# HG changeset patch # User galaxyp # Date 1605547512 0 # Node ID 3cf31069762441cfa6b7864a5f35be46752fcc3e # Parent 9b61227976d60304583e6c34a42292412753989b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 79157337a253a1c2fce2ad1739668c66b6c54df1" diff -r 9b61227976d6 -r 3cf310697624 msconvert.xml --- a/msconvert.xml Sat Jul 25 18:13:58 2020 -0400 +++ b/msconvert.xml Mon Nov 16 17:25:12 2020 +0000 @@ -7,7 +7,7 @@ chambm/pwiz-skyline-i-agree-to-the-vendor-licenses:@FULL_VERSION@ - + diff -r 9b61227976d6 -r 3cf310697624 msconvert_macros.xml --- a/msconvert_macros.xml Sat Jul 25 18:13:58 2020 -0400 +++ b/msconvert_macros.xml Mon Nov 16 17:25:12 2020 +0000 @@ -1,7 +1,7 @@ 3.0.19052 @VERSION@-089e81090 - + /dev/null; echo \$?) && + if [ "\$CAN_SUDO" -eq "0" ]; then + uid=`id -u` && + gid=`id -g` && + WINE="wine64_anyuser"; + else + WINE="wine64" && + ## create a writable copy of wine prefix (since copying fails for some html + ## stderr and exit code is swallowed) + export WINEPREFIX=\$(mktemp -d) && + (cp -a /wineprefix64/* \$WINEPREFIX 2> /dev/null || true); + fi + && + \$WINE msconvert ${inputmask} + --outdir outputs --${output_type} - - #if $general_options.combineIonMobilitySpectra: - --combineIonMobilitySpectra - #end if - - #if $general_options.simAsSpectra: - --simAsSpectra - #end if - - #if $general_options.srmAsSpectra: - --srmAsSpectra - #end if - - #if $general_options.acceptZeroLengthSpectra: - --acceptZeroLengthSpectra - #end if - - #if $general_options.ignoreUnknownInstrumentError: - --ignoreUnknownInstrumentError - #end if + $general_options.combineIonMobilitySpectra + $general_options.simAsSpectra + $general_options.srmAsSpectra + $general_options.acceptZeroLengthSpectra + $general_options.ignoreUnknownInstrumentError #if $general_options.scan_summing.do_scan_summing: --filter "scanSumming precursorTol=$general_options.scan_summing.precursorTol scanTimeTol=$general_options.scan_summing.scanTimeTol ionMobilityTol=$general_options.scan_summing.ionMobilityTol" @@ -181,8 +178,8 @@ #if str($filtering.analyzer) != "false" --filter "analyzer $filtering.analyzer" #end if - - ## OUTPUT ENCODING + + ## OUTPUT ENCODING #set $mz_encoding = str($settings.mz_encoding) #set $intensity_encoding = str($settings.intensity_encoding) #if $mz_encoding == $intensity_encoding @@ -217,14 +214,21 @@ #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}' + && + if [ "\$CAN_SUDO" -eq "0" ]; then + sudo chown \$uid:\$gid 'outputs/${os.path.splitext($basename)[0]}.${output_type}' && + sudo mv 'outputs/${os.path.splitext($basename)[0]}.${output_type}' '${output}'; + else + mv 'outputs/${os.path.splitext($basename)[0]}.${output_type}' '${output}'; + fi #else - && sudo chown \$uid:\$gid 'outputs' -R && 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' + && if [ "\$CAN_SUDO" -ne "0" ]; then + mv '$output_refinement_name' '$output_refinement'; + fi #end if ]]> @@ -243,7 +247,7 @@ -
+
@@ -407,7 +411,7 @@
- + @@ -462,7 +466,7 @@
- + @@ -474,10 +478,10 @@ - - - - + + + + @@ -514,7 +518,7 @@
- + @@ -646,7 +650,7 @@ - + @@ -736,7 +740,7 @@ - + diff -r 9b61227976d6 -r 3cf310697624 msconvert_macros.xml.orig --- a/msconvert_macros.xml.orig Sat Jul 25 18:13:58 2020 -0400 +++ /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 - - -
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
- - -
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
- -
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
- -
- - - - - - - - - - - - - - - - - - -
-
- - - - - 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}} - - - -