# HG changeset patch # User galaxyp # Date 1551381284 18000 # Node ID cc5ccfa8ee28cb3a1b36bdb930b0f4d5eaac4776 # Parent 9d5de24e6ef782f3cc79ff2e5c9bd1824c30a7e9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 3c189141a9dd1d44d44af82ccd9b6e9d3742f93d diff -r 9d5de24e6ef7 -r cc5ccfa8ee28 msconvert_macros.xml --- a/msconvert_macros.xml Sat Feb 23 06:25:48 2019 -0500 +++ b/msconvert_macros.xml Thu Feb 28 14:14:44 2019 -0500 @@ -9,19 +9,30 @@ #set $ext = $input.ext ## sanitize display name for use as temp filename - #set basename = $re.sub(r'[^\w\.\-\+]','_',$input.element_identifier) + #set basename = $re.sub(r'[^\w ,.\-+]','_',$input.element_identifier) #if $ext == 'wiff': ln -s '${input.extra_files_path}/wiff' '${basename}.wiff' && ln -s '${input.extra_files_path}/wiff_scan' '${basename}.wiff.scan' && + #set inputmask = "'"+$basename+"'" #elif $ext.endswith('tar'): ln -s '$input' '${basename}' && tar xf '${basename}' && #set basename = $os.path.splitext($basename)[0] + #if $ext.startswith('waters'): + #set inputmask = '*.raw' + #elif $ext.startswith('agilent') or $ext.startswith('bruker'): + #set inputmask = '*.d' + #elif $ext.startswith('wiff'): + #set inputmask = '*.wiff *.wiff2' + #else + #raise RuntimeError("Unrecognized type of tar (${ext})") + #end if #else ln -s '$input' '${basename}' && + #set inputmask = "'"+$basename+"'" #end if - + #if $data_processing.precursor_refinement.use_mzrefinement #set input_ident_name = ".".join((os.path.splitext($basename)[0], $data_processing.precursor_refinement.input_ident.ext)) #set output_refinement_name = os.path.splitext($basename)[0] + '.mzRefinement.tsv' @@ -31,7 +42,7 @@ uid=`id -u` && gid=`id -g` && - wine64_anyuser msconvert '${basename}' + wine64_anyuser msconvert ${inputmask} --outdir outputs --${output_type} diff -r 9d5de24e6ef7 -r cc5ccfa8ee28 msconvert_macros.xml.orig --- a/msconvert_macros.xml.orig Sat Feb 23 06:25:48 2019 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,897 +0,0 @@ - - 3.0.19052 - @VERSION@-089e81090 - - - - 0 - --runIndexSet " - #for $index in $general_options.multi_run_output.run_index_set - [${index.from},${index.to}] - #end for - " - #end if - #else - --runIndexSet $general_options.multi_run_output.runIndexSet - #end if - - ## Strip sourceFile location since it is meaningless on HPC systems and causes problems with functional tests - --stripLocationFromSourceFiles - - ## DATA PROCESSING FILTERS (NOTE: FOR VENDOR METHOD TO WORK, PEAK PICKING MUST BE THE FIRST FILTER!) - #if $data_processing.peak_picking.pick_peaks - --filter "peakPicking $data_processing.peak_picking.pick_peaks_algorithm msLevel=$data_processing.peak_picking.pick_peaks_ms_levels" - #end if - - #if $data_processing.precursor_refinement.use_mzrefinement - --filter "mzRefiner $input_ident_name - msLevels=$data_processing.precursor_refinement.precursor_refinement_ms_levels - thresholdScore=$data_processing.precursor_refinement.thresholdScore - thresholdValue=$data_processing.precursor_refinement.thresholdValue - thresholdStep=$data_processing.precursor_refinement.thresholdStep - maxSteps=$data_processing.precursor_refinement.thresholdMaxSteps assumeHighRes=1" - #end if - - #if str($data_processing.charge_state_calculation.charge_state_calculation_method) == "predictor" - --filter "chargeStatePredictor - overrideExistingCharge=$data_processing.charge_state_calculation.predictor_overrideExistingCharge - minMultipleCharge=$data_processing.charge_state_calculation.minMultipleCharge - maxMultipleCharge=$data_processing.charge_state_calculation.maxMultipleCharge - singleChargeFractionTIC=$data_processing.charge_state_calculation.singleChargeFractionTIC - maxKnownCharge=$data_processing.charge_state_calculation.maxKnownCharge" - #else if str($data_processing.charge_state_calculation.charge_state_calculation_method) == "turbocharger" - --filter "turbocharger - minCharge=$data_processing.charge_state_calculation.minCharge - maxCharge=$data_processing.charge_state_calculation.maxCharge - precursorsBefore=$data_processing.charge_state_calculation.precursorsBefore - precursorsAfter=$data_processing.charge_state_calculation.precursorsAfter - halfIsoWidth=$data_processing.charge_state_calculation.halfIsoWidth - defaultMinCharge=$data_processing.charge_state_calculation.defaultMinCharge - defaultMaxCharge=$data_processing.charge_state_calculation.defaultMaxCharge" - #end if - - #for threshold_entry in $data_processing.thresholds - --filter "threshold $threshold_entry.threshold_type $threshold_entry.value $threshold_entry.orientation" - #end for - - #if $data_processing.filter_mz_windows.do_mzwindow_filter - --filter "mzWindow [$data_processing.filter_mz_windows.mz_window_from,$data_processing.filter_mz_windows.mz_window_to]" - #end if - - #if $data_processing.etd_filtering.do_etd_filtering - --filter "ETDFilter $data_processing.etd_filtering.remove_precursor - $data_processing.etd_filtering.remove_charge_reduced - $data_processing.etd_filtering.remove_neutral_loss - $data_processing.etd_filtering.blanket_removal - $data_processing.etd_filtering.matching_tolerance$data_processing.etd_filtering.matching_tolerance_units" - #end if - - #if $data_processing.ms2denoise.denoise - --filter "MS2Denoise $data_processing.ms2denoise.num_peaks $data_processing.ms2denoise.window_width $data_processing.ms2denoise.relax" - #end if - - #if str($data_processing.ms2deisotope) == "true" - --filter "MS2Deisotope" - #end if - - - ## SCAN INCLUSION/EXCLUSION FILTERS - #if str($filtering.activation) != "false" - --filter "activation $filtering.activation" - #end if - - #if len($filtering.indices) > 0 - --filter "index - #for $index in $filtering.indices - [${index.from},${index.to}] - #end for - " - #end if - - #if len($filtering.scan_numbers) > 0 - --filter "scanNumber - #for $scan_number in $filtering.scan_numbers - [${scan_number.from},${scan_number.to}] - #end for - " - #end if - - #if $filtering.strip_it.value - --filter "stripIT" - #end if - - #if $filtering.filter_ms_levels.do_ms_level_filter - --filter "msLevel [$filtering.filter_ms_levels.ms_level_from, $filtering.filter_ms_levels.ms_level_to]" - #end if - - #if str($filtering.polarity) != "false" - --filter "polarity $filtering.polarity" - #end if - - #if str($filtering.analyzer) != "false" - --filter "analyzer $filtering.analyzer" - #end if - - ## OUTPUT ENCODING - #set $mz_encoding = str($settings.mz_encoding) - #set $intensity_encoding = str($settings.intensity_encoding) - #if $mz_encoding == $intensity_encoding - #if $mz_encoding == "64" - --64 - #else - --32 - #end if - #else - --mz${mz_encoding} - --inten${intensity_encoding} - #end if - - #set binary_compression = str($settings.binary_compression) - #if $binary_compression == "zlib" - --zlib - #else if $binary_compression == "numpressLinearPic" - --numpressLinear --numpressPic - #else if $binary_compression == "numpressLinearSlof" - --numpressLinear --numpressSlof - #else if $binary_compression == "numpressLinear" - --numpressLinear - #else if $binary_compression == "numpressPic" - --numpressPic - #else if $binary_compression == "numpressSlof" - --numpressSlof - #end if - - #if $settings.gzip_compression - --gzip - #end if - - #if $general_options.multi_run_output.do_multi_run_output == 'false': - --outfile '${os.path.splitext($basename)[0]}' - && sudo mv 'outputs/${os.path.splitext($basename)[0]}.${output_type}' '${output}' && sudo chown \$uid:\$gid '${output}' - #else - && sudo chown \$uid:\$gid 'outputs'/* - && ls -la outputs/ - #end if - - #if $data_processing.precursor_refinement.use_mzrefinement - && sudo mv '$output_refinement_name' '$output_refinement' && sudo chown \$uid:\$gid '$output_refinement' - #end if -]]> - - - - - - True == value - - - -<<<<<<< HEAD - - - - - -======= - - - - - ->>>>>>> 4d10e7e3d0c5541f26c6de354471c71aa0e61213 - - -
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- - - - - general_options['multi_run_output']['do_multi_run_output'] == False - - - - - - - - - data_processing['precursor_refinement']['use_mzrefinement'] == True - - - general_options['multi_run_output']['do_multi_run_output'] == True - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -<<<<<<< HEAD - - -======= - - ->>>>>>> 4d10e7e3d0c5541f26c6de354471c71aa0e61213 - - - - -<<<<<<< HEAD - - -======= - - ->>>>>>> 4d10e7e3d0c5541f26c6de354471c71aa0e61213 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -**What it does** - -Converts mass spectrometry (MS) files: proprietary MS vendor formats can be converted to open MS formats (mzML, mzXML, MGF, MS1/MS2) and open formats can be converted to other open formats. Additional options such as filtering and/or precursor recalculation are available. - -You can view the original documentation here_. - -.. _here: http://proteowizard.sourceforge.net/tools/msconvert.html - - - - - 10.1093/bioinformatics/btn323 - @misc{toolsGalaxyP, author = {Chilton, J, Chambers MC, et al.}, title = {Galaxy Proteomics Tools}, publisher = {GitHub}, journal = {GitHub repository}, - year = {2015}, url = {https://github.com/galaxyproteomics/tools-galaxyp}} - - - -