| Previous changeset 0:4f7d6bec667f (2016-04-08) Next changeset 2:edb33e8224c6 (2019-02-23) |
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Commit message:
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 6674ecccbb39a4bd7e379d6e8969ccec0069c2f1 |
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modified:
idconvert.xml |
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added:
test-data/Rpal_01.mzid |
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removed:
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.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-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.mzML |
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| diff -r 4f7d6bec667f -r 9e6e840d6b52 idconvert.xml --- a/idconvert.xml Fri Apr 08 16:07:32 2016 -0400 +++ b/idconvert.xml Mon Aug 08 10:43:52 2016 -0400 |
| [ |
| @@ -1,34 +1,44 @@ <tool id="idconvert" name="idconvert" version="@VERSION@.0"> <description>Convert mass spectrometry identification files</description> - <macros> <import>msconvert_macros.xml</import> </macros> - <expand macro="generic_requirements" /> - + <stdio> + <exit_code range="1:" /> + <regex match="Error" + source="both" + level="fatal" + description="Error" /> + </stdio> <command> <![CDATA[ -#set input_name -ln -s $input input.${input.extension} -idconvert input - +#import os.path +#set $input_name = '.'.join([$os.path.basename(str($from.input)),str($from.input.extension).replace('xml','.xml')]) +ln -s "$from.input" "$input_name" && +idconvert $input_name +#if str($to_format) == 'pep.xml': +--pepXML +#elif str($to_format) == 'text': +--text +#end if +--outdir outdir +&& cp outdir/* $output ]]> </command> - <inputs> <conditional name="from"> <param name="from_format" type="select" label="Convert from"> <option value="mzid">mzIdentML (mzid)</option> + <option value="pepxml">pepXML (pepxml)</option> <option value="protxml">protXML (protxml)</option> - <option value="pepxml">pepXML (pepxml)</option> </param> <when value="mzid"> <param name="input" type="data" format="pepxml,protxml,mzid" label="MS mzIdentML (mzid)" /> </when> <when value="protxml"> <param name="input" type="data" format="protxml" label="MS pepXML (pepxml)" /> - <param name="pepxml" type="data" format="pepxml" label="MS Identification" /> + <param name="pepxml" type="data" format="pepxml" multiple="true" label="MS Identification" /> </when> <when value="pepxml"> <param name="input" type="data" format="pepxml" label="MS Identification" /> @@ -36,14 +46,78 @@ </conditional> <param name="to_format" type="select" label="Convert to"> <option value="mzid">mzIdentML (mzid)</option> - <option value="pepxml">pepXML (pepxml)</option> + <option value="pep.xml">pepXML (pepxml)</option> <option value="text">text</option> </param> </inputs> - + <outputs> + <data format="mzid" name="output" label="${from.input.name.rsplit('.',1)[0]}.${to_format}"> + <change_format> + <when input="to_format" value="pep.xml" format="pepxml" /> + <when input="to_format" value="text" format="txt" /> + </change_format> + </data> + </outputs> <tests> + <test> + <param name="input" value="Rpal_01.pepXML" /> + <param name="from_format" value="pepxml" /> + <param name="to_format" value="mzid" /> + <output name="output_psms"> + <assert_contents> + <has_text text="MzIdentML" /> + <has_text text="VIKKSTTGRVLSDDILVIRKGEIAARNASHKMR" /> + </assert_contents> + </output> + </test> + <test> + <param name="input" value="Rpal_01.mzid" /> + <param name="from_format" value="mzid" /> + <param name="to_format" value="pep.xml" /> + <output name="output_psms"> + <assert_contents> + <has_text text="msms_pipeline_analysis" /> + <has_text text="VIKKSTTGRVLSDDILVIRKGEIAARNASHKMR" /> + </assert_contents> + </output> + </test> </tests> <help> +<![CDATA[ +idconvert [options] [filemasks] +Convert mass spec identification file formats. + +Return value: # of failed files. + +Options: + -f [ --filelist ] arg : specify text file containing filenames + -o [ --outdir ] arg (=.) : set output directory ('-' for stdout) [.] + -c [ --config ] arg : configuration file (optionName=value) + -e [ --ext ] arg : set extension for output files [mzid|pepXML|txt] + --mzIdentML : write mzIdentML format [default] + --pepXML : write pepXML format + --text : write hierarchical text format + -v [ --verbose ] : display detailed progress information +Examples: + +# convert sequest.pepXML to sequest.mzid +idconvert sequest.pepXML + +# convert sequest.protXML to sequest.mzid +# Also reads any pepXML file referenced in the +# protXML file if available. If the protXML +# file has been moved from its original location, +# the pepXML will still be found if it has also +# been moved to the same position relative to the +# protXML file. This relative position is determined +# by reading the protXML protein_summary:summary_xml +# and protein_summary_header:source_files values. +idconvert sequest.protXML + +# convert mascot.mzid to mascot.pepXML +idconvert mascot.mzid --pepXML + +]]> </help> <expand macro="citations" /> </tool> |
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| diff -r 4f7d6bec667f -r 9e6e840d6b52 msconvert_wrapper.py --- a/msconvert_wrapper.py Fri Apr 08 16:07:32 2016 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| [ |
| b'@@ -1,298 +0,0 @@\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 4f7d6bec667f -r 9e6e840d6b52 test-data/D100930_yeast_SCX10S_rak_ft8E_pc_01-etdfilter.mzML --- a/test-data/D100930_yeast_SCX10S_rak_ft8E_pc_01-etdfilter.mzML Fri Apr 08 16:07:32 2016 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| b'@@ -1,4759 +0,0 @@\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="D100930_yeast_SCX10S_rak_ft8E_pc_01" version="1.1.0">\n- <cvList count="2">\n- <cv id="MS" fullName="Proteomics Standards Initiative Mass Spectrometry Ontology" version="3.74.0" 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" 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| diff -r 4f7d6bec667f -r 9e6e840d6b52 test-data/D100930_yeast_SCX10S_rak_ft8E_pc_01.mz5 |
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| Binary file test-data/D100930_yeast_SCX10S_rak_ft8E_pc_01.mz5 has changed |
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| diff -r 4f7d6bec667f -r 9e6e840d6b52 test-data/Rpal_01-mzRefinement.mzML --- a/test-data/Rpal_01-mzRefinement.mzML Fri Apr 08 16:07:32 2016 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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