| Previous changeset 16:545054b15d7c (2024-03-24) |
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Commit message:
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit e3d24f3dc7a9812f8fa4447c9391e5bd3b5d4dc6 |
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modified:
msconvert.xml msconvert_macros.xml |
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added:
msconvert_macros.xml.orig |
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| diff -r 545054b15d7c -r ab6c14374bc0 msconvert.xml --- a/msconvert.xml Sun Mar 24 11:13:43 2024 +0000 +++ b/msconvert.xml Thu Aug 15 16:19:28 2024 +0000 |
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| @@ -1,4 +1,4 @@ -<tool id="msconvert" name="msconvert" version="@VERSION@.3"> +<tool id="msconvert" name="msconvert" version="@VERSION@.4"> <description>Convert and/or filter mass spectrometry files</description> <macros> <import>msconvert_macros.xml</import> |
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| diff -r 545054b15d7c -r ab6c14374bc0 msconvert_macros.xml --- a/msconvert_macros.xml Sun Mar 24 11:13:43 2024 +0000 +++ b/msconvert_macros.xml Thu Aug 15 16:19:28 2024 +0000 |
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| @@ -32,7 +32,7 @@ #set inputmask = "'"+$basename+"'" #end if - #if $data_processing.precursor_refinement.use_mzrefinement + #if $data_processing.precursor_refinement.use_mzrefinement == "true" #set input_ident_name = ".".join((os.path.splitext($basename)[0], $data_processing.precursor_refinement.input_ident.ext)) #set output_refinement_name = os.path.splitext($basename)[0] + '.mzRefinement.tsv' ln -s '$data_processing.precursor_refinement.input_ident' '$input_ident_name' && @@ -65,7 +65,7 @@ --filter "scanSumming precursorTol=$general_options.scan_summing.precursorTol scanTimeTol=$general_options.scan_summing.scanTimeTol ionMobilityTol=$general_options.scan_summing.ionMobilityTol" #end if - #if $general_options.multi_run_output.do_multi_run_output: + #if $general_options.multi_run_output.do_multi_run_output == "true": #if len($general_options.multi_run_output.run_index_set) > 0 --runIndexSet " #for $index in $general_options.multi_run_output.run_index_set @@ -85,7 +85,7 @@ --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 + #if $data_processing.precursor_refinement.use_mzrefinement == "true" --filter "mzRefiner $input_ident_name msLevels=$data_processing.precursor_refinement.precursor_refinement_ms_levels thresholdScore=$data_processing.precursor_refinement.thresholdScore @@ -229,7 +229,7 @@ #end if #end if - #if $data_processing.precursor_refinement.use_mzrefinement + #if $data_processing.precursor_refinement.use_mzrefinement == "true" && mv '$output_refinement_name' '$output_refinement'; #end if ]]> @@ -560,10 +560,10 @@ </change_format> </data> <data format="tsv" name="output_refinement" label="${($input.name[:-4] if $input.name.endswith('.tar') else $input.name).rsplit('.',1)[0]}.mzRefinement.tsv"> - <filter>data_processing['precursor_refinement']['use_mzrefinement'] == True</filter> + <filter>data_processing['precursor_refinement']['use_mzrefinement'] == "true"</filter> </data> <collection name="multi_run_output_list" type="list" label="${($input.name[:-4] if $input.name.endswith('.tar') else $input.name).rsplit('.',1)[0]}.${output_type} collection"> - <filter>general_options['multi_run_output']['do_multi_run_output'] == True</filter> + <filter>general_options['multi_run_output']['do_multi_run_output'] == "true"</filter> <discover_datasets pattern="__name_and_ext__" directory="outputs" /> </collection> </outputs> |
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| diff -r 545054b15d7c -r ab6c14374bc0 msconvert_macros.xml.orig --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/msconvert_macros.xml.orig Thu Aug 15 16:19:28 2024 +0000 |
| [ |
| b'@@ -0,0 +1,897 @@\n+<macros>\n+ <token name="@VERSION@">3.0.19052</token>\n+ <token name="@FULL_VERSION@">@VERSION@-089e81090</token>\n+ \n+ <xml name="msconvertCommand">\n+ <command detect_errors="exit_code">\n+<![CDATA[\n+ #import re\n+ #set $ext = $input.ext\n+\n+ ## sanitize display name for use as temp filename\n+ #set basename = $re.sub(r\'[^\\w\\.\\-\\+]\',\'_\',$input.element_identifier)\n+\n+ #if $ext == \'wiff\':\n+ ln -s \'${input.extra_files_path}/wiff\' \'${basename}.wiff\' &&\n+ ln -s \'${input.extra_files_path}/wiff_scan\' \'${basename}.wiff.scan\' &&\n+ #elif $ext.endswith(\'tar\'):\n+ ln -s \'$input\' \'${basename}\' &&\n+ tar xf \'${basename}\' &&\n+ #set basename = $os.path.splitext($basename)[0]\n+ #else\n+ ln -s \'$input\' \'${basename}\' &&\n+ #end if\n+ \n+ #if $data_processing.precursor_refinement.use_mzrefinement\n+ #set input_ident_name = ".".join((os.path.splitext($basename)[0], $data_processing.precursor_refinement.input_ident.ext))\n+ #set output_refinement_name = os.path.splitext($basename)[0] + \'.mzRefinement.tsv\'\n+ ln -s \'$data_processing.precursor_refinement.input_ident\' \'$input_ident_name\' &&\n+ #end if\n+\n+ uid=`id -u` &&\n+ gid=`id -g` &&\n+\n+ wine64_anyuser msconvert \'${basename}\'\n+ --outdir outputs\n+ --${output_type}\n+\n+ #if $general_options.combineIonMobilitySpectra:\n+ --combineIonMobilitySpectra\n+ #end if\n+\n+ #if $general_options.simAsSpectra:\n+ --simAsSpectra\n+ #end if\n+\n+ #if $general_options.srmAsSpectra:\n+ --srmAsSpectra\n+ #end if\n+\n+ #if $general_options.acceptZeroLengthSpectra:\n+ --acceptZeroLengthSpectra\n+ #end if\n+\n+ #if $general_options.ignoreUnknownInstrumentError:\n+ --ignoreUnknownInstrumentError\n+ #end if\n+\n+ #if $general_options.scan_summing.do_scan_summing:\n+ --filter "scanSumming precursorTol=$general_options.scan_summing.precursorTol scanTimeTol=$general_options.scan_summing.scanTimeTol ionMobilityTol=$general_options.scan_summing.ionMobilityTol"\n+ #end if\n+\n+ #if $general_options.multi_run_output.do_multi_run_output:\n+ #if len($general_options.multi_run_output.run_index_set) > 0\n+ --runIndexSet "\n+ #for $index in $general_options.multi_run_output.run_index_set\n+ [${index.from},${index.to}]\n+ #end for\n+ "\n+ #end if\n+ #else\n+ --runIndexSet $general_options.multi_run_output.runIndexSet\n+ #end if\n+\n+ ## Strip sourceFile location since it is meaningless on HPC systems and causes problems with functional tests\n+ --stripLocationFromSourceFiles\n+\n+ ## DATA PROCESSING FILTERS (NOTE: FOR VENDOR METHOD TO WORK, PEAK PICKING MUST BE THE FIRST FILTER!)\n+ #if $data_processing.peak_picking.pick_peaks\n+ --filter "peakPicking $data_processing.peak_picking.pick_peaks_algorithm msLevel=$data_processing.peak_picking.pick_peaks_ms_levels"\n+ #end if\n+\n+ #if $data_processing.precursor_refinement.use_mzrefinement\n+ --filter "mzRefiner $input_ident_name\n+ msLevels=$data_processing.precursor_refinement.precursor_refinement_ms_levels\n+ thresholdScore=$data_processing.precursor_refinement.thresholdScore\n+ thresholdValue=$data_processing.precursor_refinement.thresholdValue\n+ thresholdStep=$data_processing.precursor_refinement.thresholdStep\n+ maxSteps=$data_processing.precursor_refinement.thresholdMaxSteps assumeHighRes=1"\n+ #end if\n+\n+ #if str($data_processing.charge_state_calculation.charge_state_calculation_method) == "predictor"\n+ --filter "chargeStatePredictor\n+ overrideExistingCharge=$data_processing.charge_state_calculation.predictor_overrideExistingCharge\n+ minMultipleCharge=$data_processing.charge_state_calculation.minMultipleCharge\n+ maxMultipleCharge=$data_processing.charge_state_calculation.maxMultipleCharge\n+ singleChargeFractionTIC=$data_processing.charge_state_calculation.singleChargeFractionTIC\n+ maxKnownCharge='..b'param name="indices_1|to" value="10" />\n+ <param name="indices_2|from" value="13" />\n+ <param name="indices_2|to" value="15" />\n+ <param name="binary_compression" value="numpressLinearPic" />\n+ <output name="output" file="small-index-filter.mzML" lines_diff="32" />\n+ </test>\n+ <test>\n+ <param name="input" value="small-peakpicking-cwt-allMS.mzML" />\n+ <param name="license_agreement" value="true" />\n+ <param name="output_type" value="mzml" />\n+ <param name="strip_it" value="true" />\n+ <param name="binary_compression" value="numpressLinearPic" />\n+ <output name="output" file="small-strip-it.mzML" lines_diff="100" />\n+ </test>\n+ <test>\n+ <param name="input" value="small-peakpicking-cwt-allMS.mzML" />\n+ <param name="license_agreement" value="true" />\n+ <param name="output_type" value="mzml" />\n+ <param name="do_ms_level_filter" value="true" />\n+ <param name="ms_level_from" value="2" />\n+ <param name="ms_level_to" value="2" />\n+ <param name="binary_compression" value="numpressLinearPic" />\n+ <output name="output" file="small-ms-level-filter.mzML" lines_diff="86" />\n+ </test>\n+ <test>\n+ <param name="input" value="small-peakpicking-cwt-allMS.mzML" />\n+ <param name="license_agreement" value="true" />\n+ <param name="output_type" value="mzml" />\n+ <param name="polarity" value="positive" />\n+ <param name="binary_compression" value="numpressLinearPic" />\n+ <output name="output" file="small-polarity-filter.mzML" lines_diff="114" />\n+ </test>\n+ <test>\n+ <param name="input" value="small-peakpicking-cwt-allMS.mzML" />\n+ <param name="license_agreement" value="true" />\n+ <param name="output_type" value="mzml" />\n+ <param name="analyzer" value="IT" />\n+ <param name="binary_compression" value="numpressLinearPic" />\n+ <output name="output" file="small-analyzer-filter.mzML" lines_diff="100" />\n+ </test>\n+ <test>\n+ <param name="input" value="small-peakpicking-cwt-allMS.mzML" />\n+ <param name="license_agreement" value="true" />\n+ <param name="output_type" value="mzml" />\n+ <param name="scan_numbers_0|from" value="3" />\n+ <param name="scan_numbers_0|to" value="5" />\n+ <param name="scan_numbers_1|from" value="11" />\n+ <param name="scan_numbers_1|to" value="11" />\n+ <param name="scan_numbers_2|from" value="14" />\n+ <param name="scan_numbers_2|to" value="16" />\n+ <param name="binary_compression" value="numpressLinearPic" />\n+ <output name="output" file="small-index-filter.mzML" lines_diff="86"/> <!-- the scan numbers here produce the same output as the index test above -->\n+ </test>\n+ <!--<test>\n+ <param name="input" value="small.mzML" />\n+ <param name="output_type" value="mzml" />\n+ <param name="binary_compression" value="numpressLinearPic" />\n+ <output name="output" file="small-deisotope-poisson.mzML" />\n+ </test>-->\n+ </xml>\n+ <xml name="msconvert_help">\n+**What it does**\n+\n+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.\n+\n+You can view the original documentation here_.\n+\n+.. _here: http://proteowizard.sourceforge.net/tools/msconvert.html\n+ </xml>\n+\n+ <xml name="citations">\n+ <citations>\n+ <citation type="doi">10.1093/bioinformatics/btn323</citation>\n+ <citation type="bibtex">@misc{toolsGalaxyP, author = {Chilton, J, Chambers MC, et al.}, title = {Galaxy Proteomics Tools}, publisher = {GitHub}, journal = {GitHub repository},\n+ year = {2015}, url = {https://github.com/galaxyproteomics/tools-galaxyp}}</citation> <!-- TODO: fix substitution of commit ", commit = {$sha1$}" -->\n+ </citations>\n+ </xml>\n+\n+</macros>\n' |