Mercurial > repos > galaxyp > rawtools
changeset 0:51e4aa55ea04 draft default tip
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/rawtools commit f57f55a2cb399c5cc8fdd63128970e5f875ca48e
| author | galaxyp |
|---|---|
| date | Fri, 05 Apr 2019 04:16:26 -0400 |
| parents | |
| children | |
| files | README.rst RawFileReaderLicense.md rawtools.xml test-data/really_small.raw test-data/really_small.raw_Matrix.txt test-data/really_small.raw_Ms_BP_chromatogram.txt |
| diffstat | 6 files changed, 467 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/README.rst Fri Apr 05 04:16:26 2019 -0400 @@ -0,0 +1,34 @@ +Raw Tools +======================= + +- Home: <https://github.com/kevinkovalchik/RawTools/> +- Galaxy Tool Shed: <http://toolshed.g2.bx.psu.edu/view/galaxyp/rawtools> +- Tools ID: `rawtools` + + +Description +----------- + +RawTools is an open-source and freely available package designed to perform scan data parsing and quantification, and quality control analysis of Thermo Orbitrap raw mass spectrometer files. +RawTools is written in C# and uses the Thermo RawFileReader library. + +General Requirements +-------------------- + +This tool requires .NET 4.6.2 or greater or Mono 5.0 or greater to work. + + +License +------- + +Raw Tools is a free open-source project, following an Apache License 2.0. + + +Authors +------- + +Authors and contributors: + +* Kevin Kovalchik <kovalchk@chem.ubc.ca> +* Christopher Hughes <chughes@bcgsc.ca> +* Carlos Horro Marcos <carlos.horro@uib.no>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/RawFileReaderLicense.md Fri Apr 05 04:16:26 2019 -0400 @@ -0,0 +1,51 @@ +**SOFTWARE LICENSE AGREEMENT ("License") FOR RawFileReader** + +These License terms are an agreement between you and Thermo Finnigan LLC ("Licensor"). They apply to Licensor's MSFileReader software program ("Software"), which includes documentation and any media on which you received it. These terms also apply to any updates or supplements for this Software, unless other terms accompany those items, in which case those terms apply. **If you use this Software, you accept this License. If you do not accept this License, you are prohibited from using this software. If you comply with these License terms, you have the rights set forth below.** + +1. Rights Granted: + +1.1. You may install and use this Software on any of your computing devices. + +1.2. You may distribute this Software to others, but only in combination with other software components and/or programs that you provide and subject to the distribution requirements and restrictions below. + +2. Use Restrictions: + +2.1. You may not decompile, disassemble, reverse engineer, use reflection or modify this Software. + +3. Distribution Requirements: + +If you distribute this Software to others, you agree to: + +3.1. Indemnify, defend and hold harmless the Licensor from any claims, including attorneys' fees, related to the distribution or use of this Software; + +3.2. Display the following text in your software's "About" box: " **RawFileReader reading tool. Copyright © 2016 by Thermo Fisher Scientific, Inc. All rights reserved**."; + +3.3. Require your end users to agree to a license agreement that prohibits them from redistributing this Software to others. + +4. Distribution Restrictions: + +4.1. You may not use the Licensor's trademarks in a way that suggests your software components and/or programs are provided by or are endorsed by the Licensor; and + +4.2. You may not commercially exploit this Software or products that incorporate this Software without the prior written consent of Licensor. Commercial exploitation includes, but is not limited to, charging a purchase price, license fee, maintenance fee, or subscription fee; or licensing, transferring or redistributing the Software in exchange for consideration of any kind. + +4.3. Your rights to this Software do not include any license, right, power or authority to subject this Software in whole or in part to any of the terms of an Excluded License. "Excluded License" means any license that requires as a condition of use, modification and/or distribution of software subject to the Excluded License, that such software or other software combined and/or distributed with such software be (a) disclosed or distributed in source code form; or (b) licensed for the purpose of making derivative works. Without limiting the foregoing obligation, you are specifically prohibited from distributing this Software with any software that is subject to the General Public License (GPL) or similar license in a manner that would create a combined work. + +5. Additional Terms Applicable to Software: + +5.1. This Software is licensed, not sold. This License only gives you some rights to use this Software; the Licensor reserves all other rights. Unless applicable law gives you more rights despite this limitation, you may use this Software only as expressly permitted in this License. + +5.2. Licensor has no obligation to fix, update, supplement or support this Software. + +5.3. This Software is not designed, manufactured or intended for any use requiring fail-safe performance in which the failure of this Software could lead to death, serious personal injury or severe physical and environmental damage ("High Risk Activities"), such as the operation of aircraft, medical or nuclear facilities. You agree not to use, or license the use of, this Software in connection with any High Risk Activities. + +5.4. Your rights under this License terminate automatically if you breach this License in any way. Termination of this License will not affect any of your obligations or liabilities arising prior to termination. The following sections of this License shall survive termination: 2.1, 3.1, 3.2, 3.3, 4.1, 4.2, 4.3, 5.1, 5.2, 5.3, 5.5, 5.6, 5.7, 5.8, and 5.9. + +5.5. This Software is subject to United States export laws and regulations. You agree to comply with all domestic and international export laws and regulations that apply to this Software. These laws include restrictions on destinations, end users and end use. + +5.6. This License shall be construed and controlled by the laws of the State of California, U.S.A., without regard to conflicts of law. You consent to the jurisdiction of the state and federal courts situated in the State of California in any action arising under this License. The application of the U.N. Convention on Contracts for the International Sale of Goods to this License is hereby expressly excluded. If any provision of this License shall be deemed unenforceable or contrary to law, the rest of this License shall remain in full effect and interpreted in an enforceable manner that most nearly captures the intent of the original language. + +5.7. THIS SOFTWARE IS LICENSED "AS IS". YOU BEAR ALL RISKS OF USING IT. LICENSOR GIVES NO AND DISCLAIMS ALL EXPRESS AND IMPLIED WARRANTIES, REPRESENTATIONS OR GUARANTEES. YOU MAY HAVE ADDITIONAL CONSUMER RIGHTS UNDER YOUR LOCAL LAWS WHICH THIS LICENSE CANNOT CHANGE. TO THE EXTENT PERMITTED UNDER YOUR LOCAL LAWS, LICENSOR EXCLUDES THE IMPLIED WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. + +5.8. LICENSOR'S TOTAL LIABILITY TO YOU FOR DIRECT DAMAGES ARISING UNDER THIS LICENSE IS LIMITED TO U.S. $1.00. YOU CANNOT RECOVER ANY OTHER DAMAGES, INCLUDING CONSEQUENTIAL, LOST PROFITS, SPECIAL, INDIRECT OR INCIDENTAL DAMAGES, EVEN IF LICENSOR IS EXPRESSLY MADE AWARE OF THE POSSIBILITY THEREOF OR IS NEGLIGENT. THIS LIMITATION APPLIES TO ANYTHING RELATED TO THIS SOFTWARE, SERVICES, CONTENT (INCLUDING CODE) ON THIRD PARTY INTERNET SITES, OR THIRD PARTY PROGRAMS, AND CLAIMS FOR BREACH OF CONTRACT, BREACH OF WARRANTY, GUARANTEE OR CONDITION, STRICT LIABILITY, NEGLIGENCE, OR OTHER TORT TO THE EXTENT PERMITTED BY APPLICABLE LAW. + +5.9. Use, duplication or disclosure of this Software by the U.S. Government is subject to the restricted rights applicable to commercial computer software (under FAR 52.227019 and DFARS 252.227-7013 or parallel regulations). The manufacturer for this purpose is Thermo Finnigan LLC, 355 River Oaks Parkway, San Jose, California 95134, U.S.A.
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/rawtools.xml Fri Apr 05 04:16:26 2019 -0400 @@ -0,0 +1,279 @@ +<tool id="rawtools" name="Raw Tools" version="@RAWTOOLS_VERSION@.@TOOL_SUBVERSION@" profile="16.04"> + <description> + Perform scan data parsing, quantification and quality control analysis of Thermo Orbitrap raw mass spectrometer files. + </description> + <macros> + <token name="@RAWTOOLS_VERSION@">1.4.2</token> + <token name="@TOOL_SUBVERSION@">0</token> + <xml name="input_fasta"> + <param format="fasta" name="input_database" type="data" label="Protein Database" + help="Select FASTA database from history"/> + </xml> + </macros> + <requirements> + <requirement type="package" version="@RAWTOOLS_VERSION@">rawtools</requirement> + </requirements> + <command detect_errors="exit_code"> +<![CDATA[ + #from datetime import datetime + #import json + #import os + #import re + #set $exp_str = "Galaxy_Experiment_%s" % datetime.now().strftime("%Y%m%d%H%M%s") + #set $samp_str = "Sample_%s" % datetime.now().strftime("%Y%m%d%H%M%s") + #set $temp_stderr = "rawtools_stderr" + #set $bin_dir = "bin" + + mkdir output && + cwd=`pwd` && + ## TODO: To remove this patch when dropping support for Galaxy 17_09, adding profile="18.01" to the tool. + export HOME=\$cwd && + + mkdir raws_folder && + #for $input_raw in $input_raws: + #set $input_name = re.sub('[^\w\-\.]', '_',$input_raw.element_identifier.split('/')[-1].replace(".raw", "") + ".raw") + ln -s -f '${input_raw}' './raws_folder/${input_name}' && + #end for + + ##################### + ## Raw Tools ## + ##################### + (rawtools.sh + + ## PARSING AND QUANTIFICATION OPTIONS + + ## If any processing option is enabled in parsing & quantification, "parse" command is mandatory + #if $pq_options.pq_conditional.matrix_select == "yes" or $pq_options.chromatogram_conditional.chromatogram_select == "yes" or $pq_options.mgf_conditional.mgf_select == "yes" or $pq_options.metrics_boolean == "yes": + parse + #end if + --directory ./raws_folder + + ## Generates Matrix file + #if $pq_options.pq_conditional.matrix_select == "yes": + --parse + #end if + + ## Generates quantification information + #if $pq_options.pq_conditional.matrix_select == "yes" and $pq_options.pq_conditional.q_conditional.q_select == "yes" : + --quant + --labelingreagent ${pq_options.pq_conditional.q_conditional.q_labeling_reagent} + #end if + + ## Unlabeled quant + #if $pq_options.pq_conditional.matrix_select == "yes" and $pq_options.pq_conditional.unlabeledquant_boolean == "yes": + --unlabeledquant + #end if + + ## Generates Mgf file + #if $pq_options.mgf_conditional.mgf_select == "yes": + --writemgf + --masscutoff ${pq_options.mgf_conditional.mgf_masscutoff} + ## DEPRECATED --intensitycutoff ${pq_options.mgf_conditional.mgf_intensitycutoff} + #if $pq_options.mgf_conditional.mgf_refinement == "yes": + -R + #end if + #end if + + ## Generates chromatogram file + #if $pq_options.chromatogram_conditional.chromatogram_select == "yes": + --chro ${pq_options.chromatogram_conditional.chromatogram_type}${pq_options.chromatogram_conditional.chromatogram_order} + #end if + + ## Generates metrics file + #if $pq_options.metrics_boolean == "yes": + --metrics + #end if + + --out \$cwd/output + + 2>> $temp_stderr) && + + cat $temp_stderr 2>&1; +]]> + </command> + <inputs> + <param format="thermo.raw" name="input_raws" type="data" label="Raw file" multiple="true" + help="Select the raw file from history"/> + <param name="license_agreement" type="boolean" label="Do you agree to the vendor licenses?" help="This tool uses a proprietary vendor library; to run it you must agree to the vendor license. Read it at https://github.com/kevinkovalchik/RawTools/blob/master/RawFileReaderLicense"> + <validator type="expression" message="You must agree to the vendor license to run RawTools.">True == value</validator> + </param> + <section name="pq_options" expanded="true" title="Parsing and Quantification"> + <conditional name="pq_conditional"> + <param name="matrix_select" type="select" + label="Create Matrix file" + help="Parses raw file meta and scan data and creates a tab-delimited text file."> + <option value="yes" selected="True">Yes</option> + <option value="no" >No</option> + </param> + <when value="yes"> + <conditional name="q_conditional"> + <param name="q_select" type="select" + label="Quantification" + help="Also quantifies reporter ions and write results to output matrix."> + <option value="yes" >Yes</option> + <option value="no" selected="True">No</option> + </param> + <when value="yes"> + <param name="q_labeling_reagent" label="Labeling reagent" type="select" + help="Reagents used to label peptides."> + <option value="TMT0" selected="True">TMT0</option> + <option value="TMT2" >TMT2</option> + <option value="TMT6" >TMT6</option> + <option value="TMT10" >TMT10</option> + <option value="TMT11" >TMT11</option> + <option value="iTRAQ4" >iTRAQ4</option> + <option value="iTRAQ8" >iTRAQ8</option> + </param> + </when> + <when value="no" /> + </conditional> + <param name="unlabeledquant_boolean" label="Unlabeled quant" type="boolean" truevalue="yes" falsevalue="no" + help="Calculate areas of precursor peaks and writes them to the matrix file as ParentPeakArea column."/> + </when> + <when value="no" /> + </conditional> + + <conditional name="mgf_conditional"> + <param name="mgf_select" type="select" label="Creates a mgf file" + help="Creates a standard MGF file."> + <option value="yes" >Yes</option> + <option value="no" selected="True">No</option> + </param> + <when value="yes"> + <param name="mgf_masscutoff" label="Mass cutoff" value="0" type="float" + help="Specify a mass cutoff to be applied when generating MGF files. May be of use if removal of reporter ions is desired prior to searching of MS2 spectra."/> + <!--<param name="mgf_intensitycutoff" label="Intensity cutoff" value="0" type="float" + help="Relative intensity cutoff for ions included in a MGF file. The value is relative to the highest intensity ion found in a given scan."/> + --> + <param name="mgf_refinement" label="Precursor mass and charge refinement" type="boolean" truevalue="yes" falsevalue="no" checked="false" + help="Refine precursor charge and monoisotopic mass assignments. Highly recommended if monoisotopic precursor selection was turned off in the instrument method (or peptide match on a QE instrument)."/> + + </when> + <when value="no" /> + </conditional> + <conditional name="chromatogram_conditional"> + <param name="chromatogram_select" type="select" + label="Create chromatogram" + help="Creates a text file of chromatographic data for investigation or plotting."> + <option value="yes" >Yes</option> + <option value="no" selected="True">No</option> + </param> + <when value="yes"> + <param name="chromatogram_type" label="Chromatogram type" type="select" help="MS Level"> + <option value="1" selected="True">MS1</option> + <option value="2" >MS2</option> + <option value="3" >MS3</option> + </param> + <param name="chromatogram_order" label="Chromatogram order" type="select" help="MS Order"> + <option value="T" >TIC</option> + <option value="B" >Base peak</option> + <option value="TB" selected="True">TIC and base peak</option> + </param> + </when> + <when value="no" /> + </conditional> + <param name="metrics_boolean" label="Create metrics" type="boolean" truevalue="yes" falsevalue="no" + help="Creates a text file containing general metrics about the Ms run." /> + + </section> + + <!-- TODO: QUALITY CONTROL + <section name="quality_control_options" expanded="false" title="Quality control"> + + </section> + --> + + </inputs> + <outputs> + <!-- Matrix --> + + <collection name="output_matrix" type="list" label="${tool.name} - ${on_string}: Matrix"> + <filter>pq_options['pq_conditional']['matrix_select'] == "yes"</filter> + <discover_datasets pattern="(?P<designation>.+)\.raw_Matrix.txt" ext="txt" directory="output"/> + </collection> + + <!-- MGF file --> + + <collection name="output_mgf" type="list" label="${tool.name} - ${on_string}: MGF"> + <filter>pq_options['mgf_conditional']['mgf_select'] == "yes"</filter> + <discover_datasets pattern="(?P<designation>.+)\.mgf" ext="mgf" directory="output"/> + </collection> + + <!-- Chromatogram file --> + + <collection name="output_chromatogram" type="list" label="${tool.name} - ${on_string}: Chromatogram" > + <filter>pq_options['chromatogram_conditional']['chromatogram_select'] == "yes"</filter> + <discover_datasets pattern="(?P<designation>.+)\.raw_Ms_BP_chromatogram.txt" ext="txt" directory="output"/> + </collection> + + <!-- Metrics file --> + + <collection name="output_metrics" type="list" label="${tool.name} - ${on_string}: Metrics" > + <filter>pq_options['metrics_boolean'] is True</filter> + <discover_datasets pattern="(?P<designation>.+)\.raw_Metrics.txt" ext="txt" directory="output"/> + </collection> + </outputs> + <tests> + + <!-- Test Matrix --> + <test> + <param name="input_raws" value="really_small.raw" ftype="thermo.raw"/> + <param name="license_agreement" value="true" /> + <param name="pq_conditional|matrix_select" value="yes"/> + <output_collection name="output_matrix" type="list"> + <element name="really_small" file="really_small.raw_Matrix.txt" ftype="txt" compare="sim_size" delta="3000"/> + </output_collection> + </test> + + <!-- Test mgf conversion --> + <test> + <param name="input_raws" value="really_small.raw" ftype="thermo.raw"/> + <param name="license_agreement" value="true" /> + <param name="pq_conditional|matrix_select" value="no"/> + <param name="mgf_conditional|mgf_select" value="yes"/> + <param name="mgf_conditional|mgf_refinement" value="yes"/> + <output_collection name="output_mgf" type="list"> + <element name="really_small.raw" ftype="mgf"> + <assert_contents> + <has_text text="PEPMASS=675.248779296875"/> + <has_text text="RTINSECONDS=73.863181104"/> + <has_text text="SCANS=36"/> + <has_text text="121.31165 920.2368"/> + </assert_contents> + </element> + </output_collection> + </test> + <!-- Test chromatogram --> + <test> + <param name="input_raws" value="really_small.raw" ftype="thermo.raw"/> + <param name="license_agreement" value="true" /> + <param name="pq_conditional|matrix_select" value="no"/> + <param name="chromatogram_conditional|chromatogram_select" value="yes"/> + <output_collection name="output_chromatogram" type="list" > + <element name="really_small" file="really_small.raw_Ms_BP_chromatogram.txt" ftype="txt" compare="sim_size" delta="3000"/> + </output_collection> + </test> + + + </tests> + <help> +**What it does** + +RawTools is an open-source and freely available package designed to perform scan data parsing and quantification, and quality control analysis (to be developed in further versions) of Thermo Orbitrap raw mass spectrometer files. + +RawTools is written in C# and uses the Thermo RawFileReader library. RawTools is the replacement for RawQuant Python package. + +https://github.com/kevinkovalchik/RawTools + +**License** + +Raw Tools is a free open-source project, following an Apache License 2.0. + +RawFileReader reading tool. Copyright © 2016 by Thermo Fisher Scientific, Inc. All rights reserved. +Using this software implies the acceptance of RawFileReader license terms. + + </help> + <citations> + <citation type="doi">doi:10.1021/acs.jproteome.8b00721</citation> + </citations> +</tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/really_small.raw_Matrix.txt Fri Apr 05 04:16:26 2019 -0400 @@ -0,0 +1,35 @@ +MS2ScanNumber MS1ScanNumber MS2RetTime MS1RetTime DutyCycle MS2ScansPerCycle ParentIonMass MonoisotopicMass PrecursorCharge MS1IsolationInterference ParentPeakFound ParentPeakArea PeakFirstScan PeakMaxScan PeakLastScan BaseLinePeakWidth(s) PeakParentScanIntensity PeakMaxIntensity MS2IonInjectionTime MS1IonInjectionTime HCDEnergy MS2MedianIntensity MS1MedianIntensity +36 34 1.2310530184 1.21863295253333 0.601650768000002 1 675.248779296875 675.248779296875 2 0 True 167.717466421987 30 34 44 0.121015541333333 3464.98901367188 3464.98901367188 86 120 40 1330.77886962891 1135.81408691406 +38 35 1.24093018346667 1.22866046533333 0.593574847999996 1 407.919311523438 407.919311523438 3 0 True 36.2006497039203 32 35 39 0.0506705653333333 1348.14978027344 1348.14978027344 86 120 40 1343.35278320313 951.714965820313 +48 46 1.33196873146667 1.31970900238333 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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/really_small.raw_Ms_BP_chromatogram.txt Fri Apr 05 04:16:26 2019 -0400 @@ -0,0 +1,68 @@ +RetentionTime Intensity +0.89012589865 70424.4453125 +0.900221537066667 43581.56640625 +0.9100631456 36189.62109375 +0.919923499733333 80402.6640625 +0.930017091733333 7351.78759765625 +0.939863016533333 26657.404296875 +0.949712762933333 56096.26953125 +0.959729349866667 27086.078125 +0.969662583466667 19528.15625 +0.9796812808 61581.19921875 +0.989727160533333 81736.828125 +0.9998289248 32915.4140625 +1.00966218 27084.865234375 +1.01952249493333 15145.7265625 +1.02952865333333 44113.359375 +1.03946188506667 43779.6640625 +1.04931593173333 60325.5625 +1.05932834 40868.9765625 +1.06925323813333 20006.193359375 +1.07926137998333 37677.6953125 +1.089284284 14483.6708984375 +1.09936748238333 9640.0419921875 +1.10938205706667 18692.513671875 +1.1192320672 68367.0625 +1.12925260746667 79986.0390625 +1.1391858344 23875.185546875 +1.14903364506667 8841.4697265625 +1.15888152186667 36995.28125 +1.1687939064 12944.7939453125 +1.17882296533333 12285.0517578125 +1.18884371866667 15632.9111328125 +1.1989272952 29951.84765625 +1.20878522853333 29406.24609375 +1.21863295253333 90770.40625 +1.22866046533333 44973.32421875 +1.23855337946667 24537.724609375 +1.24959786053333 38378.23046875 +1.25994727706667 64326.21484375 +1.26985948158333 61519.15625 +1.27989484773333 48447.40625 +1.28991559493333 4981.7685546875 +1.29983850666667 24010.84375 +1.3096882712 41144.33984375 +1.31970900238333 85588.8984375 +1.32957589838333 38952.93359375 +1.33999603013333 96739.28125 +1.35037742933333 74771.09375 +1.36023153413333 40585.83984375 +1.37015649386667 113374.8828125 +1.38017916853333 84225.609375 +1.39019163545 27672.724609375 +1.40012481893333 153310.375 +1.40998103838333 123278.6328125 +1.41999132958333 78768.1953125 +1.42992453013333 83976.5625 +1.43995167306667 231040.046875 +1.44999134213333 1098570.625 +1.46004625733333 3295294 +1.47065747253333 5527336 +1.48069924293333 17924452 +1.4887905816 16887438 +1.49739083571667 18132246 +1.52459171678333 9375929 +1.54722693971667 3632126 +1.57372438638333 82251.9609375 +1.58474805438333 163374.328125 +1.5947900096 84607.90625