| Next changeset 1:d2f75a01c428 (2020-04-28) |
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"planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" |
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README.rst RawFileReaderLicense.md macros.xml sample_filter.xml test-data/MTBLS79_mzml_triplicates.zip test-data/batch04_QC17_rep01_262.mzML test-data/batch04_QC17_rep01_262.txt test-data/batch04_QC17_rep01_262_2_263_3_264.txt test-data/batch04_QC17_rep01_262_scan5.txt test-data/batch04_QC17_rep02_263.mzML test-data/batch04_QC17_rep02_263.txt test-data/batch04_QC17_rep02_263_scan5.txt test-data/batch04_QC17_rep03_264.mzML test-data/batch04_QC17_rep03_264.txt test-data/batch04_QC17_rep03_264_scan5.txt test-data/batch04_QC18_rep01_280.txt test-data/batch04_QC18_rep02_281.txt test-data/batch04_QC18_rep03_282.txt test-data/batch04_S01_average.txt test-data/batch04_S01_rep01_247_2_248_3_249.txt test-data/batch_04_QC18_mzml_triplicate.zip test-data/filelist_merge.txt test-data/filelist_mzml_QC17_triplicate.txt test-data/filelist_mzml_triplicates.txt test-data/merged_01.h5 test-data/merged_02.h5 test-data/peak_matrix_as.txt test-data/peak_matrix_as_bf.txt test-data/peak_matrix_as_bf_compr.txt test-data/peak_matrix_as_bf_rmbs.txt test-data/peak_matrix_as_bf_sf.txt test-data/peak_matrix_as_bf_sf_compr.txt test-data/peak_matrix_as_bf_sf_mv.txt test-data/peak_matrix_as_bf_sf_mz.txt test-data/peak_matrix_as_bf_sf_mz_compr.txt test-data/peak_matrix_as_bf_sf_within.txt test-data/peak_matrix_as_bf_sf_within_compr.txt test-data/peak_matrix_as_mz.txt test-data/peak_matrix_as_mz_compr.txt test-data/peak_matrix_as_t.txt test-data/peak_matrix_hdf5_to_txt_comprehensive_snr.txt test-data/peak_matrix_hdf5_to_txt_intensity.txt test-data/peak_matrix_hdf5_to_txt_mz.txt test-data/peak_matrix_hdf5_to_txt_snr.txt test-data/pls.h5 test-data/pls_QC18.h5 test-data/pls_rf.h5 test-data/pls_scan5.h5 test-data/pm_as.h5 test-data/pm_as_bf.h5 test-data/pm_as_bf_rmbs.h5 test-data/pm_as_bf_sf.h5 test-data/pm_as_bf_sf_mv.h5 test-data/pm_as_bf_sf_within.h5 test-data/report_pls_01.xt test-data/report_pls_02.xt test-data/report_pls_rf_01.txt test-data/report_pls_rf_02.txt test-data/report_pls_rf_03.txt test-data/report_pls_scan5.txt test-data/sample_list_after_bf.txt test-data/sample_list_after_mv_filter.txt test-data/samplelist_1.txt test-data/samplelist_2.txt |
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| diff -r 000000000000 -r 415fe844ec6c README.rst --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/README.rst Sat Apr 11 16:48:56 2020 -0400 |
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| @@ -0,0 +1,66 @@ +Galaxy tool wrappers for DIMSpy +======================== +|Build Status (Travis)| |Git| |Bioconda| |License| + +Galaxy tool wrappers for Python package DIMSpy: data processing of direct-infusion mass spectrometry (DIMS)-based metabolomics and lipidomics data + +Source code: https://github.com/computational-metabolomics/dimspy + +PyPI (The Python Package Index): https://pypi.org/project/dimspy + + +Version +-------- +v1.4.0+Galaxy0 (`DIMSpy v1.4.0 <https://pypi.org/project/dimspy/1.4.0/>`_) + + +Galaxy +------- +`Galaxy <https://galaxyproject.org>`_ is an open, web-based platform for data intensive biomedical research. Whether on the free public server or your own instance, you can perform, reproduce, and share complete analyses. + + +Authors, contributors & Contacts +---------------------------------- + - Ralf J. M. Weber (r.j.weber@bham.ac.uk) - `University of Birmingham (UK) <http://www.birmingham.ac.uk/index.aspx>`_ + - Thomas N. Lawson (tnl495@bham.ac.uk) - `University of Birmingham (UK) <http://www.birmingham.ac.uk/index.aspx>`_ + - Martin R. Jones (m.r.jones.1@bham.ac.uk) - `University of Birmingham (UK) <http://www.birmingham.ac.uk/index.aspx>`_ + + +Bugs +---- +Please report any bugs that you find `here <https://github.com/computational-metabolomics/dimspy-galaxy/issues>`_. +Or fork the repository on `GitHub <https://github.com/computational-metabolomics/dimspy-galaxy/>`_ +and create a pull request (PR). We welcome all contributions, and we +will help you to make the PR if you are new to `git`. + + +Changes +------- +v1.4.0+galaxy0 + - First stable release + - Final release (Python 2-based version `DIMSpy <https://pypi.org/project/dimspy/1.4.0/>`_) + + +Licenses +------- +DIMSpy and Galaxy tools are released under the GNU General Public License v3.0 (see `LICENSE file <https://github.com/computational-metabolomics/dimspy-galaxy/blob/master/LICENSE>`_) + +**Third-party licenses and copyright** + +RawFileReader reading tool. Copyright © 2016 by Thermo Fisher Scientific, Inc. All rights reserved. See `RawFileReaderLicense <https://github.com/computational-metabolomics/dimspy/blob/master/RawFileReaderLicense.rst>`_ for licensing information. +Using DIMSpy software for processing Thermo Fisher Scientific *.raw files implies the acceptance of the RawFileReader license terms. +Anyone receiving RawFileReader as part of a larger software distribution (in the current context, as part of DIMSpy) is considered an "end user" under +section 3.3 of the RawFileReader License, and is not granted rights to redistribute RawFileReader. + + +.. |Build Status (Travis)| image:: https://img.shields.io/travis/computational-metabolomics/dimspy-galaxy.svg?style=flat&maxAge=3600&label=Travis-CI + :target: https://travis-ci.com/computational-metabolomics/dimspy-galaxy + +.. |Git| image:: https://img.shields.io/badge/repository-GitHub-blue.svg?style=flat&maxAge=3600 + :target: https://github.com/computational-metabolomics/dimspy + +.. |Bioconda| image:: https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat&maxAge=3600 + :target: http://bioconda.github.io/recipes/dimspy/README.html + +.. |License| image:: https://img.shields.io/badge/License-GPL%20v3-blue.svg + :target: https://www.gnu.org/licenses/gpl-3.0.html |
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| diff -r 000000000000 -r 415fe844ec6c RawFileReaderLicense.md --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/RawFileReaderLicense.md Sat Apr 11 16:48:56 2020 -0400 |
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| @@ -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. $1.00. YOU CANNOT RECOVER ANY OTHER DAMAGES, INCLUDING CONSEQUENTIAL, LOST PROFITS, SPECIAL, INDIRECT OR INCIDENTAL DAMAGES, EVEN IF LICENSOR IS EXPRESSLY MADE AWARE OF THE POSSIBILITY THEREOF OR IS NEGLIGENT. THIS LIMITATION APPLIES TO ANYTHING RELATED TO THIS SOFTWARE, SERVICES, CONTENT (INCLUDING CODE) ON THIRD PARTY INTERNET SITES, OR THIRD PARTY PROGRAMS, AND CLAIMS FOR BREACH OF CONTRACT, BREACH OF WARRANTY, GUARANTEE OR CONDITION, STRICT LIABILITY, NEGLIGENCE, OR OTHER TORT TO THE EXTENT PERMITTED BY APPLICABLE LAW. + +5.9. Use, duplication or disclosure of this Software by the U.S. Government is subject to the restricted rights applicable to commercial computer software (under FAR 52.227019 and DFARS 252.227-7013 or parallel regulations). The manufacturer for this purpose is Thermo Finnigan LLC, 355 River Oaks Parkway, San Jose, California 95134, U.S.A. |
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| diff -r 000000000000 -r 415fe844ec6c macros.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros.xml Sat Apr 11 16:48:56 2020 -0400 |
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| b'@@ -0,0 +1,310 @@\n+<macros>\n+ <token name="@TOOL_VERSION@">1.4.0</token>\n+ <token name="@GALAXY_TOOL_VERSION@">0</token>\n+\n+ <xml name="requirements">\n+ <requirements>\n+ <requirement type="package" version="@TOOL_VERSION@">dimspy</requirement>\n+ </requirements>\n+ </xml>\n+ \n+ <token name="@HDF5_PM_TO_TXT@">\n+ dimspy hdf5-pm-to-txt\n+ --input \'$hdf5_file_out\'\n+ --output \'$matrix_file_out\'\n+ --delimiter $delimiter\n+ --attribute_name $hdf5_to_txt.matrix_attr\n+ --representation-samples $hdf5_to_txt.representation_samples\n+ </token>\n+\n+ <token name="@HDF5_PM_TO_TXT_COMPREHENSIVE@">\n+ dimspy hdf5-pm-to-txt\n+ --input \'$hdf5_file_out\'\n+ --output \'$matrix_comprehensive_file_out\'\n+ --delimiter $delimiter\n+ --comprehensive\n+ --attribute_name $hdf5_to_txt.matrix_attr\n+ --representation-samples $hdf5_to_txt.representation_samples\n+ </token>\n+\n+ <xml name="hdf5_pm_to_txt">\n+ <section name="hdf5_to_txt" title="Show options for addtional output (*.tsv files)" expanded="False">\n+ <param name="standard" type="boolean" checked="false" truevalue="true" falsevalue="false" label="Standard output?" help="Set to "yes" to produce a "standard" Peak Matrix (i.e. m/z and intensity)."/>\n+ <param name="comprehensive" type="boolean" checked="false" truevalue="true" falsevalue="false" label="Comprehensive output?" help="Set to "yes" to produce a Peak Matrix with additional information (e.g. m/z and intensity, rsd, missing values)."/>\n+ <param name="representation_samples" type="select" label="Should the rows or columns represent the samples?" help="">\n+ <option value="rows" selected="true">Rows</option>\n+ <option value="columns">Columns</option>\n+ </param>\n+ <param name="matrix_attr" type="select" label="The Peak Matrix should contain ... values" help="">\n+ <option value="intensity" selected="true">Intensity</option>\n+ <option value="mz">m/z</option>\n+ <option value="snr">Signal-to-noise ratio (SNR)</option>\n+ </param>\n+ </section>\n+ </xml>\n+\n+ <xml name="outputs_peak_intensity_matrix">\n+ <data name="hdf5_file_out" format="h5" label="${tool.name} on ${on_string}: Peak Intensity Matrix (HDF5 file)"/>\n+ <data name="matrix_file_out" format="tsv" label="${tool.name} on ${on_string}: Peak Intensity Matrix">\n+ <filter>hdf5_to_txt["standard"] is True</filter>\n+ </data>\n+ <data name="matrix_comprehensive_file_out" format="tsv" label="${tool.name} on ${on_string}: Peak Intensity Matrix (comprehensive)" >\n+ <filter>hdf5_to_txt["comprehensive"] is True</filter>\n+ </data>\n+ </xml>\n+ \n+ <xml name="citations">\n+ <citations>\n+ <citation type="doi">10.1038/nprot.2016.156</citation>\n+ <citation type="doi">10.1038/sdata.2014.12</citation>\n+ <citation type="doi">10.1021/ac062446p</citation>\n+ <citation type="doi">10.1021/ac2001803</citation>\n+ <yield />\n+ </citations>\n+ </xml>\n+ \n+ <token name="@example_filelist@"><![CDATA[\n+\n+ +-------------------------+----------------+---------------+-----------+--------------------+-----------+\n+ | **filename** | **classLabel** | **replicate** | **batch** | **injectionOrder** | **[...]** |\n+ +-------------------------+----------------+---------------+-----------+--------------------+-----------+\n+ | sample_rep1.raw | sample | 1 | 1 | 1 | [...] |\n+ +-------------------------+----------------+---------------+-----------+--------------------+-----------+\n+ | sample_rep2.raw | sample | 2 | 1 | 2 | [...] |\n+ '..b'----+----------+----------+----------+---------+\n+ | Control_10 | 2921 | 1 | 2_3_4 | 2 | 10 | Control | | 0 | 0 | 45432.2 | 0 | ... |\n+ +-------------+----------------+------------+-----------------+----------------+---------------------+-----------------+--------------+----------+----------+----------+----------+---------+\n+ | Sample_2 | 2819 | 1 | 1_2_4 | 1 | 13 | Exposed | | 0 | 3423.3 | 0 | 0 | ... |\n+ +-------------+----------------+------------+-----------------+----------------+---------------------+-----------------+--------------+----------+----------+----------+----------+---------+\n+ | Control_5 | 2877 | 1 | 2_3_4 | 2 | 18 | Control | | 0 | 0 | 49759 | 0 | ... |\n+ +-------------+----------------+------------+-----------------+----------------+---------------------+-----------------+--------------+----------+----------+----------+----------+---------+\n+ | Control_10 | 2856 | 1 | 1_2_3 | 1 | 21 | Control | | 0 | | 39890.5 | 0 | ... |\n+ +-------------+----------------+------------+-----------------+----------------+---------------------+-----------------+--------------+----------+----------+----------+----------+---------+\n+ | Sample_20 | 2855 | 1 | 1_2_4 | 1 | 25 | Exposed | | 0 | 14563.7 | 0 | 0 | ... |\n+ +-------------+----------------+------------+-----------------+----------------+---------------------+-----------------+--------------+----------+----------+----------+----------+---------+\n+ | Sample_2 | 2814 | 1 | 1_2_4 | 1 | 29 | Exposed | | 0 | 34676.4 | 0 | 0 | ... |\n+ +-------------+----------------+------------+-----------------+----------------+---------------------+-----------------+--------------+----------+----------+----------+----------+---------+\n+ | Sample_14 | 2870 | 1 | 1_2_3 | 1 | 33 | Exposed | | 0 | 13134.9 | 0 | 521.4 | ... |\n+ +-------------+----------------+------------+-----------------+----------------+---------------------+-----------------+--------------+----------+----------+----------+----------+---------+\n+ | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... |\n+ +-------------+----------------+------------+-----------------+----------------+---------------------+-----------------+--------------+----------+----------+----------+----------+---------+\n+\n+ </token>\n+\n+\n+ <token name="@github_developers_contributors@"> \n+Github respository (source code)\n+--------------------------------\n+\n+Galaxy Tool Wrappers: https://github.com/computational-metabolomics/dimspy-galaxy/\n+DIMSpy package: https://github.com/computational-metabolomics/dimspy/\n+\n+\n+Developers and contributors\n+---------------------------\n+\n+- Ralf Weber (r.j.weber@bham.ac.uk) - University of Birmingham (UK)\n+- Martin R. Jones (m.r.jones.1@bham.ac.uk) - University of Birmingham (UK)\n+- Thomas Lawson (tnl495@bham.ac.uk) - University of Birmingham (UK)\n+\n+ </token>\n+\n+ <token name="@license@"> \n+License\n+-------\n+DIMSpy is released under the GNU General Public License v3.0 (see `LICENSE file`_)\n+\n+.. _`LICENSE file`: https://github.com/computational-metabolomics/dimspy-galaxy/blob/master/LICENSE\n+\n+ </token>\n+\n+\n+</macros>\n' |
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| diff -r 000000000000 -r 415fe844ec6c sample_filter.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/sample_filter.xml Sat Apr 11 16:48:56 2020 -0400 |
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| b'@@ -0,0 +1,155 @@\n+<tool id="dimspy_sample_filter" name="Sample Filter" version="@TOOL_VERSION@+galaxy@GALAXY_TOOL_VERSION@">\n+ <description>Remove peaks that fail to appear in x-out-of-n (biological) samples</description>\n+ <macros>\n+ <import>macros.xml</import>\n+ </macros>\n+ <expand macro="requirements" />\n+ <command detect_errors="exit_code">\n+ <![CDATA[\n+ dimspy sample-filter\n+ --input \'$hdf5_file_in\'\n+ --output \'$hdf5_file_out\'\n+ --min-fraction $min_fraction\n+ ${within}\n+ #if $rsd_threshold\n+ --rsd-threshold $rsd_threshold\n+ #end if\n+ #if $qc_label\n+ --qc-label \'$qc_label\'\n+ #end if\n+ #if $hdf5_to_txt.standard\n+ &&\n+ @HDF5_PM_TO_TXT@\n+ #end if\n+ #if $hdf5_to_txt.comprehensive\n+ &&\n+ @HDF5_PM_TO_TXT_COMPREHENSIVE@\n+ #end if\n+ ]]>\n+ </command>\n+ <inputs>\n+ <param name="hdf5_file_in" argument="--input" type="data" format="h5" label="Peak Intensity Matrix (HDF5 file)" help="" />\n+ <param name="within" argument="--within" type="boolean" checked="false" truevalue="--within" falsevalue="" label="Apply sample filter within each sample class." help="" />\n+ <param name="min_fraction" argument="--min-fraction" type="float" min="0" max="1.0" value="0.5" label="Minimum fraction" help="Minimum fraction (i.e. percentage) of samples a peak has to be present" />\n+ <param name="rsd_threshold" type="hidden" value="" label="Relative standard deviation threshold" help="Leave empty to skip this step" argument="--rsd-threshold"/>\n+ <param name="qc_label" argument="--qc-label" type="hidden" value="" label="Label for the QC sample (RSD filter only)" help="Peaks that have a larger RSD than the QC peaks are removed (Leave empty to skip this step)." >\n+ <validator type="regex" message="Value may include alphanumeric characters, underscores, dashes and spaces.">[A-Za-z0-9_\\- ]*</validator>\n+ </param>\n+ <param name="delimiter" argument="--delimiter" type="hidden" value="tab" label="" help=""/>\n+ <expand macro="hdf5_pm_to_txt" />\n+ </inputs>\n+ <outputs>\n+ <expand macro="outputs_peak_intensity_matrix" />\n+ </outputs>\n+ <tests>\n+ <test>\n+ <param name="hdf5_file_in" value="pm_as_bf.h5" ftype="h5"/>\n+ <param name="within" value=""/>\n+ <param name="min_fraction" value="0.5"/>\n+ <param name="rsd_threshold" value=""/>\n+ <param name="qc_label" value=""/>\n+ <param name="delimiter" value="tab"/>\n+ <conditional name="hdf5_to_txt">\n+ <param name="standard" value="True"/>\n+ <param name="comprehensive" value="True"/>\n+ <param name="representation_samples" value="rows"/>\n+ <param name="matrix_attr" value="intensity"/>\n+ </conditional>\n+ <output name="hdf5_file_out" file="pm_as_bf_sf.h5" ftype="h5" compare="sim_size"/>\n+ <output name="matrix_file_out" file="peak_matrix_as_bf_sf.txt" ftype="tsv" compare="sim_size"/>\n+ <output name="matrix_comprehensive_file_out" file="peak_matrix_as_bf_sf_compr.txt" ftype="tsv"/>\n+ </test>\n+ <test>\n+ <param name="hdf5_file_in" value="pm_as_bf.h5" ftype="h5"/>\n+ <param name="within" value=""/>\n+ <param name="min_fraction" value="0.5"/>\n+ <param name="rsd_threshold" value=""/>\n+ <param name="qc_label" value=""/>\n+ <param name="delimiter" value="tab"/>\n+ <conditional name="hdf5_to_txt">\n+ <param name="standard" value="True"/>\n+ <param name="comprehensive" value="True"/>\n+ <param name="representation_samples" value="columns"/>\n+ <param name="matrix_attr" value="mz"/>\n+ </conditional>\n+ <output name="hdf5_file_ou'..b' <conditional name="hdf5_to_txt">\n+ <param name="standard" value="True"/>\n+ <param name="comprehensive" value="True"/>\n+ <param name="representation_samples" value="rows"/>\n+ <param name="matrix_attr" value="intensity"/>\n+ </conditional>\n+ <output name="hdf5_file_out" file="pm_as_bf_sf_within.h5" ftype="h5" compare="sim_size"/>\n+ <output name="matrix_file_out" file="peak_matrix_as_bf_sf_within.txt" ftype="tsv"/>\n+ <output name="matrix_comprehensive_file_out" file="peak_matrix_as_bf_sf_within_compr.txt" ftype="tsv"/>\n+ </test>\n+ </tests>\n+ <help>\n+-------------\n+Sample Filter\n+-------------\n+\n+..\n+\n+----------------------------------------------\n+\n+Description\n+-----------\n+\n+Standard DIMS processing workflow: Process Scans -> Replicate Filter -> Align Samples -> [Missing values sample filter] -> Blank Filter -> **Sample Filter** -> Matrix processing -> Statistics\n+\n+|\n+\n+There are many and varied reasons why a peak may not have been detected in all study samples, including: due to having an intensity (concentration) close to the signal-to-noise limit of the system; due to having been present in only one of the study classes (e.g. a drug administered to the \xe2\x80\x98treatment\xe2\x80\x99 class samples); due to ion suppression/enhancement effects in the mass spectrometer source region; etc. The Sample Filter tool allows users to remove peaks from the input peak intensity matrix that were detected in fewer-than a user-defined minimum number of study samples. \n+\n+------------------------------------\n+\n+Parameters\n+-----------\n+\n+**Peak Intensity Matrix (HDF5 file)** (REQUIRED) - a HDF5 file containing the peak intensity matrix to undergo sample filtering.\n+\n+\n+**Apply sample filter within each sample class** (REQUIRED; default **No**) \n+\n+ - **No** - check across ALL classes simultaneously whether greater-than the user-defined \xe2\x80\x9cMinimum fraction\xe2\x80\x9d of samples contained an intensity value for a specific mass spectral peak.\n+\n+ - **Yes** - check within EACH class separately whether greater-than the user-defined \xe2\x80\x9cMinimum fraction\xe2\x80\x9d of samples contained an intensity value for a specific mass spectral peak. \n+\n+ **IMPORTANT**: if in ANY class a peak is detected in greater-than the user-defined minimum fraction of samples, then the peak is retained in the output peak matrix. For classes in which this condition is not met, the peak intensity recorded for that peak (if any) will still be presented in the output peak matrix. If no peak intensity was recorded in a sample, then a \xe2\x80\x980\xe2\x80\x99 is inserted in to the peak matrix.\n+\n+\n+**Minimum fraction** (REQUIRED, default 0.5) - a numeric value between 0 and 1 indicating the proportion of study samples in which a peak must have a recorded intensity value in order for it to be retained in the output peak intensity matrix; e.g. 0.5 means that at least 50% of samples (whether assessed across all classes, or within each class individually) must have a recorded intensity value for a specific peak in order for it to be retained in the output peak matrix.\n+\n+|\n+\n+@help_options_addtional_output@\n+\n+-------------------------------\n+\n+\n+Output file(s)\n+--------------\n+\n+**IMPORTANT** - in all outputs except for the (optional) comprehensive output, if fewer-than the user-defined \xe2\x80\x9cMinimum fraction\xe2\x80\x9d of samples (whether assessed within a class, or across all classes) had a recorded intensity value (either within or across classes) for a given peak, then that peak will be removed from the output peak matrix. Note that when assessing within classes, only one class needs to have recorded intensity values in greater-than the "Minimum fraction" of samples in order for the peak to be retained in the output peak matrix.\n+\n+@help_outputs_matrix@\n+\n+-------------------------------------\n+\n+@github_developers_contributors@\n+@license@\n+ </help>\n+ <expand macro="citations" />\n+</tool>\n+\n' |
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No newline at end of file\n' |
| b |
| diff -r 000000000000 -r 415fe844ec6c test-data/batch04_QC17_rep01_262_2_263_3_264.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/batch04_QC17_rep01_262_2_263_3_264.txt Sat Apr 11 16:48:56 2020 -0400 |
| b |
| b'@@ -0,0 +1,436 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No newline at end of file\n' |
| b |
| diff -r 000000000000 -r 415fe844ec6c test-data/batch04_QC17_rep01_262_scan5.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/batch04_QC17_rep01_262_scan5.txt Sat Apr 11 16:48:56 2020 -0400 |
| b |
| @@ -0,0 +1,16 @@ +mz intensity snr present fraction rsd occurrence purity snr_flag fraction_flag flags +118.086253583 259112.28125 108.590310357 1 1.0 nan 1.0 1.0 1 1 1 +132.075569347 292439.75 122.557383463 1 1.0 nan 1.0 1.0 1 1 1 +132.07609471 1416429.125 593.605511635 1 1.0 nan 1.0 1.0 1 1 1 +132.076675568 13824452.0 5793.63326953 1 1.0 nan 1.0 1.0 1 1 1 +132.077210117 1575695.125 660.351650744 1 1.0 nan 1.0 1.0 1 1 1 +132.10191987 313542.46875 131.401235894 1 1.0 nan 1.0 1.0 1 1 1 +133.080118521 416953.09375 174.739173443 1 1.0 nan 1.0 1.0 1 1 1 +136.04814365 456499.09375 191.312345477 1 1.0 nan 1.0 1.0 1 1 1 +140.068182551 1010273.5625 423.391431575 1 1.0 nan 1.0 1.0 1 1 1 +146.117590681 349931.4375 146.651340563 1 1.0 nan 1.0 1.0 1 1 1 +147.075656347 265543.125 111.285386466 1 1.0 nan 1.0 1.0 1 1 1 +147.076406922 1787055.75 748.929914018 1 1.0 nan 1.0 1.0 1 1 1 +148.003903094 628156.9375 263.251731901 1 1.0 nan 1.0 1.0 1 1 1 +148.060455078 628223.0 263.279417765 1 1.0 nan 1.0 1.0 1 1 1 +156.042176052 358481.28125 150.23445975 1 1.0 nan 1.0 1.0 1 1 1 \ No newline at end of file |
| b |
| diff -r 000000000000 -r 415fe844ec6c test-data/batch04_QC17_rep02_263.mzML --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/batch04_QC17_rep02_263.mzML Sat Apr 11 16:48:56 2020 -0400 |
| b |
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No newline at end of file\n' |
| b |
| diff -r 000000000000 -r 415fe844ec6c test-data/batch04_QC17_rep02_263_scan5.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/batch04_QC17_rep02_263_scan5.txt Sat Apr 11 16:48:56 2020 -0400 |
| b |
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| b |
| diff -r 000000000000 -r 415fe844ec6c test-data/batch04_QC17_rep03_264.mzML --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/batch04_QC17_rep03_264.mzML Sat Apr 11 16:48:56 2020 -0400 |
| b |
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No newline at end of file\n' |
| b |
| diff -r 000000000000 -r 415fe844ec6c test-data/batch04_QC17_rep03_264_scan5.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/batch04_QC17_rep03_264_scan5.txt Sat Apr 11 16:48:56 2020 -0400 |
| b |
| @@ -0,0 +1,16 @@ +mz intensity snr present fraction rsd occurrence purity snr_flag fraction_flag flags +118.086251246 317588.40625 119.748138639 1 1.0 nan 1.0 1.0 1 1 1 +132.075558769 336786.0625 126.986701372 1 1.0 nan 1.0 1.0 1 1 1 +132.076089225 1503678.875 566.968890702 1 1.0 nan 1.0 1.0 1 1 1 +132.076675013 16059164.0 6055.18009867 1 1.0 nan 1.0 1.0 1 1 1 +132.077209793 1795780.75 677.10721797 1 1.0 nan 1.0 1.0 1 1 1 +132.101921999 285028.125 107.471137978 1 1.0 nan 1.0 1.0 1 1 1 +133.08011769 461302.875 173.93632621 1 1.0 nan 1.0 1.0 1 1 1 +136.04813844 506052.625 190.80942095 1 1.0 nan 1.0 1.0 1 1 1 +140.068171152 1307694.5 493.072099615 1 1.0 nan 1.0 1.0 1 1 1 +146.117584259 391558.0 147.638707038 1 1.0 nan 1.0 1.0 1 1 1 +147.075637569 322906.625 121.753396966 1 1.0 nan 1.0 1.0 1 1 1 +147.07639398 2336210.5 880.878688697 1 1.0 nan 1.0 1.0 1 1 1 +148.003903003 731813.9375 275.933740404 1 1.0 nan 1.0 1.0 1 1 1 +148.060453166 780531.875 294.303058109 1 1.0 nan 1.0 1.0 1 1 1 +156.042166811 522879.53125 197.154081721 1 1.0 nan 1.0 1.0 1 1 1 \ No newline at end of file |
| b |
| diff -r 000000000000 -r 415fe844ec6c test-data/batch04_QC18_rep01_280.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/batch04_QC18_rep01_280.txt Sat Apr 11 16:48:56 2020 -0400 |
| b |
| b'@@ -0,0 +1,546 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No newline at end of file\n' |
| b |
| diff -r 000000000000 -r 415fe844ec6c test-data/batch04_QC18_rep02_281.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/batch04_QC18_rep02_281.txt Sat Apr 11 16:48:56 2020 -0400 |
| b |
| b'@@ -0,0 +1,502 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No newline at end of file\n' |
| b |
| diff -r 000000000000 -r 415fe844ec6c test-data/batch04_QC18_rep03_282.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/batch04_QC18_rep03_282.txt Sat Apr 11 16:48:56 2020 -0400 |
| b |
| b'@@ -0,0 +1,516 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No newline at end of file\n' |
| b |
| diff -r 000000000000 -r 415fe844ec6c test-data/batch04_S01_average.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/batch04_S01_average.txt Sat Apr 11 16:48:56 2020 -0400 |
| b |
| b'@@ -0,0 +1,238 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No newline at end of file\n' |
| b |
| diff -r 000000000000 -r 415fe844ec6c test-data/batch04_S01_rep01_247_2_248_3_249.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/batch04_S01_rep01_247_2_248_3_249.txt Sat Apr 11 16:48:56 2020 -0400 |
| b |
| b'@@ -0,0 +1,238 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No newline at end of file\n' |
| b |
| diff -r 000000000000 -r 415fe844ec6c test-data/batch_04_QC18_mzml_triplicate.zip |
| b |
| Binary file test-data/batch_04_QC18_mzml_triplicate.zip has changed |
| b |
| diff -r 000000000000 -r 415fe844ec6c test-data/filelist_merge.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/filelist_merge.txt Sat Apr 11 16:48:56 2020 -0400 |
| b |
| @@ -0,0 +1,14 @@ +filename classLabel +batch04_B02_rep01_301.mzML blank +batch04_B02_rep02_302.mzML blank +batch04_B02_rep03_303.mzML blank +batch04_S01_rep01_247.mzML sample +batch04_S01_rep02_248.mzML sample +batch04_S01_rep03_249.mzML sample +batch04_QC17_rep01_262.mzML QC +batch04_QC17_rep02_263.mzML QC +batch04_QC17_rep03_264.mzML QC +batch04_QC18_rep01_280.mzML QC +batch04_QC18_rep02_281.mzML QC +batch04_QC18_rep03_282.mzML QC + |
| b |
| diff -r 000000000000 -r 415fe844ec6c test-data/filelist_mzml_QC17_triplicate.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/filelist_mzml_QC17_triplicate.txt Sat Apr 11 16:48:56 2020 -0400 |
| b |
| @@ -0,0 +1,5 @@ +filename replicate injectionOrder classLabel +batch04_QC17_rep01_262.mzML 1 1 QC +batch04_QC17_rep02_263.mzML 2 2 QC +batch04_QC17_rep03_264.mzML 3 3 QC + |
| b |
| diff -r 000000000000 -r 415fe844ec6c test-data/filelist_mzml_triplicates.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/filelist_mzml_triplicates.txt Sat Apr 11 16:48:56 2020 -0400 |
| b |
| @@ -0,0 +1,10 @@ +filename replicate injectionOrder classLabel +batch04_B02_rep01_301.mzML 1 1 blank +batch04_B02_rep02_302.mzML 2 2 blank +batch04_B02_rep03_303.mzML 3 3 blank +batch04_QC17_rep01_262.mzML 1 4 QC +batch04_QC17_rep02_263.mzML 2 5 QC +batch04_QC17_rep03_264.mzML 3 6 QC +batch04_S01_rep01_247.mzML 1 7 sample +batch04_S01_rep02_248.mzML 2 8 sample +batch04_S01_rep03_249.mzML 3 9 sample |
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| diff -r 000000000000 -r 415fe844ec6c test-data/merged_01.h5 |
| b |
| Binary file test-data/merged_01.h5 has changed |
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| diff -r 000000000000 -r 415fe844ec6c test-data/merged_02.h5 |
| b |
| Binary file test-data/merged_02.h5 has changed |
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| diff -r 000000000000 -r 415fe844ec6c test-data/peak_matrix_as.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/peak_matrix_as.txt Sat Apr 11 16:48:56 2020 -0400 |
| b |
| b'@@ -0,0 +1,4 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No newline at end of file\n' |
| b |
| diff -r 000000000000 -r 415fe844ec6c test-data/peak_matrix_as_bf.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/peak_matrix_as_bf.txt Sat Apr 11 16:48:56 2020 -0400 |
| b |
| b'@@ -0,0 +1,4 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No newline at end of file\n' |
| b |
| diff -r 000000000000 -r 415fe844ec6c test-data/peak_matrix_as_bf_compr.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/peak_matrix_as_bf_compr.txt Sat Apr 11 16:48:56 2020 -0400 |
| b |
| b'@@ -0,0 +1,10 @@\n+mz\tmissing 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No newline at end of file\n' |
| b |
| diff -r 000000000000 -r 415fe844ec6c test-data/peak_matrix_as_bf_rmbs.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/peak_matrix_as_bf_rmbs.txt Sat Apr 11 16:48:56 2020 -0400 |
| b |
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No newline at end of file\n' |
| b |
| diff -r 000000000000 -r 415fe844ec6c test-data/peak_matrix_as_bf_sf.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/peak_matrix_as_bf_sf.txt Sat Apr 11 16:48:56 2020 -0400 |
| b |
| b'@@ -0,0 +1,4 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No newline at end of file\n' |
| b |
| diff -r 000000000000 -r 415fe844ec6c test-data/peak_matrix_as_bf_sf_compr.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/peak_matrix_as_bf_sf_compr.txt Sat Apr 11 16:48:56 2020 -0400 |
| b |
| b'@@ -0,0 +1,11 @@\n+mz\tmissing 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No newline at end of file\n' |
| b |
| diff -r 000000000000 -r 415fe844ec6c test-data/peak_matrix_as_bf_sf_mv.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/peak_matrix_as_bf_sf_mv.txt Sat Apr 11 16:48:56 2020 -0400 |
| b |
| b'@@ -0,0 +1,3 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8_3_249\t75661.9152344\t29157.5138579\t69397.7929688\t171352.920833\t33188.405136\t32625.4074508\t47105.5606771\t32450.8670573\t101834.059896\t45483.2532552\t37785.3966146\t87564.9338542\t449483.561458\t2035922.99167\t20506869.8\t2360257.82083\t51068.0911459\t80324.7497396\t275370.386979\t36743.0329427\t126032.773438\t40203.8609375\t148157.292969\t571837.39375\t53255.8532986\t61401.8567708\t40844.759375\t58446.9075521\t399714.763542\t33801.1007161\t35140.682487\t91467.1914063\t46092.2585937\t59685.0216146\t75417.1070313\t27727.3874024\t67655.2373698\t421695.090625\t53353.3583333\t30312.1079055\t176395.807813\t39563.0611545\t92778.5830729\t368217.978125\t2589303.19167\t39939.0320963\t50918.9657552\t142174.205729\t861803.833333\t71481.8338542\t59911.4585937\t343706.757292\t29198.8929986\t88914.2354166\t136740.753646\t85044.7835938\t40625.5928819\t314133.819287\t30864.4441821\t91214.1764915\t48946.6908045\t79060.7282631\t3998792.83144\t350395.191367\t28647.7264323\t27727.4832012\t231284.080374\t111374.140684\t950393.925663\t69493.0027423\t47600.7256846\t110465.472577\t157527.609217\t67019.9925525\t83479.8228378\t63670.523911\t628735.534091\t41198.208067\t59509.2936691\t109159.824712\t47887.6653153\t29075.0419116\t71806.3585365\t156071.826665\t68531.7921106\t57407.8662603\t376787.278014\t284592.552715\t31272.8382162\t35768.1149138\t163282.826468\t64573.8773378\t428675.28125\t42556.8198538\t28555.8812397\t540260.536616\t8535363.9053\t637690.522254\t53398.3073805\t99238.2958689\t604875.090751\t27713.4003581\t45013.9758424\t85621.5451783\t34503.327617\t27492.0458985\t50703.6310369\t27876.122526\t34248.8084902\t274465.635496\t73848.1836727\t868657.55161\t100127.096335\t107189.000769\t74855.1697246\t44218.4837536\t78263.7571812\t22698.1600329\t34816.5754464\t313890.845387\t37872.1027871\t31850.4178075\t137319.952901\t1254363.10516\t138911.806386\t22508.9044922\t96194.9694569\t71786.9004216\t83165.9085937\t22083.0000543\t44524.1178386\t53219.1476252\t563467.506151\t61452.0262835\t121461.770077\t22174.7870939\t234800.567807\t37164.1391245\t45122.2787822\t434254.057589\t37092.6867095\t25167.2324755\t24355.0742513\t163861.212078\t23160.4090286\t45369.4699901\t42101.4501798\t105624.266332\t63188.0389819\t52955.5375868\t25661.128635\t28190.3489056\t45349.4178076\t52889.2135107\t37808.0831721\t43880.4109995\t574059.297421\t57604.3296999\t78127.0883308\t42197.1028739\t41416.6056052\t110157.383321\t35188.0299851\t133851.823128\t1030898.46736\t179443.65744\t74687.6008309\t9470685.43492\t83400.0044767\t144474.419469\t1424719.79246\t475144.365873\t108507.602058\t83007.3273065\t83981.0337054\t29854.6649034\t29646.7611002\t118081.919841\t152571.8\t87342.6934896\t33841.5495567\t33583.9862155\t21959.403428\t34300.0228508\t29778.2274353\t146305.931791\t175021.826208\t38369.6506696\t125281.944211\t333543.300996\t78079.7740385\t108447.628663\t40548.6571836\t18431.7802843\t69388.9127175\t24770.5678568\t22212.354832\t154255.921804\t1063613.37901\t31026.9425061\t225684.520175\t62285.5514108\t19884.966638\t203560.854567\t60629.8506611\t23161.9888822\t40219.9194211\t29817.9132111\t32708.1322116\t84717.5342548\t24053.9997747\t24988.0221354\t20138.1137925\t21167.997496\t34787.1693209\t37938.5930489\t21314.306265\t71192.1812984\t20811.2708312\t15828.4004729\t14286.5203961\t717237.77353\t321793.089844\t196613.679988\t59718.0442291\t47967.01163\t3177844.60844\t102904.264724\t22302.9383347\t988971.083066\t231091.970987\t121895.147887\t59537.7919504\t18404.367872\t14867.3283224\t392976.702791\t107441.149189\n\\ No newline at end of file\n' |
| b |
| diff -r 000000000000 -r 415fe844ec6c test-data/peak_matrix_as_bf_sf_mz.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/peak_matrix_as_bf_sf_mz.txt Sat Apr 11 16:48:56 2020 -0400 |
| b |
| b'@@ -0,0 +1,238 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No newline at end of file\n' |
| b |
| diff -r 000000000000 -r 415fe844ec6c test-data/peak_matrix_as_bf_sf_mz_compr.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/peak_matrix_as_bf_sf_mz_compr.txt Sat Apr 11 16:48:56 2020 -0400 |
| b |
| b'@@ -0,0 +1,897 @@\n+mz\tpresent\toccurrence\tpurity\trsd_all\tblank_flag\tfraction_flag\tflags\tbatch04_B02_rep01_301_2_302_3_303\tbatch04_QC17_rep01_262_2_263_3_264\tbatch04_S01_rep01_247_2_248_3_249\n+missing 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No newline at end of file\n' |
| b |
| diff -r 000000000000 -r 415fe844ec6c test-data/peak_matrix_as_bf_sf_within.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/peak_matrix_as_bf_sf_within.txt Sat Apr 11 16:48:56 2020 -0400 |
| b |
| b'@@ -0,0 +1,4 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No newline at end of file\n' |
| b |
| diff -r 000000000000 -r 415fe844ec6c test-data/peak_matrix_as_bf_sf_within_compr.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/peak_matrix_as_bf_sf_within_compr.txt Sat Apr 11 16:48:56 2020 -0400 |
| b |
| b'@@ -0,0 +1,11 @@\n+mz\tmissing values\ttags_classLabel\ttags_untyped\t95.0854867136\t96.0477230462\t97.0647529114\t97.1011384065\t98.9954998691\t99.0804011767\t101.003118017\t101.059284262\t101.059667337\t101.777300408\t101.781524007\t102.127686063\t102.970223555\t103.038951206\t103.075318834\t104.106972509\t105.003234195\t105.090964311\t107.070230246\t107.085062328\t107.085488315\t109.100703053\t109.101137314\t111.08040236\t111.116786045\t112.052301283\t113.059666808\t113.096051485\t114.065677969\t114.066170487\t114.091302909\t115.036557299\t115.075318293\t115.111705216\t116.070599012\t116.985382141\t116.98587154\t117.054583395\t117.090968646\t118.086253653\t119.085485311\t120.980267261\t120.980786531\t121.00756219\t121.064754009\t123.013845316\t123.055288913\t123.116788199\t125.095487802\t125.096051948\t126.021940468\t127.075321735\t127.111706998\t128.010843476\t128.994858336\t129.090369007\t129.090974735\t129.127358602\t130.049222294\t130.049863468\t130.964513436\t130.965138358\t131.009836808\t131.010517825\t131.018942036\t131.070233883\t131.085482301\t131.106615399\t132.074583988\t132.075008963\t132.075567318\t132.076101717\t132.076671348\t132.077202011\t132.077992635\t132.078371418\t132.10124611\t132.101899697\t133.034572295\t133.073124466\t133.073801709\t133.078935658\t133.079460494\t133.080118687\t133.080632528\t133.085244134\t133.08588551\t133.100506766\t133.101138251\t133.105278546\t134.080996946\t134.986830233\t134.996465421\t135.002862414\t135.044024062\t135.079258734\t135.079764229\t135.08038938\t135.08097732\t135.100884718\t135.101532646\t135.116137118\t135.116787748\t136.021508699\t136.04691347\t136.047429382\t136.048119883\t136.048697166\t136.061765976\t136.073251744\t136.083096309\t136.083761924\t136.940051855\t137.029491761\t137.045065286\t137.045773739\t137.056596193\t137.057269511\t137.058997556\t137.059672042\t137.094876372\t137.095391733\t137.096043901\t137.096633067\t137.132444496\t138.091309182\t138.099413241\t139.015603989\t139.036530811\t139.072917036\t139.074630285\t139.075322774\t139.111014214\t139.111701664\t140.066921905\t140.067478979\t140.06819156\t140.068751041\t140.106954463\t140.115061283\t141.015855767\t141.05218138\t141.071577375\t141.087852717\t141.088567109\t141.090252262\t141.090971445\t141.127355825\t142.047430796\t142.086228559\t142.121881522\t142.122604088\t142.158992032\t142.94808538\t143.001525805\t143.085493568\t143.10588682\t143.106624835\t143.988083681\t144.080733504\t144.101942195\t144.980789437\t145.047092142\t145.101135997\t145.122261684\t146.116764318\t146.117593543\t146.165212548\t146.99644084\t147.075026099\t147.07563403\t147.076381496\t147.076979975\t147.080407767\t147.112840746\t147.116791771\t148.002470297\t148.003082516\t148.003895413\t148.004529246\t148.059020674\t148.059628878\t148.060463029\t148.061104039\t148.079812778\t149.002478676\t149.022503043\t149.023281113\t149.044827912\t149.059672206\t149.063819045\t149.09606266\t149.132443185\t149.999720327\t150.975955392\t150.976840465\t152.022107353\t152.106952838\t155.106635915\t156.041293988\t156.04209741\t156.076741027\t156.989754618\t157.045485596\t158.040247352\t158.117532287\t158.921989272\t159.027720801\t159.065165762\t160.133198751\t161.128432541\t162.110690219\t162.111590644\t162.112377858\t162.113089295\t163.045136563\t163.114854206\t163.115822095\t163.148118188\t163.976056014\t163.976865689\t163.977780102\t165.97362311\t165.975937112\t166.086251818\t166.950728597\t167.021727034\t167.104235181\t168.00575923\t169.058369029\t169.122302355\t170.031627109\t170.032608751\t170.117542392\t171.036000371\t171.10155643\t172.03075001\t172.131391412\t172.132189987\t172.133058362\t172.984687975\t173.080840757\t173.132465407\t173.136536346\t174.112454069\t174.89594473\t175.001680018\t175.118963541\t175.148114856\t176.102979229\t177.134608611\t179.128465135\t180.099485034\t181.064781256\t183.135542334\t184.09440398\t186.1488452\t187.125928194\t188.126027407\t188.126982017\t188.127958364\t189.052399827\t189.112130373\t189.131443965\t189.159733638\t191.040098978\t191.104244442\t191.106642836\t191.139020145\t191.143026735\t191.164168196\t193.001987153\t193.107326275\t193.122293797\t193.158657464\t194.112909063\t194.113937225\t194.115013807\t194.162041956\t195.017597191\t195.099164614\t195.118489509\t195.122688'..b'7\t46718.5139013\t37164.1391245\t45122.2787822\t434254.057589\t0.0\t37092.6867095\t34855.5437965\t0.0\t0.0\t0.0\t0.0\t0.0\t111267.406263\t0.0\t0.0\t0.0\t0.0\t115616.861148\t25167.2324755\t33594.2303323\t0.0\t24355.0742513\t0.0\t163861.212078\t23160.4090286\t21964.9843811\t0.0\t45369.4699901\t42101.4501798\t0.0\t105624.266332\t0.0\t41616.8141059\t22512.4054512\t0.0\t0.0\t0.0\t28694.5055215\t293367.556771\t0.0\t63188.0389819\t77919.4854353\t0.0\t0.0\t22437.2196777\t52955.5375868\t25661.128635\t0.0\t42299.4517795\t0.0\t0.0\t22295.725614\t0.0\t0.0\t28190.3489056\t108440.803026\t0.0\t71139.6292659\t0.0\t0.0\t0.0\t0.0\t0.0\t52879.8920449\t33920.1825983\t402248.862153\t32328.1328559\t22020.1567735\t0.0\t186318.821652\t0.0\t0.0\t22403.277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No newline at end of file\n' |
| b |
| diff -r 000000000000 -r 415fe844ec6c test-data/peak_matrix_as_mz.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/peak_matrix_as_mz.txt Sat Apr 11 16:48:56 2020 -0400 |
| b |
| b'@@ -0,0 +1,4 @@\n+mz\t95.0854867136\t96.0477230462\t97.0647529114\t97.1011384065\t98.9954998691\t99.0804011767\t101.003118017\t101.059284262\t101.059667337\t101.777300408\t101.781524007\t102.127686063\t102.970223555\t103.038951206\t103.075318834\t104.106972509\t105.003234195\t105.090964311\t107.070230246\t107.085062328\t107.085488315\t109.100703053\t109.101137314\t111.08040236\t111.116786045\t112.052301283\t113.059666808\t113.096051485\t114.065677969\t114.066170487\t114.091302909\t115.036557299\t115.075318293\t115.111705216\t116.070599012\t116.985382141\t116.98587154\t117.054583395\t117.090968646\t118.086253653\t119.085485311\t120.980267261\t120.980786531\t121.00756219\t121.064754009\t123.013845316\t123.055288913\t123.116788199\t125.095487802\t125.096051948\t126.021940468\t127.075321735\t127.111706998\t128.010843476\t128.994858336\t129.090369007\t129.090974735\t129.127358602\t130.049222294\t130.049863468\t130.964513436\t130.965138358\t131.009836808\t131.010517825\t131.018942036\t131.070233883\t131.085482301\t131.106615399\t132.074583988\t132.075008963\t132.075567318\t132.076101717\t132.076671348\t132.077202011\t132.077992635\t132.078371418\t132.10124611\t132.101899697\t133.034572295\t133.073124466\t133.073801709\t133.078935658\t133.079460494\t133.080118687\t133.080632528\t133.085244134\t133.08588551\t133.100506766\t133.101138251\t133.105278546\t134.080996946\t134.986830233\t134.996465421\t135.002862414\t135.044024062\t135.079258734\t135.079764229\t135.08038938\t135.08097732\t135.100884718\t135.101532646\t135.116137118\t135.116787748\t136.021508699\t136.04691347\t136.047429382\t136.048119883\t136.048697166\t136.061765976\t136.073251744\t136.083096309\t136.083761924\t136.940051855\t137.029491761\t137.045065286\t137.045773739\t137.056596193\t137.057269511\t137.058997556\t137.059672042\t137.094876372\t137.095391733\t137.096043901\t137.096633067\t137.132444496\t138.091309182\t138.099413241\t139.015603989\t139.036530811\t139.072917036\t139.074630285\t139.075322774\t139.111014214\t139.111701664\t140.066921905\t140.067478979\t140.06819156\t140.068751041\t140.106954463\t140.115061283\t141.015855767\t141.05218138\t141.071577375\t141.087852717\t141.088567109\t141.090252262\t141.090971445\t141.127355825\t142.047430796\t142.086228559\t142.121881522\t142.122604088\t142.158992032\t142.94808538\t143.001525805\t143.085493568\t143.10588682\t143.106624835\t143.988083681\t144.080733504\t144.101942195\t144.980789437\t145.047092142\t145.101135997\t145.122261684\t146.116764318\t146.117593543\t146.165212548\t146.99644084\t147.075026099\t147.07563403\t147.076381496\t147.076979975\t147.080407767\t147.112840746\t147.116791771\t148.002470297\t148.003082516\t148.003895413\t148.004529246\t148.059020674\t148.059628878\t148.060463029\t148.061104039\t148.079812778\t149.002478676\t149.022503043\t149.023281113\t149.044827912\t149.059672206\t149.063819045\t149.09606266\t149.132443185\t149.999720327\t150.975955392\t150.976840465\t152.022107353\t152.106952838\t155.106635915\t156.041293988\t156.04209741\t156.076741027\t156.989754618\t157.045485596\t158.040247352\t158.117532287\t158.921989272\t159.027720801\t159.065165762\t160.133198751\t161.128432541\t162.110690219\t162.111590644\t162.112377858\t162.113089295\t163.045136563\t163.114854206\t163.115822095\t163.148118188\t163.976056014\t163.976865689\t163.977780102\t165.97362311\t165.975937112\t166.086251818\t166.950728597\t167.021727034\t167.104235181\t168.00575923\t169.058369029\t169.122302355\t170.031627109\t170.032608751\t170.117542392\t171.036000371\t171.10155643\t172.03075001\t172.131391412\t172.132189987\t172.133058362\t172.984687975\t173.080840757\t173.132465407\t173.136536346\t174.112454069\t174.89594473\t175.001680018\t175.118963541\t175.148114856\t176.102979229\t177.134608611\t179.128465135\t180.099485034\t181.064781256\t183.135542334\t184.09440398\t186.1488452\t187.125928194\t188.126027407\t188.126982017\t188.127958364\t189.052399827\t189.112130373\t189.131443965\t189.159733638\t191.040098978\t191.104244442\t191.106642836\t191.139020145\t191.143026735\t191.164168196\t193.001987153\t193.107326275\t193.122293797\t193.158657464\t194.112909063\t194.113937225\t194.115013807\t194.162041956\t195.017597191\t195.099164614\t195.118489509\t195.122688638\t195.137953706\t195.174329384\t196.093111731'..b'45101195\t249.045247385\t249.153255588\t249.155420706\t0.0\t250.158789317\t250.213845847\t0.0\t0.0\t0.0\t0.0\t0.0\t254.247533265\t0.0\t0.0\t0.0\t0.0\t256.263179588\t257.041913932\t257.091126293\t0.0\t258.109823957\t0.0\t260.185324487\t260.196573871\t261.188683931\t0.0\t262.128216617\t262.16460197\t0.0\t263.145926453\t0.0\t263.236647595\t264.172129098\t0.0\t0.0\t0.0\t265.250038827\t265.252251512\t0.0\t266.187758572\t266.255625979\t0.0\t0.0\t268.263174107\t269.08772033\t270.109874888\t0.0\t270.278807885\t0.0\t0.0\t273.005664599\t0.0\t0.0\t276.1802052\t276.229422561\t0.0\t278.245081352\t0.0\t0.0\t0.0\t0.0\t0.0\t280.263139386\t282.276325668\t282.278750921\t283.282130163\t284.294422258\t0.0\t292.203326231\t0.0\t0.0\t292.2606964\t293.071370521\t293.206676616\t0.0\t296.065995008\t0.0\t0.0\t0.0\t0.0\t298.992898459\t0.0\t0.0\t302.242399929\t302.245428093\t303.24878925\t0.0\t304.260752744\t304.263413947\t0.0\t305.264411781\t306.219393536\t0.0\t306.267785589\t0.0\t0.0\t0.0\t307.04384865\t0.0\t308.047278029\t308.091094314\t0.0\t308.235022494\t309.042061331\t310.047025746\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t316.203748156\t0.0\t316.320989966\t317.114987803\t318.213669955\t318.215895358\t318.219220098\t0.0\t318.240338563\t319.222752972\t0.0\t0.0\t320.217554344\t320.224871533\t0.0\t320.229134825\t320.231111598\t320.234519196\t320.241626804\t0.0\t320.255685787\t320.974811232\t0.0\t321.232197081\t321.234786853\t321.238176947\t0.0\t0.0\t322.229522709\t322.233119641\t322.241737876\t322.250687978\t0.0\t323.236505464\t0.0\t326.948386194\t0.0\t328.067250132\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t332.028913499\t0.0\t0.0\t0.0\t334.214273542\t0.0\t334.250668262\t334.271616498\t0.0\t0.0\t336.229929268\t0.0\t336.948764624\t0.0\t0.0\t338.341734428\t0.0\t0.0\t0.0\t0.0\t346.047033578\t348.070427363\t0.0\t348.266379527\t0.0\t350.25403947\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t366.203836216\t0.0\t0.0\t0.0\t0.0\t368.219386882\t0.0\t369.22284541\t0.0\t0.0\t370.052050654\t0.0\t370.247962938\t0.0\t371.326452665\t372.206249404\t372.245046935\t372.329856912\t0.0\t374.203335574\t0.0\t0.0\t376.297232822\t377.300657538\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t384.206323385\t0.0\t385.316989323\t386.025874125\t386.221768966\t0.0\t0.0\t0.0\t387.225262028\t0.0\t387.332638188\t0.0\t388.218983046\t389.222358733\t0.0\t0.0\t0.0\t393.358426888\t394.279817501\t0.0\t395.337633663\t0.0\t396.308075518\t396.341053427\t0.0\t398.020297889\t398.032874064\t0.0\t0.0\t0.0\t399.357767697\t400.157203497\t0.0\t0.0\t407.293469086\t408.007897242\t408.020525014\t408.308085494\t408.951037638\t0.0\t0.0\t409.161823425\t0.0\t0.0\t0.0\t0.0\t411.332645717\t413.348274197\t413.373403903\t414.006828619\t0.0\t415.156868323\t416.084280734\t423.981765103\t424.281866106\t0.0\t425.135298418\t425.285292567\t426.138881798\t0.0\t427.13386107\t427.142901643\t0.0\t429.262746682\t435.061172652\t435.330083765\t435.988638501\t0.0\t0.0\t443.233520419\t0.0\t445.248985812\t445.98895613\t446.252511258\t0.0\t450.329735454\t451.962532082\t453.068896429\t453.112601976\t0.0\t0.0\t454.04005321\t0.0\t457.042996949\t461.332795944\t0.0\t461.962809831\t0.0\t467.23109072\t0.0\t0.0\t469.055315064\t0.0\t0.0\t469.410670251\t470.013885023\t0.0\t471.061108818\t471.13283571\t0.0\t0.0\t473.01699606\t0.0\t0.0\t0.0\t476.227413736\t0.0\t0.0\t479.335260946\t0.0\t0.0\t483.017348311\t483.075303021\t0.0\t483.944760702\t484.311374779\t484.323911019\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t499.918623596\t0.0\t0.0\t0.0\t0.0\t0.0\t515.413178882\t0.0\t0.0\t516.416626946\t0.0\t517.396435931\t0.0\t0.0\t518.250004364\t0.0\t519.253388986\t519.295091303\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t527.183407917\t531.408057826\t0.0\t0.0\t0.0\t0.0\t532.439740342\t533.249741237\t0.0\t0.0\t535.520104813\t537.378500181\t537.394422417\t537.535644564\t0.0\t538.398326377\t0.0\t0.0\t0.0\t539.391034626\t539.401891838\t0.0\t0.0\t0.0\t545.40662442\t545.423134445\t546.42664666\t547.419387343\t547.430522439\t547.460189893\t548.285476369\t549.289092376\t0.0\t550.360250738\t553.348894953\t553.367647289\t0.0\t553.376284114\t0.0\t553.388587287\t0.0\t554.278572222\t554.35522838\t554.371478456\t0.0\t554.393049185\t0.0\t555.366533294\t555.374371686\t0.0\t556.370106746\t0.0\t557.073628299\t557.09505812\t557.501974295\t558.505341074\t559.151249619\t559.517386251\t561.535808365\t563.551216499\t564.554790108\t569.345464898\t569.363508407\t570.367357412\t571.361841884\n\\ No newline at end of file\n' |
| b |
| diff -r 000000000000 -r 415fe844ec6c test-data/peak_matrix_as_mz_compr.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/peak_matrix_as_mz_compr.txt Sat Apr 11 16:48:56 2020 -0400 |
| b |
| b'@@ -0,0 +1,9 @@\n+mz\tmissing values\ttags_injectionOrder\ttags_classLabel\ttags_replicates\ttags_untyped\t95.0854867136\t96.0477230462\t97.0647529114\t97.1011384065\t98.9954998691\t99.0804011767\t101.003118017\t101.059284262\t101.059667337\t101.777300408\t101.781524007\t102.127686063\t102.970223555\t103.038951206\t103.075318834\t104.106972509\t105.003234195\t105.090964311\t107.070230246\t107.085062328\t107.085488315\t109.100703053\t109.101137314\t111.08040236\t111.116786045\t112.052301283\t113.059666808\t113.096051485\t114.065677969\t114.066170487\t114.091302909\t115.036557299\t115.075318293\t115.111705216\t116.070599012\t116.985382141\t116.98587154\t117.054583395\t117.090968646\t118.086253653\t119.085485311\t120.980267261\t120.980786531\t121.00756219\t121.064754009\t123.013845316\t123.055288913\t123.116788199\t125.095487802\t125.096051948\t126.021940468\t127.075321735\t127.111706998\t128.010843476\t128.994858336\t129.090369007\t129.090974735\t129.127358602\t130.049222294\t130.049863468\t130.964513436\t130.965138358\t131.009836808\t131.010517825\t131.018942036\t131.070233883\t131.085482301\t131.106615399\t132.074583988\t132.075008963\t132.075567318\t132.076101717\t132.076671348\t132.077202011\t132.077992635\t132.078371418\t132.10124611\t132.101899697\t133.034572295\t133.073124466\t133.073801709\t133.078935658\t133.079460494\t133.080118687\t133.080632528\t133.085244134\t133.08588551\t133.100506766\t133.101138251\t133.105278546\t134.080996946\t134.986830233\t134.996465421\t135.002862414\t135.044024062\t135.079258734\t135.079764229\t135.08038938\t135.08097732\t135.100884718\t135.101532646\t135.116137118\t135.116787748\t136.021508699\t136.04691347\t136.047429382\t136.048119883\t136.048697166\t136.061765976\t136.073251744\t136.083096309\t136.083761924\t136.940051855\t137.029491761\t137.045065286\t137.045773739\t137.056596193\t137.057269511\t137.058997556\t137.059672042\t137.094876372\t137.095391733\t137.096043901\t137.096633067\t137.132444496\t138.091309182\t138.099413241\t139.015603989\t139.036530811\t139.072917036\t139.074630285\t139.075322774\t139.111014214\t139.111701664\t140.066921905\t140.067478979\t140.06819156\t140.068751041\t140.106954463\t140.115061283\t141.015855767\t141.05218138\t141.071577375\t141.087852717\t141.088567109\t141.090252262\t141.090971445\t141.127355825\t142.047430796\t142.086228559\t142.121881522\t142.122604088\t142.158992032\t142.94808538\t143.001525805\t143.085493568\t143.10588682\t143.106624835\t143.988083681\t144.080733504\t144.101942195\t144.980789437\t145.047092142\t145.101135997\t145.122261684\t146.116764318\t146.117593543\t146.165212548\t146.99644084\t147.075026099\t147.07563403\t147.076381496\t147.076979975\t147.080407767\t147.112840746\t147.116791771\t148.002470297\t148.003082516\t148.003895413\t148.004529246\t148.059020674\t148.059628878\t148.060463029\t148.061104039\t148.079812778\t149.002478676\t149.022503043\t149.023281113\t149.044827912\t149.059672206\t149.063819045\t149.09606266\t149.132443185\t149.999720327\t150.975955392\t150.976840465\t152.022107353\t152.106952838\t155.106635915\t156.041293988\t156.04209741\t156.076741027\t156.989754618\t157.045485596\t158.040247352\t158.117532287\t158.921989272\t159.027720801\t159.065165762\t160.133198751\t161.128432541\t162.110690219\t162.111590644\t162.112377858\t162.113089295\t163.045136563\t163.114854206\t163.115822095\t163.148118188\t163.976056014\t163.976865689\t163.977780102\t165.97362311\t165.975937112\t166.086251818\t166.950728597\t167.021727034\t167.104235181\t168.00575923\t169.058369029\t169.122302355\t170.031627109\t170.032608751\t170.117542392\t171.036000371\t171.10155643\t172.03075001\t172.131391412\t172.132189987\t172.133058362\t172.984687975\t173.080840757\t173.132465407\t173.136536346\t174.112454069\t174.89594473\t175.001680018\t175.118963541\t175.148114856\t176.102979229\t177.134608611\t179.128465135\t180.099485034\t181.064781256\t183.135542334\t184.09440398\t186.1488452\t187.125928194\t188.126027407\t188.126982017\t188.127958364\t189.052399827\t189.112130373\t189.131443965\t189.159733638\t191.040098978\t191.104244442\t191.106642836\t191.139020145\t191.143026735\t191.164168196\t193.001987153\t193.107326275\t193.122293797\t193.158657464\t194.112909063\t194.113937225\t194.115013807\t194.162041956\t195.017597191\t195'..b'45101195\t249.045247385\t249.153255588\t249.155420706\t0.0\t250.158789317\t250.213845847\t0.0\t0.0\t0.0\t0.0\t0.0\t254.247533265\t0.0\t0.0\t0.0\t0.0\t256.263179588\t257.041913932\t257.091126293\t0.0\t258.109823957\t0.0\t260.185324487\t260.196573871\t261.188683931\t0.0\t262.128216617\t262.16460197\t0.0\t263.145926453\t0.0\t263.236647595\t264.172129098\t0.0\t0.0\t0.0\t265.250038827\t265.252251512\t0.0\t266.187758572\t266.255625979\t0.0\t0.0\t268.263174107\t269.08772033\t270.109874888\t0.0\t270.278807885\t0.0\t0.0\t273.005664599\t0.0\t0.0\t276.1802052\t276.229422561\t0.0\t278.245081352\t0.0\t0.0\t0.0\t0.0\t0.0\t280.263139386\t282.276325668\t282.278750921\t283.282130163\t284.294422258\t0.0\t292.203326231\t0.0\t0.0\t292.2606964\t293.0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No newline at end of file\n' |
| b |
| diff -r 000000000000 -r 415fe844ec6c test-data/peak_matrix_as_t.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/peak_matrix_as_t.txt Sat Apr 11 16:48:56 2020 -0400 |
| b |
| b'@@ -0,0 +1,894 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No newline at end of file\n' |
| b |
| diff -r 000000000000 -r 415fe844ec6c test-data/peak_matrix_hdf5_to_txt_comprehensive_snr.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/peak_matrix_hdf5_to_txt_comprehensive_snr.txt Sat Apr 11 16:48:56 2020 -0400 |
| b |
| b'@@ -0,0 +1,11 @@\n+mz\tmissing 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No newline at end of file\n' |
| b |
| diff -r 000000000000 -r 415fe844ec6c test-data/peak_matrix_hdf5_to_txt_intensity.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/peak_matrix_hdf5_to_txt_intensity.txt Sat Apr 11 16:48:56 2020 -0400 |
| b |
| b'@@ -0,0 +1,897 @@\n+mz\tpresent\toccurrence\tpurity\trsd_all\tblank_flag\tfraction_flag\tflags\tbatch04_B02_rep01_301_2_302_3_303\tbatch04_QC17_rep01_262_2_263_3_264\tbatch04_S01_rep01_247_2_248_3_249\n+missing 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No newline at end of file\n' |
| b |
| diff -r 000000000000 -r 415fe844ec6c test-data/peak_matrix_hdf5_to_txt_mz.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/peak_matrix_hdf5_to_txt_mz.txt Sat Apr 11 16:48:56 2020 -0400 |
| b |
| b'@@ -0,0 +1,4 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No newline at end of file\n' |
| b |
| diff -r 000000000000 -r 415fe844ec6c test-data/peak_matrix_hdf5_to_txt_snr.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/peak_matrix_hdf5_to_txt_snr.txt Sat Apr 11 16:48:56 2020 -0400 |
| b |
| b'@@ -0,0 +1,4 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707\t19.0299005103\t14.8620174687\t154.679537445\t42.921133024\n+batch04_S01_rep01_247_2_248_3_249\t29.1450101692\t11.4029541309\t26.6706097673\t65.9129785479\t12.8361207096\t12.5887141682\t18.1738870974\t12.5029416526\t39.2420940643\t17.5236947432\t14.5521229306\t33.7015165238\t172.921630576\t783.074503416\t7890.53014739\t908.060331335\t19.7999598644\t31.0065089557\t106.320383274\t14.1627966488\t48.5067629241\t15.4655233304\t57.0005637827\t220.002640213\t20.2645705597\t23.6425345661\t15.7389691415\t22.4742009609\t153.800490893\t12.9021969764\t13.5289343462\t35.1791189379\t17.8027145046\t22.9101033887\t29.0717840023\t10.4351781971\t26.0012626069\t162.171595168\t20.5234147547\t11.7347068919\t68.0448555761\t15.209643774\t35.7072823486\t141.614224422\t995.488692629\t15.3596100852\t19.626216186\t54.8042362232\t332.410853955\t27.5707172754\t23.0818703511\t132.401997754\t11.352292313\t34.1915179905\t52.7082207875\t32.6922781816\t16.7298237531\t129.373547053\t12.7332443974\t37.6588394362\t20.1752219396\t32.6255898833\t1649.89025387\t144.575605326\t11.8182139938\t11.4577517246\t95.4530369747\t45.9819102429\t392.376498483\t28.6812937849\t19.6600308029\t45.5710384955\t65.0245470428\t27.6596723274\t34.4479945792\t26.2370255633\t259.109789326\t16.9909428614\t24.5757517546\t45.0510309736\t19.7665266095\t12.0902301177\t29.6325758677\t64.4142199996\t28.2921152043\t23.6056160166\t155.109908421\t117.512065403\t12.7732910828\t14.759327\t67.4040483492\t26.6529754807\t176.988021752\t17.5671512792\t11.8161616815\t222.972124841\t3525.53976256\t263.377489596\t22.0258326279\t40.9965299845\t249.834282356\t11.4210228614\t18.5953076191\t35.3365523063\t14.2361444326\t11.2876774111\t20.9367772161\t11.5275722745\t14.1466575878\t113.357580204\t30.4918200742\t358.677860537\t41.2184943593\t44.2327665617\t30.9008074552\t18.2433951854\t32.3166525292\t11.7615071479\t17.9647800696\t161.862502292\t19.539131141\t16.4229752553\t70.8119997843\t646.791207011\t71.6622317938\t11.6676296228\t49.6346364686\t36.9962397464\t42.8220250099\t11.5269539356\t22.9558739192\t27.4410772485\t290.575242551\t31.6793065631\t62.6602968912\t11.4656015113\t121.121197186\t19.1667556434\t23.2561335574\t223.913527883\t19.1146764412\t13.0070937558\t12.5300643331\t84.5048169726\t11.9952981643\t23.3776659038\t21.702191176\t54.4286459454\t32.5792303817\t27.277565931\t13.2493745891\t14.5218996643\t23.3774057332\t20.3142241481\t14.5305001268\t16.8158418665\t220.080362075\t22.0781658101\t30.006752663\t16.159203984\t15.8490953533\t42.2571291115\t13.514541111\t51.2980983968\t395.004885103\t68.7928077379\t28.6226900936\t3628.29618503\t31.9664090314\t55.4092030284\t545.672030518\t181.948983687\t41.5621679602\t31.7855620533\t32.1722225497\t11.5835913921\t11.3845749449\t45.2281762965\t58.4538694971\t33.4367058724\t12.9887217159\t13.0354007449\t13.4972177977\t21.05986485\t18.2935739723\t89.8372157561\t106.444029387\t23.3553817068\t76.6293564426\t200.365390026\t47.7423326559\t66.5581176078\t24.915301286\t11.3751403225\t42.5010621501\t15.2219615383\t13.6225768138\t93.170038069\t649.769086575\t18.7622178523\t137.910560001\t38.047406797\t12.1897174967\t131.518907352\t39.1682927832\t14.9572361498\t25.9559281077\t19.2532003976\t21.1105985765\t54.7118976534\t15.1767110975\t16.1073993052\t12.9750653887\t13.6749271877\t22.4408723712\t24.5162391824\t16.3589347091\t55.7023528125\t16.274560588\t12.4047150391\t11.2490564201\t551.885046616\t247.444133255\t153.680848731\t46.6732912371\t37.7174316228\t2496.18228347\t82.0966312828\t17.4906830242\t777.190722473\t181.653269998\t95.7877629621\t46.7377488266\t14.4233930202\t11.5941650138\t305.739047439\t83.6481389716\n\\ No newline at end of file\n' |
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| diff -r 000000000000 -r 415fe844ec6c test-data/report_pls_01.xt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/report_pls_01.xt Sat Apr 11 16:48:56 2020 -0400 |
| [ |
| @@ -0,0 +1,73 @@ +filename event scans peaks median_rsd +batch04_B02_rep01_301.mzML FTMS + p ESI w SIM ms [70.00-170.00] 10 125 8.16474487133 +batch04_B02_rep01_301.mzML FTMS + p ESI w SIM ms [140.00-240.00] 10 118 7.91689453929 +batch04_B02_rep01_301.mzML FTMS + p ESI w SIM ms [210.00-310.00] 14 66 7.68607124086 +batch04_B02_rep01_301.mzML FTMS + p ESI w SIM ms [280.00-380.00] 14 59 7.3571823389 +batch04_B02_rep01_301.mzML FTMS + p ESI w SIM ms [350.00-450.00] 14 38 7.81073302387 +batch04_B02_rep01_301.mzML FTMS + p ESI w SIM ms [420.00-520.00] 12 31 7.11304069203 +batch04_B02_rep01_301.mzML FTMS + p ESI w SIM ms [490.00-590.00] 14 45 6.30005138853 +batch04_B02_rep01_301.mzML SIM-Stitch NA 482 7.76858437374 +batch04_B02_rep02_302.mzML FTMS + p ESI w SIM ms [70.00-170.00] 10 128 8.07600991574 +batch04_B02_rep02_302.mzML FTMS + p ESI w SIM ms [140.00-240.00] 10 125 8.03864926779 +batch04_B02_rep02_302.mzML FTMS + p ESI w SIM ms [210.00-310.00] 14 65 7.44888873374 +batch04_B02_rep02_302.mzML FTMS + p ESI w SIM ms [280.00-380.00] 14 61 6.29657260707 +batch04_B02_rep02_302.mzML FTMS + p ESI w SIM ms [350.00-450.00] 14 47 7.01271931319 +batch04_B02_rep02_302.mzML FTMS + p ESI w SIM ms [420.00-520.00] 12 31 7.3500419991 +batch04_B02_rep02_302.mzML FTMS + p ESI w SIM ms [490.00-590.00] 14 43 7.37566447385 +batch04_B02_rep02_302.mzML SIM-Stitch NA 500 7.68715459068 +batch04_B02_rep03_303.mzML FTMS + p ESI w SIM ms [70.00-170.00] 10 123 9.16935154458 +batch04_B02_rep03_303.mzML FTMS + p ESI w SIM ms [140.00-240.00] 10 118 7.55444375891 +batch04_B02_rep03_303.mzML FTMS + p ESI w SIM ms [210.00-310.00] 15 66 7.78351619427 +batch04_B02_rep03_303.mzML FTMS + p ESI w SIM ms [280.00-380.00] 14 57 6.27056997549 +batch04_B02_rep03_303.mzML FTMS + p ESI w SIM ms [350.00-450.00] 13 44 8.20380544323 +batch04_B02_rep03_303.mzML FTMS + p ESI w SIM ms [420.00-520.00] 12 32 8.26327800306 +batch04_B02_rep03_303.mzML FTMS + p ESI w SIM ms [490.00-590.00] 14 45 8.21592686599 +batch04_B02_rep03_303.mzML SIM-Stitch NA 485 8.03552677192 +batch04_QC17_rep01_262.mzML FTMS + p ESI w SIM ms [70.00-170.00] 10 79 7.03196696794 +batch04_QC17_rep01_262.mzML FTMS + p ESI w SIM ms [140.00-240.00] 11 80 7.76766561352 +batch04_QC17_rep01_262.mzML FTMS + p ESI w SIM ms [210.00-310.00] 14 61 8.15363335888 +batch04_QC17_rep01_262.mzML FTMS + p ESI w SIM ms [280.00-380.00] 14 54 6.06465919921 +batch04_QC17_rep01_262.mzML FTMS + p ESI w SIM ms [350.00-450.00] 13 38 6.24970496714 +batch04_QC17_rep01_262.mzML FTMS + p ESI w SIM ms [420.00-520.00] 13 19 7.42363265295 +batch04_QC17_rep01_262.mzML FTMS + p ESI w SIM ms [490.00-590.00] 13 38 7.08865209918 +batch04_QC17_rep01_262.mzML SIM-Stitch NA 369 7.18546096997 +batch04_QC17_rep02_263.mzML FTMS + p ESI w SIM ms [70.00-170.00] 10 77 7.67971252743 +batch04_QC17_rep02_263.mzML FTMS + p ESI w SIM ms [140.00-240.00] 11 76 7.40959870023 +batch04_QC17_rep02_263.mzML FTMS + p ESI w SIM ms [210.00-310.00] 14 61 8.07007716689 +batch04_QC17_rep02_263.mzML FTMS + p ESI w SIM ms [280.00-380.00] 15 53 6.56434715809 +batch04_QC17_rep02_263.mzML FTMS + p ESI w SIM ms [350.00-450.00] 13 43 6.01206175751 +batch04_QC17_rep02_263.mzML FTMS + p ESI w SIM ms [420.00-520.00] 13 19 6.89479622473 +batch04_QC17_rep02_263.mzML FTMS + p ESI w SIM ms [490.00-590.00] 13 41 6.82339923038 +batch04_QC17_rep02_263.mzML SIM-Stitch NA 370 7.32153403689 +batch04_QC17_rep03_264.mzML FTMS + p ESI w SIM ms [70.00-170.00] 10 76 7.06684475755 +batch04_QC17_rep03_264.mzML FTMS + p ESI w SIM ms [140.00-240.00] 11 77 7.70812724744 +batch04_QC17_rep03_264.mzML FTMS + p ESI w SIM ms [210.00-310.00] 14 62 7.27381932537 +batch04_QC17_rep03_264.mzML FTMS + p ESI w SIM ms [280.00-380.00] 14 56 6.85168250471 +batch04_QC17_rep03_264.mzML FTMS + p ESI w SIM ms [350.00-450.00] 13 44 8.1369518449 +batch04_QC17_rep03_264.mzML FTMS + p ESI w SIM ms [420.00-520.00] 13 22 9.04310387911 +batch04_QC17_rep03_264.mzML FTMS + p ESI w SIM ms [490.00-590.00] 13 44 8.17119973043 +batch04_QC17_rep03_264.mzML SIM-Stitch NA 381 7.63853989932 +batch04_S01_rep01_247.mzML FTMS + p ESI w SIM ms [70.00-170.00] 10 67 6.9449339373 +batch04_S01_rep01_247.mzML FTMS + p ESI w SIM ms [140.00-240.00] 12 74 7.56562141338 +batch04_S01_rep01_247.mzML FTMS + p ESI w SIM ms [210.00-310.00] 14 63 7.25018452732 +batch04_S01_rep01_247.mzML FTMS + p ESI w SIM ms [280.00-380.00] 15 51 6.83402648161 +batch04_S01_rep01_247.mzML FTMS + p ESI w SIM ms [350.00-450.00] 13 46 6.86311688031 +batch04_S01_rep01_247.mzML FTMS + p ESI w SIM ms [420.00-520.00] 13 30 7.56433662729 +batch04_S01_rep01_247.mzML FTMS + p ESI w SIM ms [490.00-590.00] 14 47 7.38328588939 +batch04_S01_rep01_247.mzML SIM-Stitch NA 378 7.20481827147 +batch04_S01_rep02_248.mzML FTMS + p ESI w SIM ms [70.00-170.00] 10 68 7.61402326633 +batch04_S01_rep02_248.mzML FTMS + p ESI w SIM ms [140.00-240.00] 11 74 6.91382809333 +batch04_S01_rep02_248.mzML FTMS + p ESI w SIM ms [210.00-310.00] 15 63 7.81020674999 +batch04_S01_rep02_248.mzML FTMS + p ESI w SIM ms [280.00-380.00] 14 52 6.67116706795 +batch04_S01_rep02_248.mzML FTMS + p ESI w SIM ms [350.00-450.00] 14 49 7.47235757299 +batch04_S01_rep02_248.mzML FTMS + p ESI w SIM ms [420.00-520.00] 13 29 9.18092932673 +batch04_S01_rep02_248.mzML FTMS + p ESI w SIM ms [490.00-590.00] 13 50 7.49743321145 +batch04_S01_rep02_248.mzML SIM-Stitch NA 385 7.44772817369 +batch04_S01_rep03_249.mzML FTMS + p ESI w SIM ms [70.00-170.00] 10 70 8.14059659419 +batch04_S01_rep03_249.mzML FTMS + p ESI w SIM ms [140.00-240.00] 11 72 6.70234634239 +batch04_S01_rep03_249.mzML FTMS + p ESI w SIM ms [210.00-310.00] 14 60 8.31220999647 +batch04_S01_rep03_249.mzML FTMS + p ESI w SIM ms [280.00-380.00] 15 51 6.64301911594 +batch04_S01_rep03_249.mzML FTMS + p ESI w SIM ms [350.00-450.00] 14 48 6.5996960655 +batch04_S01_rep03_249.mzML FTMS + p ESI w SIM ms [420.00-520.00] 13 30 7.38454762189 +batch04_S01_rep03_249.mzML FTMS + p ESI w SIM ms [490.00-590.00] 13 50 9.08654743835 +batch04_S01_rep03_249.mzML SIM-Stitch NA 381 7.56306270833 |
| b |
| diff -r 000000000000 -r 415fe844ec6c test-data/report_pls_02.xt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/report_pls_02.xt Sat Apr 11 16:48:56 2020 -0400 |
| [ |
| @@ -0,0 +1,25 @@ +filename event scans peaks median_rsd +batch04_QC18_rep01_280.mzML FTMS + p ESI w SIM ms [70.00-170.00] 10 62 9.10679576511 +batch04_QC18_rep01_280.mzML FTMS + p ESI w SIM ms [140.00-240.00] 11 66 8.37633825047 +batch04_QC18_rep01_280.mzML FTMS + p ESI w SIM ms [210.00-310.00] 14 30 13.8609519301 +batch04_QC18_rep01_280.mzML FTMS + p ESI w SIM ms [280.00-380.00] 14 43 11.9950166441 +batch04_QC18_rep01_280.mzML FTMS + p ESI w SIM ms [350.00-450.00] 13 32 10.1868114169 +batch04_QC18_rep01_280.mzML FTMS + p ESI w SIM ms [420.00-520.00] 12 15 11.2326559481 +batch04_QC18_rep01_280.mzML FTMS + p ESI w SIM ms [490.00-590.00] 13 24 14.1641211658 +batch04_QC18_rep01_280.mzML SIM-Stitch NA 272 10.8339327639 +batch04_QC18_rep02_281.mzML FTMS + p ESI w SIM ms [70.00-170.00] 10 56 10.022274693 +batch04_QC18_rep02_281.mzML FTMS + p ESI w SIM ms [140.00-240.00] 11 47 16.5074895025 +batch04_QC18_rep02_281.mzML FTMS + p ESI w SIM ms [210.00-310.00] 14 47 10.32312253 +batch04_QC18_rep02_281.mzML FTMS + p ESI w SIM ms [280.00-380.00] 14 46 7.96958465718 +batch04_QC18_rep02_281.mzML FTMS + p ESI w SIM ms [350.00-450.00] 14 30 8.39097430939 +batch04_QC18_rep02_281.mzML FTMS + p ESI w SIM ms [420.00-520.00] 12 16 9.67349503755 +batch04_QC18_rep02_281.mzML FTMS + p ESI w SIM ms [490.00-590.00] 12 27 9.46664767552 +batch04_QC18_rep02_281.mzML SIM-Stitch NA 269 10.0625229083 +batch04_QC18_rep03_282.mzML FTMS + p ESI w SIM ms [70.00-170.00] 10 69 7.5232876329 +batch04_QC18_rep03_282.mzML FTMS + p ESI w SIM ms [140.00-240.00] 11 71 7.71867980771 +batch04_QC18_rep03_282.mzML FTMS + p ESI w SIM ms [210.00-310.00] 14 50 7.01093076419 +batch04_QC18_rep03_282.mzML FTMS + p ESI w SIM ms [280.00-380.00] 14 49 7.24728641458 +batch04_QC18_rep03_282.mzML FTMS + p ESI w SIM ms [350.00-450.00] 14 39 8.26255528557 +batch04_QC18_rep03_282.mzML FTMS + p ESI w SIM ms [420.00-520.00] 13 20 8.48394726745 +batch04_QC18_rep03_282.mzML FTMS + p ESI w SIM ms [490.00-590.00] 13 41 5.46125101547 +batch04_QC18_rep03_282.mzML SIM-Stitch NA 339 7.33323994646 |
| b |
| diff -r 000000000000 -r 415fe844ec6c test-data/report_pls_rf_01.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/report_pls_rf_01.txt Sat Apr 11 16:48:56 2020 -0400 |
| b |
| @@ -0,0 +1,4 @@ +name peaks peaks_3oo3 median_rsd_3oo3 +batch04_B02_rep01_301_2_302_3_303 487 421 12.3353334905 +batch04_QC17_rep01_262_2_263_3_264 364 321 7.90853836608 +batch04_S01_rep01_247_2_248_3_249 383 331 5.34421558583 |
| b |
| diff -r 000000000000 -r 415fe844ec6c test-data/report_pls_rf_02.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/report_pls_rf_02.txt Sat Apr 11 16:48:56 2020 -0400 |
| b |
| @@ -0,0 +1,4 @@ +name peaks peaks_3oo3 median_rsd_3oo3 +batch04_B02_rep01_301_2_302_3_303 487 421 12.3353334905 +batch04_QC17_rep01_262_2_263_3_264 364 321 7.90853836608 +batch04_S01_rep01_247_2_248_3_249 383 331 5.34421558583 |
| b |
| diff -r 000000000000 -r 415fe844ec6c test-data/report_pls_rf_03.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/report_pls_rf_03.txt Sat Apr 11 16:48:56 2020 -0400 |
| b |
| @@ -0,0 +1,2 @@ +name peaks peaks_3oo3 median_rsd_3oo3 +batch04_QC17_rep01_262_2_263_3_264 15 15 8.60246934744 |
| b |
| diff -r 000000000000 -r 415fe844ec6c test-data/report_pls_scan5.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/report_pls_scan5.txt Sat Apr 11 16:48:56 2020 -0400 |
| [ |
| @@ -0,0 +1,4 @@ +filename event scans peaks median_rsd +batch04_QC17_rep01_262.mzML FTMS + p ESI w SIM ms [70.00-170.00] 1 15 nan +batch04_QC17_rep02_263.mzML FTMS + p ESI w SIM ms [70.00-170.00] 1 15 nan +batch04_QC17_rep03_264.mzML FTMS + p ESI w SIM ms [70.00-170.00] 1 15 nan |
| b |
| diff -r 000000000000 -r 415fe844ec6c test-data/sample_list_after_bf.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/sample_list_after_bf.txt Sat Apr 11 16:48:56 2020 -0400 |
| b |
| @@ -0,0 +1,3 @@ +filename injectionOrder replicates classLabel +batch04_QC17_rep01_262_2_263_3_264 4 1_2_3 QC +batch04_S01_rep01_247_2_248_3_249 7 1_2_3 sample |
| b |
| diff -r 000000000000 -r 415fe844ec6c test-data/sample_list_after_mv_filter.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/sample_list_after_mv_filter.txt Sat Apr 11 16:48:56 2020 -0400 |
| b |
| @@ -0,0 +1,3 @@ +filename classLabel +batch04_QC17_rep01_262_2_263_3_264 QC +batch04_S01_rep01_247_2_248_3_249 sample |
| b |
| diff -r 000000000000 -r 415fe844ec6c test-data/samplelist_1.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/samplelist_1.txt Sat Apr 11 16:48:56 2020 -0400 |
| b |
| @@ -0,0 +1,4 @@ +filename injectionOrder replicates classLabel +batch04_B02_rep01_301_2_302_3_303 1 1_2_3 blank +batch04_QC17_rep01_262_2_263_3_264 4 1_2_3 QC +batch04_S01_rep01_247_2_248_3_249 7 1_2_3 sample |
| b |
| diff -r 000000000000 -r 415fe844ec6c test-data/samplelist_2.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/samplelist_2.txt Sat Apr 11 16:48:56 2020 -0400 |
| b |
| @@ -0,0 +1,4 @@ +filename injectionOrder replicates classLabel +batch04_B02_rep01_301_2_302_3_303 1 1_2_3 blank +batch04_QC17_rep01_262_2_263_3_264 4 1_2_3 QC +batch04_S01_rep01_247_2_248_3_249 7 1_2_3 sample |