| Previous changeset 10:9d5de24e6ef7 (2019-02-23) Next changeset 12:9ec469ff191a (2019-03-22) |
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Commit message:
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 3c189141a9dd1d44d44af82ccd9b6e9d3742f93d |
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modified:
msconvert_macros.xml |
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removed:
msconvert_macros.xml.orig |
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| 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} |
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| 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 |
| [ |
| b'@@ -1,897 +0,0 @@\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' |