0" optional="true" label="maximumFDRToInclude for pepXML import" help="(Only for pepXML import) Include spectra with global FDR no greater than this in the library. Default is 999.0"/> - <param name="setFragmentation" type="select" label="Set the fragmentation type of all spectra, overriding existing information"> - <option value="dataset" selected="true">Search Single Spectrum file and output results as a dataset</option> - <option value="collection">Search Multiple Spectrum files and output results as a collection</option> - </param> <param name="setFragmentation" type="select" optional="true" label="Set the fragmentation type of all spectra, overriding existing information" > <help>Default is off (determined from the data files). Examples: CID, ETD, CID-QTOF, HCD. The latter two are treated as high-mass accuracy spectra. @@ -243,98 +239,101 @@ </xml> <token name="@LIBRARY_MANIPULATION_OPTIONS@"> -#if $library_manipulation.filterCriteria is not None: +#if str($library_manipulation.filterCriteria) != '': filterCriteria = $library_manipulation.filterCriteria #end if -#if $library_manipulation.combineAction is not None: +#if str($library_manipulation.combineAction) != 'None': combineAction = $library_manipulation.combineAction #end if #if $library_manipulation.build.buildAction != 'NONE': buildAction = $library_manipulation.build.buildAction #if $library_manipulation.build.buildAction in ['BEST_REPLICATE','CONSENSUS']: -#if $library_manipulation.build.build_bc_action.minimumNumReplicates is not None: +#if str($library_manipulation.build.build_bc_action.minimumNumReplicates) != '': minimumNumReplicates = $library_manipulation.build.build_bc_action.minimumNumReplicates #end if -#if $library_manipulation.build.build_bc_action.removeDissimilarReplicates is not None: +#if str($library_manipulation.build.build_bc_action.removeDissimilarReplicates) in ['true','false']: removeDissimilarReplicates = $library_manipulation.build.build_bc_action.removeDissimilarReplicates #end if -#if $library_manipulation.build.build_bc_action.peakQuorum is not None: +#if str($library_manipulation.build.build_bc_action.peakQuorum) != '': peakQuorum = $library_manipulation.build.build_bc_action.peakQuorum #end if -#if $library_manipulation.build.build_bc_action.maximumNumPeaksUsed is not None: +#if str($library_manipulation.build.build_bc_action.maximumNumPeaksUsed) != '': maximumNumPeaksUsed = $library_manipulation.build.build_bc_action.maximumNumPeaksUsed #end if -#if $library_manipulation.build.build_bc_action.maximumNumReplicates is not None: +#if str($library_manipulation.build.build_bc_action.maximumNumReplicates) != '': maximumNumReplicates = $library_manipulation.build.build_bc_action.maximumNumReplicates #end if -#if $library_manipulation.build.build_bc_action.maximumNumPeaksKept is not None: +#if str($library_manipulation.build.build_bc_action.maximumNumPeaksKept) != '': maximumNumPeaksKept = $library_manipulation.build.build_bc_action.maximumNumPeaksKept #end if -#if $library_manipulation.build.build_bc_action.replicateWeight is not None: +#if str($library_manipulation.build.build_bc_action.replicateWeight) != 'None': replicateWeight = $library_manipulation.build.build_bc_action.replicateWeight #end if -#if $library_manipulation.build.build_bc_action.recordRawSpectra is not None: +#if str($library_manipulation.build.build_bc_action.recordRawSpectra) in ['true','false']: recordRawSpectra = $library_manipulation.build.build_bc_action.recordRawSpectra #end if #end if #if $library_manipulation.build.buildAction == 'DECOY': -#if $library_manipulation.build.build_d_action.decoyConcatenate is not None: +#if str($library_manipulation.build.build_d_action.decoyConcatenate) in ['true','false']: decoyConcatenate = $library_manipulation.build.build_d_action.decoyConcatenate #end if -#if $library_manipulation.build.build_d_action.decoySizeRatio is not None: +#if str($library_manipulation.build.build_d_action.decoySizeRatio) != '': decoySizeRatio = $library_manipulation.build.build_d_action.decoySizeRatio #end if -#if $library_manipulation.build.build_d_action.decoyPrecursorSwap is not None: +#if str($library_manipulation.build.build_d_action.decoyPrecursorSwap) in ['true','false']: decoyPrecursorSwap = $library_manipulation.build.build_d_action.decoyPrecursorSwap #end if #end if #if $library_manipulation.build.buildAction == 'USER_SPECIFIED_MODS': -#if $library_manipulation.build.build_m_action.allowableModTokens is not None: +#if str($library_manipulation.build.build_m_action.allowableModTokens) != '': allowableModTokens = $library_manipulation.build.build_m_action.allowableModTokens #end if #end if #if $library_manipulation.build.buildAction == 'QUALITY_FILTER': -#if $library_manipulation.build.build_q_action.minimumNumReplicates is not None: +#if str($library_manipulation.build.build_q_action.minimumNumReplicates) != '': minimumNumReplicates = $library_manipulation.build.build_q_action.minimumNumReplicates #end if -#if $library_manipulation.build.build_q_action.qualityLevelRemove is not None: +#if str($library_manipulation.build.build_q_action.qualityLevelRemove) != '': qualityLevelRemove = $library_manipulation.build.build_q_action.qualityLevelRemove #end if -#if $library_manipulation.build.build_q_action.qualityLevelMark is not None: +#if str($library_manipulation.build.build_q_action.qualityLevelMark) != '': qualityLevelMark = $library_manipulation.build.build_q_action.qualityLevelMark #end if -#if $library_manipulation.build.build_q_action.qualityPenalizeSingletons is not None: +#if str($library_manipulation.build.build_q_action.qualityPenalizeSingletons) in ['true','false']: qualityPenalizeSingletons = $library_manipulation.build.build_q_action.qualityPenalizeSingletons #end if -#if $library_manipulation.build.build_q_action.qualityImmuneProbThreshold is not None: +#if str($library_manipulation.build.build_q_action.qualityImmuneProbThreshold) != '': qualityImmuneProbThreshold = $library_manipulation.build.build_q_action.qualityImmuneProbThreshold #end if -#if $library_manipulation.build.build_q_action.qualityImmuneMultipleEngines is not None: +#if str($library_manipulation.build.build_q_action.qualityImmuneMultipleEngines) in ['true','false']: qualityImmuneMultipleEngines = $library_manipulation.build.build_q_action.qualityImmuneMultipleEngines #end if #end if #end if -#if $library_manipulation.reduceSpectra is not None: +#if str($library_manipulation.reduceSpectra) != '': reduceSpectra = $library_manipulation.reduceSpectra #end if -#if $library_manipulation.minimumNumPeaksToInclude is not None: +#if str($library_manipulation.reannotatePeaks) in ['true','false']: +reannotatePeaks = $library_manipulation.reannotatePeaks +#end if +#if str($library_manipulation.minimumNumPeaksToInclude) != '': minimumNumPeaksToInclude = $library_manipulation.minimumNumPeaksToInclude #end if -#if $library_manipulation.minimumMRMQ3MZ is not None: +#if str($library_manipulation.minimumMRMQ3MZ) != '': minimumMRMQ3MZ = $library_manipulation.minimumMRMQ3MZ #end if -#if $library_manipulation.maximumMRMQ3MZ is not None: +#if str($library_manipulation.maximumMRMQ3MZ) != '': maximumMRMQ3MZ = $library_manipulation.maximumMRMQ3MZ #end if #if $library_manipulation.db.refresh == 'yes': refreshDatabase = $library_manipulation.db.refreshDatabase -#if $library_manipulation.db.refreshDeleteUnmapped is not None: +#if str($library_manipulation.db.refreshDeleteUnmapped) in ['true','false']: refreshDeleteUnmapped = $library_manipulation.db.refreshDeleteUnmapped #end if -#if $library_manipulation.db.refreshDeleteMultimapped is not None: +#if str($library_manipulation.db.refreshDeleteMultimapped) in ['true','false']: refreshDeleteMultimapped = $library_manipulation.db.refreshDeleteMultimapped #end if -#if $library_manipulation.db.refreshTrypticOnly is not None: +#if str($library_manipulation.db.refreshTrypticOnly) in ['true','false']: refreshTrypticOnly = $library_manipulation.db.refreshTrypticOnly #end if #end if @@ -363,7 +362,7 @@ label="maximumNumPeaksKept" help="De-noise single spectra by keeping only this number of the most intense peaks. Will not affect consensus spectra of more than one replicate. Default is 150"/> <param name="replicateWeight" type="select" optional="true" label="replicateWeight Default: signal-to-noise ratio" > - <help> How to combine peptides from multiple files + <help> Select the type of score to weigh and rank the replicates. </help> <option value="NONE">NONE</option> <option value="SN">Use a measure of signal-to-noise ratio as the weight.</option> @@ -454,7 +453,7 @@ <param name="filterCriteria" type="text" value="" optional="true" label="filterCriteria"> <help><![CDATA[ Filter library by criteria. Keep only those entries satisfying the predicate. - The preicate should in the form "<attr> <op> <value>". + The predicate should in the form "<attr> <op> <value>". <attr> can refer to any of the fields and any comment entries. <op> can be ==, !=, <, >, <=, >=, =~ and !~. Multiple predicates can be separated by either & (AND logic) or | (OR logic), but not both.
--- a/spectrast_create.xml Wed Jul 25 10:58:17 2018 -0400 +++ b/spectrast_create.xml Wed Jul 25 14:41:20 2018 -0400 @@ -10,13 +10,13 @@ ## pepxml datasets #set $input_files = [] #for $px in $pepxml_files: - #set $input_name = $re.sub('[.]?pep[.]?xml$','',$re.sub('[ ]','_',$input.display_name.split('/')[-1])) + '.pep.xml' + #set $input_name = $re.sub('[.]?pep[.]?xml$', '' ,$re.sub('[ ]', '_', $px.display_name.split('/')[-1])) + '.pep.xml' #silent $input_files.append($input_name) ln -s -f '${px}' '${input_name}' && #end for #set $input_names = ' '.join($input_files) python $__tool_directory__/link_scan_datasets.py - #for spectrum_file in spectrum_files: + #for $spectrum_file in $spectrum_files: -n '$spectrum_file.display_name' -f '$spectrum_file' #end for $input_names && @@ -26,10 +26,11 @@ '$spectrastParams' #end if '$spectrast_params' -o spectrast_create.params && - mkdir -p libdir && - spectrast -cFspectrast_create.params -cN'libdir/library' $input_names && + mkdir -p outdir && + spectrast -cFspectrast_create.params -cN'outdir/library' $input_names && + find * && mkdir -p '$output.files_path' && - for i in library.splib library.sptxt library.spidx library.pepidx; do if [ -e outdir/${i} ]; then cp -p outdir/${i} '$output.files_path'; fi; done + for i in library.splib library.sptxt library.spidx library.pepidx; do if [ -e outdir/\${i} ]; then cp -p outdir/\${i} '$output.files_path'; fi; done ]]></command> <configfiles> <configfile name="spectrast_params"><![CDATA[#slurp
--- a/spectrast_filter.xml Wed Jul 25 10:58:17 2018 -0400 +++ b/spectrast_filter.xml Wed Jul 25 14:41:20 2018 -0400 @@ -11,21 +11,21 @@ '$spectrastParams' #end if '$spectrast_params' -o spectrast_create.params && - mkdir -p libdir && - spectrast -cFspectrast_create.params -cN'libdir/library' + mkdir -p outdir && + spectrast -cFspectrast_create.params -cN'outdir/library' #for $splib_file in $splib_files: ${splib_file.extra_files_path}/library.splib #end for && mkdir -p '$output.files_path' && - for i in library.splib library.sptxt library.spidx library.pepidx; do if [ -e outdir/${i} ]; then cp -p outdir/${i} '$output.files_path'; fi; done + for i in library.splib library.sptxt library.spidx library.pepidx; do if [ -e outdir/\${i} ]; then cp -p outdir/\${i} '$output.files_path'; fi; done ]]> </command> <configfiles> <configfile name="spectrast_params"><![CDATA[#slurp ]]> @LIBRARY_CREATE_OPTIONS@ -@LIBRARY_MANIPULATION_OPTIONS +@LIBRARY_MANIPULATION_OPTIONS@ </configfile> </configfiles> <inputs>
--- a/spectrast_import.xml Wed Jul 25 10:58:17 2018 -0400 +++ b/spectrast_import.xml Wed Jul 25 14:41:20 2018 -0400 @@ -13,7 +13,7 @@ mkdir -p libdir && spectrast -cN'libdir/library' '$input_name' | tee '$output' && mkdir -p '$output.files_path' && - for i in library.splib library.sptxt library.spidx library.pepidx; do if [ -e outdir/${i} ]; then cp -p outdir/${i} '$output.files_path'; fi; done + for i in library.splib library.sptxt library.spidx library.pepidx; do if [ -e outdir/\${i} ]; then cp -p outdir/\${i} '$output.files_path'; fi; done ]]></command> <inputs> <param name="input" type="data" format="ms2,msp,hlf" label="Spectral library ms2, msp, or hlf"
--- a/spectrast_params.py Wed Jul 25 10:58:17 2018 -0400 +++ b/spectrast_params.py Wed Jul 25 14:41:20 2018 -0400 @@ -14,7 +14,8 @@ 'remark', 'binaryFormat', 'writeDtaFiles', - 'writeMgfFiles', + 'writeMgfFile', + 'writePAIdent', 'removeDecoyProteins', 'plotSpectra', 'minimumProbabilityToInclude', @@ -41,10 +42,8 @@ 'refreshDeleteUnmapped', 'refreshDeleteMultimapped', 'reannotatePeaks', - 'minimumNumPeaksToInclude', 'minimumMRMQ3MZ', 'maximumMRMQ3MZ', - 'minimumNumPeaksToInclude', 'refreshTrypticOnly', 'minimumNumReplicates', 'removeDissimilarReplicates', @@ -84,7 +83,8 @@ 'remark', 'binaryFormat', 'writeDtaFiles', - 'writeMgfFiles', + 'writeMgfFile', + 'writePAIdent', 'removeDecoyProteins', 'plotSpectra', 'minimumProbabilityToInclude', @@ -111,10 +111,8 @@ 'refreshDeleteUnmapped', 'refreshDeleteMultimapped', 'reannotatePeaks', - 'minimumNumPeaksToInclude', 'minimumMRMQ3MZ', 'maximumMRMQ3MZ', - 'minimumNumPeaksToInclude', 'refreshTrypticOnly', 'minimumNumReplicates', 'removeDissimilarReplicates',