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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty |
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README job_conf.xml.sample msconvert_macros.xml msconvert_win.xml msconvert_wrapper.py test-data/D100930_yeast_SCX10S_rak_ft8E_pc_01-etdfilter.mzML test-data/D100930_yeast_SCX10S_rak_ft8E_pc_01.mz5 test-data/Rpal_01-mzRefinement.mzML test-data/Rpal_01.mz5 test-data/Rpal_01.pepXML test-data/Rpal_01.pepXML.mzRefinement.tsv test-data/small-activation.mzML test-data/small-analyzer-filter.mzML test-data/small-chargeStatePredictor.mzML test-data/small-deisotope-poisson.mzML test-data/small-deisotope.mzML test-data/small-denoise.mzML test-data/small-index-filter.mzML test-data/small-ms-level-filter.mzML test-data/small-mzWindow.mzML test-data/small-numpressL.mzML test-data/small-numpressLP.mzML test-data/small-numpressLS.mzML test-data/small-numpressP.mzML test-data/small-numpressS.mzML test-data/small-peakpicking-cwt-allMS.mzML test-data/small-peakpicking-vendor-ms1.mgf test-data/small-polarity-filter.mzML test-data/small-strip-it.mzML test-data/small-threshold.mzML test-data/small-turbocharger.mzML test-data/small-zlib-32.mzXML test-data/small-zlib-64.mz5 test-data/small.RAW test-data/small.mzML |
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| diff -r 000000000000 -r f8cf3be564bb README --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/README Fri Apr 08 16:09:02 2016 -0400 |
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| @@ -0,0 +1,15 @@ +**NOTE** +This tool must be run on a Windows Operating System. + +Your system administrator will need to: + + - install proteowizard on a windows server + http://proteowizard.sourceforge.net/downloads.shtml + + - install the galaxy pulsar rest server on the windows server + http://pulsar.readthedocs.org/en/latest/ + + - setup the galaxy job_conf.xml to send msconvert jobs to the windows server via pulsar + https://wiki.galaxyproject.org/Admin/Config/Performance/Cluster + https://wiki.galaxyproject.org/Admin/Config/Jobs + http://pulsar.readthedocs.org/en/latest/job_managers.html |
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| diff -r 000000000000 -r f8cf3be564bb job_conf.xml.sample --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/job_conf.xml.sample Fri Apr 08 16:09:02 2016 -0400 |
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| @@ -0,0 +1,88 @@ +<?xml version="1.0"?> +<job_conf> + <plugins workers="4"> + <!-- "workers" is the number of threads for the runner's work queue. + The default from <plugins> is used if not defined for a <plugin>. + --> + <plugin id="plugin_local" type="runner" load="galaxy.jobs.runners.local:LocalJobRunner"/> + <plugin id="plugin_pulsar_rest" type="runner" load="galaxy.jobs.runners.pulsar:PulsarRESTJobRunner"> + <!-- Allow optimized HTTP calls with libcurl (defaults to urllib) --> + <!-- <param id="transport">curl</param> --> + <!-- *Experimental Caching*: Next parameter enables caching. + Likely will not work with newer features such as MQ support. + If this is enabled be sure to specify a `file_cache_dir` in + the remote Pulsar's servers main configuration file. + --> + <!-- <param id="cache">True</param> --> + </plugin> + </plugins> + + <destinations default="destination_local"> + <destination id="destination_local" runner="plugin_local"/> + + <destination id="destination_winserver_pulsar_rest" runner="plugin_pulsar_rest"> + <param id="manager">_default_</param> + <param id="url">http://winserver.myu.edu:8900/</param> + <!-- If set, private_token must match token in remote Pulsar's + configuration. --> + <param id="private_token">your_ultra-secret_magic_token_here</param> + <!-- Uncomment the following statement to disable file staging (e.g. + if there is a shared file system between Galaxy and the Pulsar + server). Alternatively action can be set to 'copy' - to replace + http transfers with file system copies, 'remote_transfer' to cause + the Pulsar to initiate HTTP transfers instead of Galaxy, or + 'remote_copy' to cause Pulsar to initiate file system copies. + If setting this to 'remote_transfer' be sure to specify a + 'galaxy_url' attribute on the runner plugin above. + --> + <!-- <param id="default_file_action">none</param> --> + <!-- The above option is just the default, the transfer behavior + none|copy|http can be configured on a per path basis via the + following file. See Pulsar documentation for more details and + examples. + --> + <!-- <param id="file_action_config">file_actions.yaml</param> --> + <!-- The non-legacy Pulsar runners will attempt to resolve Galaxy + dependencies remotely - to enable this set a tool_dependency_dir + in Pulsar's configuration (can work with all the same dependency + resolutions mechanisms as Galaxy - tool Shed installs, Galaxy + packages, etc...). To disable this behavior, set the follow parameter + to none. To generate the dependency resolution command locally + set the following parameter local. + --> + <!-- <param id="dependency_resolution">none</params> --> + <!-- Uncomment following option to enable setting metadata on remote + Pulsar server. The 'use_remote_datatypes' option is available for + determining whether to use remotely configured datatypes or local + ones (both alternatives are a little brittle). + --> + <!-- <param id="remote_metadata">true</param> --> + <!-- <param id="use_remote_datatypes">false</param> --> + <!-- <param id="remote_property_galaxy_home">/path/to/remote/galaxy-central</param> --> + <!-- If remote Pulsar server is configured to run jobs as the real user, + uncomment the following line to pass the current Galaxy user + along. + --> + <!-- <param id="submit_user">$__user_name__</param> --> + <!-- Various other submission parameters can be passed along to the Pulsar + whose use will depend on the remote Pulsar's configured job manager. + For instance: + --> + <!-- <param id="submit_native_specification">-P bignodes -R y -pe threads 8</param> --> + <!-- Disable parameter rewriting and rewrite generated commands + instead. This may be required if remote host is Windows machine + but probably not otherwise. + --> + <!-- <param id="rewrite_parameters">false</params> --> + </destination> + + </destinations> + + <tools> + <tool id="msconvert_win" destination="destination_winserver_pulsar_rest"/> + </tools> + +</job_conf> + + + |
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| diff -r 000000000000 -r f8cf3be564bb msconvert_macros.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/msconvert_macros.xml Fri Apr 08 16:09:02 2016 -0400 |
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| b'@@ -0,0 +1,675 @@\n+<macros>\n+ <xml name="generic_requirements">\n+ <requirements>\n+ <requirement type="package" version="3.0.9016">proteowizard</requirement>\n+ </requirements>\n+ </xml>\n+ <token name="@VERSION@">3.0</token>\n+ \n+ <xml name="msconvertCommand">\n+ <command interpreter="python">\n+<![CDATA[\n+ #import re\n+ #set $ext = $input.ext\n+ msconvert_wrapper.py\n+ #if $ext == \'wiff\':\n+ #set basename = \'absciex\'\n+ #if hasattr($input, \'display_name\')\n+ #set basename = $re.sub(\'\\W\',\'_\',$input.display_name)\n+ #end if\n+ --input=${input.extra_files_path}/wiff\n+ --input_name=\'${basename}.wiff\n+ --implicit=${input.extra_files_path}/wiff_scan\n+ --input=${input.extra_files_path}/wiff_scan\n+ --input_name=\'${basename}.wiff.scan\n+ #else\n+ --input=${input}\n+ #if hasattr($input, \'display_name\')\n+ --input_name=\'${input.display_name}\'\n+ #end if\n+ #end if\n+ --output=${output}\n+ ## BEGIN_VERSION_DEFAULT\n+ --fromextension=$ext\n+ ## END_VERSION_DEFAULT\n+ --toextension=${output_type}\n+\n+ ## DATA PROCESSING FILTERS (NOTE: FOR VENDOR METHOD TO WORK, PEAK PICKING MUST BE THE FIRST FILTER!)\n+ #if $data_processing.precursor_refinement.use_mzrefinement\n+ #set $input_ident_name = $re.sub(\'\\W\',\'_\',$data_processing.precursor_refinement.input_ident.display_name)\n+ #if $data_processing.precursor_refinement.input_ident.ext == \'mzid\':\n+ #set $input_ident_name = $re.sub(\'(?i)([.]?mzid)*$\',\'.mzid\',$input_ident_name)\n+ #elif $data_processing.precursor_refinement.input_ident.ext == \'pepxml\':\n+ #set $input_ident_name = $re.sub(\'(?i)([.]?pep[.]?xml)*$\',\'.pep.xml\',$input_ident_name)\n+ #end if\n+ --ident=$data_processing.precursor_refinement.input_ident\n+ --ident_name=$input_ident_name\n+ --refinement=$output_refinement\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"\n+ #end if\n+\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 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=$data_processing.charge_state_calculation.singleChargeFractionTIC\n+ maxKnownCharge=$data_processing.charge_state_calculation.maxKnownCharge"\n+ #else if str($data_processing.charge_state_calculation.charge_state_calculation_method) == "turbocharger"\n+ --filter "turbocharger\n+ minCharge=$data_processing.charge_state_calculation.minCharge\n+ maxCharge=$data_processing.charge_state_calculation.maxCharge\n+ precursorsBefore=$data_processing.charge_state_calculation.precursorsBefore\n+ precursorsAfter=$data_processing.charge_state_calculation.precursorsAfter\n+ halfIsoWidth=$data_processing.charge_state_calculation.halfIsoWidth\n+ defaultMinCharge=$data_processing.charge_state_calculation.defaultMinCharge\n+ defaultMaxCharge=$data_processing.charge_state_calculation.defaultMaxCharge"\n+ #end if\n+\n+ #for threshold_entry in $data_processing.thresholds\n+ --filter "threshold $threshold_entry.threshold_type $thres'..b'e="mzML" />\n+ <param name="activation" value="CID" />\n+ <param name="binary_compression" value="numpressLinearPic" />\n+ <output name="output" file="small-activation.mzML" />\n+ </test>\n+ <test>\n+ <param name="input" value="small-peakpicking-cwt-allMS.mzML" />\n+ <param name="output_type" value="mzML" />\n+ <param name="indices_0|from" value="2" />\n+ <param name="indices_0|to" value="4" />\n+ <param name="indices_1|from" value="10" />\n+ <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" />\n+ </test>\n+ <test>\n+ <param name="input" value="small-peakpicking-cwt-allMS.mzML" />\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" />\n+ </test>\n+ <test>\n+ <param name="input" value="small-peakpicking-cwt-allMS.mzML" />\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" />\n+ </test>\n+ <test>\n+ <param name="input" value="small-peakpicking-cwt-allMS.mzML" />\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" />\n+ </test>\n+ <test>\n+ <param name="input" value="small-peakpicking-cwt-allMS.mzML" />\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" />\n+ </test>\n+ <test>\n+ <param name="input" value="small-peakpicking-cwt-allMS.mzML" />\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" /> <!-- 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+Allows interconversion within various mass spectrometry peak list 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' |
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| diff -r 000000000000 -r f8cf3be564bb msconvert_win.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/msconvert_win.xml Fri Apr 08 16:09:02 2016 -0400 |
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| @@ -0,0 +1,36 @@ +<tool id="msconvert_win" name="msconvert (vendor support)" version="@VERSION@.0"> + <description>Convert and/or filter mass spectrometry files (with vendor support on Windows)</description> + + <macros> + <import>msconvert_macros.xml</import> + </macros> + + <expand macro="msconvertCommand" /> + + <inputs> + <!-- TODO: add Bruker, Waters, Agilent types --> + <param format="mzml,mzxml,mz5,mgf,wiff,raw" name="input" type="data" label="Input unrefined MS data" /> + + <expand macro="msconvertInputParameters" /> + </inputs> + + <expand macro="msconvertOutput" /> + + <tests> + <expand macro="msconvert_tests" /> + + <test> + <param name="input" value="small.raw" /> + <param name="output_type" value="mgf" /> + <param name="pick_peaks" value="true" /> + <param name="pick_peaks_algorithm" value="vendor" /> + <param name="pick_peaks_ms_levels" value="1" /> + <output name="output" file="small-peakpicking-vendor-ms1.mgf" /> + </test> + + </tests> + <help> + <expand macro="msconvert_help" /> + </help> + <expand macro="citations" /> +</tool> |
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| diff -r 000000000000 -r f8cf3be564bb msconvert_wrapper.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/msconvert_wrapper.py Fri Apr 08 16:09:02 2016 -0400 |
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| b'@@ -0,0 +1,298 @@\n+#!/usr/bin/env python\n+import optparse\n+import os\n+import sys\n+import tempfile\n+import shutil\n+import subprocess\n+import re\n+import logging\n+\n+assert sys.version_info[:2] >= (2, 6)\n+\n+log = logging.getLogger(__name__)\n+working_directory = os.getcwd()\n+tmp_stderr_name = tempfile.NamedTemporaryFile(dir=working_directory, suffix=\'.stderr\').name\n+tmp_stdout_name = tempfile.NamedTemporaryFile(dir=working_directory, suffix=\'.stdout\').name\n+\n+\n+def stop_err(msg):\n+ sys.stderr.write("%s\\n" % msg)\n+ sys.exit()\n+\n+\n+def read_stderr():\n+ stderr = \'\'\n+ if(os.path.exists(tmp_stderr_name)):\n+ with open(tmp_stderr_name, \'rb\') as tmp_stderr:\n+ buffsize = 1048576\n+ try:\n+ while True:\n+ stderr += tmp_stderr.read(buffsize)\n+ if not stderr or len(stderr) % buffsize != 0:\n+ break\n+ except OverflowError:\n+ pass\n+ return stderr\n+\n+\n+def execute(command, stdin=None):\n+ try:\n+ with open(tmp_stderr_name, \'wb\') as tmp_stderr:\n+ with open(tmp_stdout_name, \'wb\') as tmp_stdout:\n+ proc = subprocess.Popen(args=command, shell=True, stderr=tmp_stderr.fileno(), stdout=tmp_stdout.fileno(), stdin=stdin, env=os.environ)\n+ returncode = proc.wait()\n+ if returncode != 0:\n+ raise Exception("Program returned with non-zero exit code %d. stderr: %s" % (returncode, read_stderr()))\n+ finally:\n+ print(( open(tmp_stderr_name, "r").read() ))\n+ print(( open(tmp_stdout_name, "r").read() ))\n+\n+\n+def delete_file(path):\n+ if os.path.exists(path):\n+ try:\n+ os.remove(path)\n+ except:\n+ pass\n+\n+\n+def delete_directory(directory):\n+ if os.path.exists(directory):\n+ try:\n+ shutil.rmtree(directory)\n+ except:\n+ pass\n+\n+\n+def symlink(source, link_name):\n+ import platform\n+ if platform.system() == \'Windows\':\n+ try:\n+ import win32file\n+ win32file.CreateSymbolicLink(source, link_name, 1)\n+ except:\n+ shutil.copy(source, link_name)\n+ else:\n+ os.symlink(source, link_name)\n+\n+\n+def copy_to_working_directory(data_file, relative_path):\n+ if os.path.abspath(data_file) != os.path.abspath(relative_path):\n+ symlink(data_file, relative_path)\n+ return relative_path\n+\n+\n+def __main__():\n+ run_script()\n+\n+#ENDTEMPLATE\n+\n+to_extensions = [\'mzML\', \'mzXML\', \'unindexed_mzML\', \'unindexed_mzXML\', \'mgf\', \'mz5\', \'txt\', \'ms2\', \'cms2\']\n+\n+\n+def str_to_bool(v):\n+ """ From http://stackoverflow.com/questions/715417/converting-from-a-string-to-boolean-in-python """\n+ return v.lower() in ["yes", "true", "t", "1"]\n+\n+\n+def _add_filter(filters_file, contents):\n+ filters_file.write("filter=%s\\n" % contents)\n+\n+\n+def _skip_line(options, file_num, line_parts):\n+ file_num_column = options.filter_table_file_column\n+ if not file_num_column:\n+ return False\n+ else:\n+ target_file_num_val = str(file_num).strip()\n+ query_file_num_val = line_parts[int(file_num_column) - 1].strip()\n+ #print "target %s, query %s" % (target_file_num_val, query_file_num_val)\n+ return target_file_num_val != query_file_num_val\n+\n+\n+def _read_table_numbers(path, options, file_num=None):\n+ unique_numbers = set([])\n+ column_num = options.filter_table_column\n+ input = open(path, "r")\n+ first_line = True\n+ for line in input:\n+ if not line:\n+ continue\n+ line = line.strip()\n+ if line.startswith("#"):\n+ first_line = False\n+ continue\n+ if column_num == None:\n+ column = line\n+ else:\n+ line_parts = line.split("\\t")\n+ if _skip_line(options, file_num, line_parts):\n+ continue\n+ column = line_parts[int(column_num) - 1]\n+ match = re.match("\\d+", column)\n+ '..b' parser.add_option(\'--binaryencoding\', dest=\'binaryencoding\', choices=[\'32\', \'64\'])\n+ parser.add_option(\'--mzencoding\', dest=\'mzencoding\', choices=[\'32\', \'64\'])\n+ parser.add_option(\'--intensityencoding\', dest=\'intensityencoding\', choices=[\'32\', \'64\'])\n+ parser.add_option(\'--zlib\', dest=\'zlib\', default="false")\n+ parser.add_option(\'--filter\', dest=\'filter\', action=\'append\', default=[])\n+ parser.add_option(\'--filters_file\', dest=\'filters_file\', default=None)\n+ parser.add_option(\'--filter_table\', default=None)\n+ parser.add_option(\'--filter_table_type\', default=\'index\', choices=[\'index\', \'number\'])\n+ parser.add_option(\'--filter_table_column\', default=None)\n+ parser.add_option(\'--filter_table_file_column\', default=None)\n+ parser.add_option(\'--debug\', dest=\'debug\', action=\'store_true\', default=False)\n+\n+ (options, args) = parser.parse_args()\n+ if len(options.inputs) < 1:\n+ stop_err("No input files to msconvert specified")\n+ if len(options.input_names) > 0 and len(options.input_names) != len(options.inputs):\n+ stop_err("Number(s) of supplied input names and input files do not match")\n+ if not options.output:\n+ stop_err("Must specify output location")\n+ input_files = []\n+ for i, input in enumerate(options.inputs):\n+ input_base = None\n+ if len(options.input_names) > i:\n+ input_base = options.input_names[i]\n+ input_base = input_base.replace("\'", "").replace("\\"", "")\n+ print("1- input_base: %s" % input_base)\n+ if not input_base:\n+ input_base = \'input%s\' % i\n+ print("2- input_base: %s" % input_base)\n+ if not input_base.lower().endswith(\'.%s\' % options.fromextension.lower()) and input not in options.implicits:\n+ input_file = \'%s.%s\' % (input_base, options.fromextension)\n+ print("3- input_base: %s" % input_base)\n+ print("3- input_file: %s" % input_file)\n+ else:\n+ input_file = input_base\n+ print("4- input_base: %s" % input_base)\n+ print("4- input_file: %s" % input_file)\n+ input_file = input_file\n+ copy_to_working_directory(input, input_file)\n+ if input in options.implicits:\n+ continue\n+ input_files.append(input_file)\n+ for i, ident in enumerate(options.idents):\n+ ident_file = options.ident_names[i]\n+ copy_to_working_directory(ident, ident_file)\n+\n+ cmd = _build_base_cmd(options,args=args)\n+ file_column = options.filter_table_file_column\n+ if not file_column:\n+ # Apply same filters to all files, just create a unviersal filter files\n+ # and run msconvert once.\n+ filters_file_path = _create_filters_file(options, debug=options.debug)\n+ cmd = "%s -c %s" % (cmd, filters_file_path)\n+ else:\n+ # Dispatching on a column to filter different files differently, need to filter\n+ # each input once with msconvert and then merge once.\n+ filtered_files = []\n+ for index, input_file in enumerate(input_files):\n+ filters_file_path = _create_filters_file(options, index + 1, debug=options.debug)\n+ filter_cmd = "%s -c %s" % (cmd, filters_file_path)\n+ filtered_output_file = _run(filter_cmd, output_dir=\'output%d\' % index, inputs=[input_file], debug=options.debug)\n+ filtered_files.append(filtered_output_file)\n+ input_files = filtered_files\n+ if len(input_files) > 1:\n+ cmd = "%s --merge" % cmd\n+ output_file = _run(cmd, output_dir=\'output\', inputs=input_files, debug=options.debug)\n+ shutil.copy(output_file, options.output)\n+ if options.refinement:\n+ # .mzRefinement.tsv\n+ files = os.listdir(os.getcwd())\n+ for fname in files:\n+ if fname.endswith(\'.mzRefinement.tsv\'):\n+ shutil.copy(fname, options.refinement)\n+ break\n+\n+def __main__():\n+ run_script()\n+\n+if __name__ == \'__main__\':\n+ __main__()\n' |
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| diff -r 000000000000 -r f8cf3be564bb test-data/D100930_yeast_SCX10S_rak_ft8E_pc_01-etdfilter.mzML --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/D100930_yeast_SCX10S_rak_ft8E_pc_01-etdfilter.mzML Fri Apr 08 16:09:02 2016 -0400 |
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| @@ -0,0 +1,2 @@ +ThresholdScore ThresholdValue Excluded (score) Excluded (mass error) MS1 Included MS1 Shift method MS1 Final stDev MS1 Tolerance for 99% MS1 Final MAD MS1 MAD Tolerance for 99% MS2 Included MS2 Shift method MS2 Final stDev MS2 Tolerance for 99% MS2 Final MAD MS2 MAD Tolerance for 99% +MyriMatch:MVH 40 <= MME <= 1.7976931348623157e+308 4390 175 1024 m/z 3.37955 10.1387 0.519682 2.31144 0 m/z 3.37955 10.1387 0.519682 2.31144 |
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| b |
| diff -r 000000000000 -r f8cf3be564bb test-data/small-zlib-64.mz5 |
| b |
| Binary file test-data/small-zlib-64.mz5 has changed |
| b |
| diff -r 000000000000 -r f8cf3be564bb test-data/small.RAW |
| b |
| Binary file test-data/small.RAW has changed |
| b |
| diff -r 000000000000 -r f8cf3be564bb test-data/small.mzML --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/small.mzML Fri Apr 08 16:09:02 2016 -0400 |
| b |
| b'@@ -0,0 +1,2757 @@\n+<?xml version="1.0" encoding="utf-8"?>\n+<indexedmzML xmlns="http://psi.hupo.org/ms/mzml" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://psi.hupo.org/ms/mzml http://psidev.info/files/ms/mzML/xsd/mzML1.1.2_idx.xsd">\n+ <mzML xmlns="http://psi.hupo.org/ms/mzml" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://psi.hupo.org/ms/mzml http://psidev.info/files/ms/mzML/xsd/mzML1.1.0.xsd" id="small" version="1.1.0">\n+ <cvList count="2">\n+ <cv id="MS" fullName="Proteomics Standards Initiative Mass Spectrometry Ontology" version="3.79.0" URI="http://psidev.cvs.sourceforge.net/*checkout*/psidev/psi/psi-ms/mzML/controlledVocabulary/psi-ms.obo"/>\n+ <cv id="UO" fullName="Unit Ontology" version="12:10:2011" URI="http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/phenotype/unit.obo"/>\n+ </cvList>\n+ <fileDescription>\n+ <fileContent>\n+ <cvParam cvRef="MS" accession="MS:1000579" name="MS1 spectrum" 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