# HG changeset patch # User galaxyp # Date 1554452186 14400 # Node ID 51e4aa55ea0444f5c56fc4960e6dc573facf5b0b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/rawtools commit f57f55a2cb399c5cc8fdd63128970e5f875ca48e diff -r 000000000000 -r 51e4aa55ea04 README.rst --- /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: +- Galaxy Tool Shed: +- 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 +* Christopher Hughes +* Carlos Horro Marcos diff -r 000000000000 -r 51e4aa55ea04 RawFileReaderLicense.md --- /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. diff -r 000000000000 -r 51e4aa55ea04 rawtools.xml --- /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 @@ + + + Perform scan data parsing, quantification and quality control analysis of Thermo Orbitrap raw mass spectrometer files. + + + 1.4.2 + 0 + + + + + + rawtools + + +> $temp_stderr) && + + cat $temp_stderr 2>&1; +]]> + + + + + True == value + +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + pq_options['pq_conditional']['matrix_select'] == "yes" + + + + + + + pq_options['mgf_conditional']['mgf_select'] == "yes" + + + + + + + pq_options['chromatogram_conditional']['chromatogram_select'] == "yes" + + + + + + + pq_options['metrics_boolean'] is True + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +**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. + + + + doi:10.1021/acs.jproteome.8b00721 + + diff -r 000000000000 -r 51e4aa55ea04 test-data/really_small.raw Binary file test-data/really_small.raw has changed diff -r 000000000000 -r 51e4aa55ea04 test-data/really_small.raw_Matrix.txt --- /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 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