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Commit message:
"planemo upload commit 9639dde5737c9aa2330bb603c2299345939407cf" |
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added:
README.md docker_container_postbuild_setup_run.txt planemo_install_history.txt test_repositories.list tools/old_w4mclassfilter.xml tools/w4mclassfilter/LICENSE tools/w4mclassfilter/README tools/w4mclassfilter/quick_test.sh tools/w4mclassfilter/run_serve.sh tools/w4mclassfilter/run_test.sh tools/w4mclassfilter/test-data/exp_med1_medoid_dm.tsv tools/w4mclassfilter/test-data/exp_med1_medoid_sm.tsv tools/w4mclassfilter/test-data/exp_med1_medoid_vm.tsv tools/w4mclassfilter/test-data/expected_dataMatrix.tsv tools/w4mclassfilter/test-data/expected_sampleMetadata.tsv tools/w4mclassfilter/test-data/expected_variableMetadata.tsv tools/w4mclassfilter/test-data/input_dataMatrix.tsv tools/w4mclassfilter/test-data/input_med1_dm.tsv tools/w4mclassfilter/test-data/input_med1_sm.tsv tools/w4mclassfilter/test-data/input_med1_vm.tsv tools/w4mclassfilter/test-data/input_nofilter_dataMatrix.tsv tools/w4mclassfilter/test-data/input_sampleMetadata.tsv tools/w4mclassfilter/test-data/input_variableMetadata.tsv tools/w4mclassfilter/test-data/rangefilter_dataMatrix.tsv tools/w4mclassfilter/test-data/rangefilter_sampleMetadata.tsv tools/w4mclassfilter/test-data/rangefilter_variableMetadata.tsv tools/w4mclassfilter/test_log.txt tools/w4mclassfilter/w4mclassfilter.xml tools/w4mclassfilter/w4mclassfilter_wrapper.R |
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removed:
README test-data/expected_dataMatrix.tsv test-data/expected_sampleMetadata.tsv test-data/expected_variableMetadata.tsv test-data/input_dataMatrix.tsv test-data/input_nofilter_dataMatrix.tsv test-data/input_sampleMetadata.tsv test-data/input_variableMetadata.tsv test-data/rangefilter_dataMatrix.tsv test-data/rangefilter_sampleMetadata.tsv test-data/rangefilter_variableMetadata.tsv w4mclassfilter.xml w4mclassfilter_wrapper.R |
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| diff -r b24ca78a425b -r 1d36ecf93e67 README --- a/README Mon Sep 03 22:28:03 2018 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,8 +0,0 @@ -Galaxy Wrapper for the w4mclassfilter R Package -<https://doi.org/10.5281/zenodo.1034793> - -This is a Galaxy tool-wrapper <https://docs.galaxyproject.org/en/latest/dev/schema.htm> -to wrap the w4mclassfilter R package <https://github.com/HegemanLab/w4mclassfilter> -for use with the Workflow4Metabolomics <http://workflow4metabolomics.org/> -flavor of Galaxy <https://galaxyproject.org/>. -The tool is built with Planemo <http://planemo.readthedocs.io/en/latest/>. |
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| diff -r b24ca78a425b -r 1d36ecf93e67 README.md --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/README.md Thu Mar 11 20:44:23 2021 +0000 |
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| b'@@ -0,0 +1,238 @@\n+[](https://zenodo.org/badge/latestdoi/90571457) Latest public release\n+\n+[](https://travis-ci.org/HegemanLab/w4mclassfilter_galaxy_wrapper) Current build status for master branch on GitHub\n+\n+[Repository \'w4mclassfilter\' in Galaxy Toolshed](https://toolshed.g2.bx.psu.edu/repository?repository_id=5f24951d82ab40fa)\n+\n+# W4M Data Subset\n+\n+#### A Galaxy tool to select a subset of Workflow4Metabolomics data\n+\n+*W4M Data Subset* is [Galaxy tool-wrapper](https://docs.galaxyproject.org/en/latest/dev/schema.htm) to wrap the\n+[w4mclassfilter R package](https://github.com/HegemanLab/w4mclassfilter) for use with the\n+[Workflow4Metabolomics](http://workflow4metabolomics.org/) flavor of\n+[Galaxy](https://galaxyproject.org/).\n+This tool was developed and tested with [planemo](http://planemo.readthedocs.io/en/latest/).\n+\n+#### Author\n+\n+Arthur Eschenlauer (University of Minnesota, esch0041@umn.edu)\n+\n+#### R package wrapped by this tool\n+\n+The *w4mclassfilter* package is available from the Hegeman lab github repository [https://github.com/HegemanLab/w4mclassfilter/releases](https://github.com/HegemanLab/w4mclassfilter/releases).\n+\n+#### Tool in Galaxy Toolshed\n+\n+The "w4mclassfilter" Galaxy tool, built from this repository, is in the main Galaxy Toolshed at [https://toolshed.g2.bx.psu.edu/repository?repository_id=5f24951d82ab40fa](https://toolshed.g2.bx.psu.edu/repository?repository_id=5f24951d82ab40fa)\n+\n+#### Tool updates\n+\n+See the **NEWS** section at the bottom of this page\n+\n+## Motivation\n+\n+LC-MS metabolomics experiments seek to resolve "features", i.e., species that have distinct chromatographic retention time ("rt") and (after ionization) mass-to-charge ratio ("*m/z*" or "mz").\n+(If a chemical is fragmented or may have a variety of adducts, several features will result.)\n+Data for a sample are collected as mass-spectral intensities, each of\n+which is associated with a position on a 2D plane with dimensions of rt\n+and *m/z*. Ideally, features would be sufficiently reproducible among\n+sample-runs to distinguish features that are similar among samples from\n+those that differ.\n+\n+For liquid chromatography, the retention time for a species can vary considerably from one chromatography\n+run to the next. The Workflow4Metabolomics suite of Galaxy tools\n+(W4M, [Giacomoni *et al.*, 2014, Guitton *et al.* 2017])\n+uses the XCMS preprocessing tools [Smith *et al.*, 2006] for "retention-time correction" to\n+align features among samples. Features may be better aligned if pooled\n+samples and blanks are included.\n+\n+Multivariate statistical tools may be used to discover clusters of\n+similar samples [Thévenot *et al.*, 2015].\n+However, once retention-time alignment of features has been achieved\n+among samples in LC-MS datasets:\n+\n+- The presence of pools and blanks may confound identification and separation of sample clusters.\n+- Multivariate statistical algorithms may be impacted by missing values or dimensions that have zero variance.\n+\n+\n+## Description\n+\n+The W4M Data Subset tool selects subsets of samples, features, or data values and conditions the data for further analysis.\n+\n+- The tool takes as input the *dataMatrix*, *sampleMetadata*, and *variableMetadata* datasets produced by W4M\\\'s XCMS and CAMERA [Kuhl *et al.*, 2012] tools.\n+- The tool produces the same trio of output datasets, modified as described below.\n+\n+This tool can perform several operations to reduce the number samples or features to be analyzed (although *this should be done only in a statistically sound manner* consistent with the nature of the experiment):\n+\n+- *Sample filtering:* Samples may be selected by designating a "sample class" column in *sampleMetadata* and specifying criteria to include or exclude samples based on the contents of this column.\n+- *Feature filtering:* Features may be selected by speci'..b'+#### New features\n+\n+* Added support for filtering out features whose attributes fall outside specified ranges. For more detail, see "Variable-range filters" above.\n+\n+#### Internal modifications\n+\n+* Now uses w4mclassfilter R package v0.98.6.\n+* Now sorts sample names and feature names in output files because some statistical tools expect the same order in dataMatrix row and column names as in the corresponding metadata files.\n+\n+### Changes in version 0.98.3\n+\n+#### New features\n+\n+* Improved reference-list.\n+\n+#### Internal modifications\n+\n+* Improved input handling.\n+* Now uses w4mclassfilter R package v0.98.3, although that version has no functional implications for this tool.\n+\n+### Changes in version 0.98.1\n+\n+#### New features\n+\n+* First release - Wrap the w4mclassfilter R package that implements filtering of W4M data matrix, variable metadata, and sample metadata by class of sample.\n+* *dataMatrix* *is* modified by the tool, so it *does* appear as an output file\n+* *sampleMetadata* *is* modified by the tool, so it *does* appear as an output file\n+* *variableMetadata* *is* modified by the tool, so it *does* appear as an output file\n+\n+#### Internal modifications\n+\n+* none\n+\n+## Citations\n+\n+Benjamini, Yoav and Hochberg, Yosef (1995) **Controlling the False Discovery Rate: A Practical and Powerful Approach to Multiple Testing.** In *Journal of the royal statistical society. Series B (Methodological), 1 (57), pp. pp. 289-300.* [http://www.jstor.org/stable/2346101](http://www.jstor.org/stable/2346101)\n+\n+Kuhl, Carsten and Tautenhahn, Ralf and Böttcher, Christoph and Larson, Tony R. and Neumann, Steffen (2011). **CAMERA: An Integrated Strategy for Compound Spectra Extraction and Annotation of Liquid Chromatography/Mass Spectrometry Data Sets.** In *Analytical Chemistry, 84 (1), pp. 283-289.* [doi:10.1021/ac202450g](http://dx.doi.org/10.1021/ac202450g)\n+\n+Giacomoni, F. and Le Corguille, G. and Monsoor, M. and Landi, M. and Pericard, P. and Petera, M. and Duperier, C. and Tremblay-Franco, M. and Martin, J.-F. and Jacob, D. and *et al.* (2014). **Workflow4Metabolomics: a collaborative research infrastructure for computational metabolomics.** In *Bioinformatics, 31 (9), pp. 1493\xe2\x80\x931495.* [doi:10.1093/bioinformatics/btu813](http://dx.doi.org/10.1093/bioinformatics/btu813)\n+\n+Guitton, Yann and Tremblay-Franco, Marie and Le Corguillé, Gildas and Martin, Jean-Fran\xc3\xa7ois and Pétéra, Mélanie and Roger-Mele, Pierrick and Delabrière, Alexis and Goulitquer, Sophie and Monsoor, Misharl and Duperier, Christophe and *et al.* (2017). **Create, run, share, publish, and reference your LC\xe2\x80\x93MS, FIA\xe2\x80\x93MS, GC\xe2\x80\x93MS, and NMR data analysis workflows with the Workflow4Metabolomics 3.0 Galaxy online infrastructure for metabolomics.** In *The International Journal of Biochemistry & Cell Biology, pp. 89-101.* [doi:10.1016/j.biocel.2017.07.002](http://dx.doi.org/10.1016/j.biocel.2017.07.002)\n+\n+Smith, Colin A. and Want, Elizabeth J. and O\'Maille, Grace and Abagyan, Ruben and Siuzdak, Gary (2006). **XCMS: Processing Mass Spectrometry Data for Metabolite Profiling Using Nonlinear Peak Alignment, Matching, and Identification.** In *Analytical Chemistry, 78 (3), pp. 779\xe2\x80\x93787.* [doi:10.1021/ac051437y](http://dx.doi.org/10.1021/ac051437y)\n+\n+Thévenot, Etienne A. and Roux, Aurélie and Xu, Ying and Ezan, Eric and Junot, Christophe (2015). **Analysis of the Human Adult Urinary Metabolome Variations with Age, Body Mass Index, and Gender by Implementing a Comprehensive Workflow for Univariate and OPLS Statistical Analyses.** In *Journal of Proteome Research, 14 (8), pp. 3322\xe2\x80\x933335.* [doi:10.1021/acs.jproteome.5b00354](http://dx.doi.org/10.1021/acs.jproteome.5b00354)\n+\n+Yekutieli, Daniel and Benjamini, Yoav (2001) **The control of the false discovery rate in multiple testing under dependency.** In *The Annals of Statistics, 29 (4), pp. 1165-1188.* [doi:10.1214/aos/1013699998](http://dx.doi.org/10.1214/aos/1013699998)\n' |
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| diff -r b24ca78a425b -r 1d36ecf93e67 docker_container_postbuild_setup_run.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/docker_container_postbuild_setup_run.txt Thu Mar 11 20:44:23 2021 +0000 |
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| @@ -0,0 +1,13 @@ +virtualenv .venv # initialize the virtual environment - do this once +. .venv/bin/activate # activate the virtual environment - do this each time you start using planemo +pip install planemo # install planemo into the virtual environment - do this once +# here is where I pull my project from github - depends on ~/.ssh +mkdir src +cd src +git clone git@github.com:HegemanLab/w4mclassfilter_galaxy_wrapper.git +cd w4mclassfilter_galaxy_wrapper/ +planemo conda_init . # initialize conda for planemo - do this once +planemo conda_install . # install the package dependencies using conda resolution - do this each time the dependencies change +./run_test.sh # wrapper that mainly does: planemo test --conda_dependency_resolution w4mclassfilter.xml +./run_serve.sh # wrapper that mainly does: planemo serve --host 0.0.0.0 --conda_dependency_resolution . +planemo shed_update -t testtoolshed . # deploy to testtoolshed - depends on ~/.planemo.yml |
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| diff -r b24ca78a425b -r 1d36ecf93e67 planemo_install_history.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/planemo_install_history.txt Thu Mar 11 20:44:23 2021 +0000 |
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| @@ -0,0 +1,24 @@ +#!/bin/bash + +# abridged transcript of the steps that I used to test this wrapper + +ruby -e "$(curl -fsSL https://raw.githubusercontent.com/Linuxbrew/install/master/install)" + +sudo apt-get install build-essential + +cat >> ~/.bashrc << . +# ACE +export PATH="/home/backdoor/.linuxbrew/bin:$PATH" +export MANPATH="/home/backdoor/.linuxbrew/share/man:$MANPATH" +export INFOPATH="/home/backdoor/.linuxbrew/share/info:$INFOPATH" +. + +brew update +brew install python +brew tap galaxyproject/tap +brew install planemo + +git clone https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper.git +cd w4mclassfilter_galaxy_wrapper/ + +./run_test.sh |
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| diff -r b24ca78a425b -r 1d36ecf93e67 test-data/expected_dataMatrix.tsv --- a/test-data/expected_dataMatrix.tsv Mon Sep 03 22:28:03 2018 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,16 +0,0 @@ - HU_017 HU_034 HU_078 HU_091 HU_093 HU_099 HU_130 HU_134 HU_138 -HMDB00191 560002 575790 785428 645785 591569 960658 639437 1092885 1409045 -HMDB00208 747080 595872 3143654 4059767 1433702 5593888 2477288 3346077 4230072 -HMDB00251 368600 94936 293988 352855 767894 268331 310918 1248919 577184 -HMDB00299 250551 456162 808657 614370 250403 768004 504108 1014041 1362408 -HMDB00512 0 280560 556003 590779 209285 342532 569970 525240 246282 -HMDB00518 0 85944 129886 175800 13154 230242 440223 315368 10657 -HMDB00715 1252089 905408 5140022 2658555 814523 2558923 4184204 3865723 3236644 -HMDB01032 2569205 1604999 26222916 257139 675754 59906109 31151730 18648127 14989438 -HMDB01101 30689 52217 229568 4763576 3878773 976436 608298 1605075 72021 -HMDB01101.1 6877586 3158 4763576 3878773 976436 831937 1605075 72021 442510 -HMDB03193 76043 44943 173175 242549 57066 559869 339188 471368 262271 -HMDB04824 374028 539206 959381 605191 310260 1253319 477995 825691 1157093 -HMDB10348 47259 60885 168264 176500 76457 610110 279156 524468 451573 -HMDB13189 2644620 1661412 2755434 593863 837865 3526136 1608814 3446611 1941527 -HMDB59717 357351 301983 1028110 1530493 270027 1378535 808334 1132813 871209 |
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| diff -r b24ca78a425b -r 1d36ecf93e67 test-data/expected_sampleMetadata.tsv --- a/test-data/expected_sampleMetadata.tsv Mon Sep 03 22:28:03 2018 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,10 +0,0 @@ -sampleMetadata injectionOrder mode age bmi gender -HU_017 2 pos 41 23.03 M -HU_034 9 pos 52 23.37 M -HU_078 34 pos 46 25.18 M -HU_091 42 pos 61 26.12 M -HU_093 43 pos 53 21.71 M -HU_099 46 pos 23 21.3 M -HU_130 63 pos 33 26.06 M -HU_134 67 pos 48 22.89 M -HU_138 68 pos 42 21.88 M |
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| diff -r b24ca78a425b -r 1d36ecf93e67 test-data/expected_variableMetadata.tsv --- a/test-data/expected_variableMetadata.tsv Mon Sep 03 22:28:03 2018 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,16 +0,0 @@ -variableMetadata name mz rt -HMDB00191 loquor 650 600 -HMDB00208 loquimini 873 476 -HMDB00251 pasamur 500 423 -HMDB00299 bantur 700 500 -HMDB00512 pantur 900 543 -HMDB00518 loquoris 870 250 -HMDB00715 loquitur 725 900 -HMDB01032 loquimur 550 425 -HMDB01101 bar 150 300 -HMDB01101.1 baz 200 225 -HMDB03193 foo 100 200 -HMDB04824 loquantur 950 522 -HMDB10348 batur 300 275 -HMDB13189 baris 800 325 -HMDB59717 bamur 125 400 |
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| diff -r b24ca78a425b -r 1d36ecf93e67 test-data/input_dataMatrix.tsv --- a/test-data/input_dataMatrix.tsv Mon Sep 03 22:28:03 2018 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,17 +0,0 @@ -dataMatrix HU_017 HU_028 HU_034 HU_051 HU_060 HU_078 HU_091 HU_093 HU_099 HU_110 HU_130 HU_134 HU_138 HU_149 HU_152 HU_175 HU_178 HU_185 HU_204 HU_208 -HMDB03193 76043 412165 44943 27242 436566 173175 242549 57066 559869 3732 339188 471368 262271 127285 451270 212500 79673 NA 891129 43907 -HMDB01101 30689 6877586 52217 3158 10789748 229568 4763576 3878773 976436 831937 608298 1605075 72021 442510 1107705 1464339 31250 2724553 891129 32742 -HMDB01101 6877586 52217 3158 10789748 229568 4763576 3878773 976436 831937 608298 1605075 72021 442510 1107705 1464339 31250 2724553 72900 891129 30689 -HMDB10348 47259 544877 60885 34582 529874 168264 176500 76457 610110 16262 279156 524468 451573 591487 433529 161069 214392 13781 891129 39315 -HMDB59717 357351 1030464 301983 67604 306862 1028110 1530493 270027 1378535 289677 808334 1132813 871209 895435 715190 1563158 784738 146195 891129 239030 -HMDB00822 14627 14627 14627 14627 14627 14627 14627 14627 14627 14627 14627 14627 14627 14627 14627 14627 14627 14627 14627 14627 -HMDB13189 2644620 727587 1661412 619181 136278 2755434 593863 837865 3526136 2003278 1608814 3446611 1941527 113937 3132404 2893445 2092753 1034666 891129 841661 -HMDB00299 250551 1046138 456162 159386 1013302 808657 614370 250403 768004 242085 504108 1014041 1362408 1057660 1110050 566050 411886 142233 891129 284775 -HMDB00191 560002 771533 575790 392284 888498 785428 645785 591569 960658 910201 639437 1092885 1409045 2292023 1246459 1945577 710519 773384 891129 622898 -HMDB00518 -34236 58249 85944 NA 342102 129886 175800 13154 230242 NA 440223 315368 10657 419508 48673 28361 514579 23108 891129 73831 -HMDB00715 1252089 2547452 905408 371059 4983588 5140022 2658555 814523 2558923 859466 4184204 3865723 3236644 2615560 3820724 3577833 2295288 625924 891129 1341900 -HMDB01032 2569205 26023086 1604999 430453 8103558 26222916 257139 675754 59906109 263055 31151730 18648127 14989438 1554658 20249262 5588731 871010 15920 891129 44276 -HMDB00208 747080 13420742 595872 1172376 7172632 3143654 4059767 1433702 5593888 5402629 2477288 3346077 4230072 7621236 8960828 10335722 7037373 1574738 891129 2540044 -HMDB04824 374028 1144386 539206 178517 1046190 959381 605191 310260 1253319 477259 477995 825691 1157093 1089284 1411802 1020206 782673 346761 891129 387811 -HMDB00512 NA 319783 280560 85009 1333877 556003 590779 209285 342532 198512 569970 525240 246282 1140422 542345 1171008 827723 222953 891129 85554 -HMDB00251 368600 616555 94936 622468 180988 293988 352855 767894 268331 167246 310918 1248919 577184 10985 335711 403815 80614 63393 891129 616061 |
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| diff -r b24ca78a425b -r 1d36ecf93e67 test-data/input_nofilter_dataMatrix.tsv --- a/test-data/input_nofilter_dataMatrix.tsv Mon Sep 03 22:28:03 2018 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,16 +0,0 @@ -dataMatrix HU_017 HU_028 HU_034 HU_051 HU_060 HU_078 HU_091 HU_093 HU_099 HU_110 HU_130 HU_134 HU_138 HU_149 HU_152 HU_175 HU_178 HU_185 HU_204 HU_208 -HMDB03193 76043 412165 44943 27242 436566 173175 242549 57066 559869 3732 339188 471368 262271 127285 451270 212500 79673 NA 891129 43907 -HMDB01101 30689 6877586 52217 3158 10789748 229568 4763576 3878773 976436 831937 608298 1605075 72021 442510 1107705 1464339 31250 2724553 891129 32742 -HMDB01101 6877586 52217 3158 10789748 229568 4763576 3878773 976436 831937 608298 1605075 72021 442510 1107705 1464339 31250 2724553 72900 891129 30689 -HMDB10348 47259 544877 60885 34582 529874 168264 176500 76457 610110 16262 279156 524468 451573 591487 433529 161069 214392 13781 891129 39315 -HMDB59717 357351 1030464 301983 67604 306862 1028110 1530493 270027 1378535 289677 808334 1132813 871209 895435 715190 1563158 784738 146195 891129 239030 -HMDB00822 14627 14627 14627 14627 14627 14627 14627 14627 14627 14627 14627 14627 14627 14627 14627 14627 14627 14627 14627 14627 -HMDB00299 250551 1046138 456162 159386 1013302 808657 614370 250403 768004 242085 504108 1014041 1362408 1057660 1110050 566050 411886 142233 891129 284775 -HMDB00191 560002 771533 575790 392284 888498 785428 645785 591569 960658 910201 639437 1092885 1409045 2292023 1246459 1945577 710519 773384 891129 622898 -HMDB00518 -34236 58249 85944 NA 342102 129886 175800 13154 230242 NA 440223 315368 10657 419508 48673 28361 514579 23108 891129 73831 -HMDB00715 1252089 2547452 905408 371059 4983588 5140022 2658555 814523 2558923 859466 4184204 3865723 3236644 2615560 3820724 3577833 2295288 625924 891129 1341900 -HMDB01032 2569205 26023086 1604999 430453 8103558 26222916 257139 675754 59906109 263055 31151730 18648127 14989438 1554658 20249262 5588731 871010 15920 891129 44276 -HMDB00208 747080 13420742 595872 1172376 7172632 3143654 4059767 1433702 5593888 5402629 2477288 3346077 4230072 7621236 8960828 10335722 7037373 1574738 891129 2540044 -HMDB04824 374028 1144386 539206 178517 1046190 959381 605191 310260 1253319 477259 477995 825691 1157093 1089284 1411802 1020206 782673 346761 891129 387811 -HMDB00512 NA 319783 280560 85009 1333877 556003 590779 209285 342532 198512 569970 525240 246282 1140422 542345 1171008 827723 222953 891129 85554 -HMDB00251 368600 616555 94936 622468 180988 293988 352855 767894 268331 167246 310918 1248919 577184 10985 335711 403815 80614 63393 891129 616061 |
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| diff -r b24ca78a425b -r 1d36ecf93e67 test-data/input_sampleMetadata.tsv --- a/test-data/input_sampleMetadata.tsv Mon Sep 03 22:28:03 2018 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,21 +0,0 @@ -sampleMetadata injectionOrder mode age bmi gender -HU_017 2 pos 41 23.03 M -HU_028 7 pos 41 23.92 F -HU_034 9 pos 52 23.37 M -HU_051 20 pos 24 23.23 F -HU_060 24 pos 55 28.72 F -HU_078 34 pos 46 25.18 M -HU_091 42 pos 61 26.12 M -HU_093 43 pos 53 21.71 M -HU_099 46 pos 23 21.3 M -HU_110 53 pos 50 20.9 F -HU_130 63 pos 33 26.06 M -HU_134 67 pos 48 22.89 M -HU_138 68 pos 42 21.88 M -HU_149 72 pos 35 19.49 F -HU_152 75 pos 26 17.58 F -HU_175 87 pos 35 21.26 F -HU_178 88 pos 60 32.87 F -HU_185 95 pos 42 21.09 F -HU_204 104 pos 31 29.06 M -HU_208 106 pos 27 18.61 F |
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| diff -r b24ca78a425b -r 1d36ecf93e67 test-data/input_variableMetadata.tsv --- a/test-data/input_variableMetadata.tsv Mon Sep 03 22:28:03 2018 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,17 +0,0 @@ -variable name mz rt -HMDB03193 foo 100 200 -HMDB01101 bar 150 300 -HMDB01101 baz 200 225 -HMDB00208 loquimini 873 476 -HMDB10348 batur 300 275 -HMDB00299 bantur 700 500 -HMDB00191 loquor 650 600 -HMDB00518 loquoris 870 250 -HMDB59717 bamur 125 400 -HMDB00822 bamini 300 199 -HMDB13189 baris 800 325 -HMDB00715 loquitur 725 900 -HMDB01032 loquimur 550 425 -HMDB04824 loquantur 950 522 -HMDB00512 pantur 900 543 -HMDB00251 pasamur 500 423 |
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| diff -r b24ca78a425b -r 1d36ecf93e67 test-data/rangefilter_dataMatrix.tsv --- a/test-data/rangefilter_dataMatrix.tsv Mon Sep 03 22:28:03 2018 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,6 +0,0 @@ - HU_017 HU_028 HU_034 HU_051 HU_060 HU_078 HU_091 HU_093 HU_099 HU_110 HU_130 HU_134 HU_138 HU_149 HU_152 HU_175 HU_178 HU_185 HU_208 -HMDB00191 19.0950724540801 19.5573683394871 19.1351832076319 18.581538968171 19.7610090032025 19.5831195045026 19.3006944055142 19.1741869272827 19.8736633887651 19.7958256457729 19.2864427002132 20.0597101691826 20.4262862563728 21.1281900906526 20.2494039981067 20.8917666482316 19.438513703552 19.5608253922588 19.2486364146654 -HMDB00208 19.5109032146715 23.6779611010349 19.1846429313023 20.1610039089984 22.7740711828923 21.5840110083096 21.9529654992985 20.451313755289 22.4154199380002 22.3652301844309 21.2403301698498 21.6740392144135 22.0122507889717 22.8615935600174 23.0952006159265 23.3011358356974 22.746605551146 20.5866803867983 21.2764220576728 -HMDB01032 21.2928905785523 24.6332887213057 20.6141409677961 18.7154961966847 22.9501240553341 24.6443247870262 17.9721889132336 19.3661386209868 25.8361997953493 18.0050049466979 24.8928089492302 24.1525273990616 23.8374429574498 20.5681658146509 24.2713659930314 22.4140893053724 19.7323297568288 13.958552715431 15.4342372710269 -HMDB01101.1 22.7134708439962 15.6722319530667 11.6247954558602 23.3631578345615 17.8085620299575 22.183613575742 21.8871689158671 19.8971659609365 19.6661147561338 19.214418735272 20.6142092807528 16.1361300108053 18.7553505325418 20.079142288524 20.4818181509538 14.9315685693242 21.3775881248719 16.1536311941017 14.9054340159519 -HMDB13189 21.3346290086766 19.4727602406215 20.6639784491577 19.2400016764968 17.0561931543153 21.3938481405109 19.1797706242895 19.6763582845664 21.7496566885488 20.9339312108399 20.6175661105571 21.7167470481744 20.8887603396637 16.7978767996065 21.5788388647145 21.4643567902489 20.9969706149343 19.9807336965562 19.6828797432404 |
| b |
| diff -r b24ca78a425b -r 1d36ecf93e67 test-data/rangefilter_sampleMetadata.tsv --- a/test-data/rangefilter_sampleMetadata.tsv Mon Sep 03 22:28:03 2018 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,20 +0,0 @@ -sampleMetadata injectionOrder mode age bmi gender -HU_017 2 pos 41 23.03 M -HU_028 7 pos 41 23.92 F -HU_034 9 pos 52 23.37 M -HU_051 20 pos 24 23.23 F -HU_060 24 pos 55 28.72 F -HU_078 34 pos 46 25.18 M -HU_091 42 pos 61 26.12 M -HU_093 43 pos 53 21.71 M -HU_099 46 pos 23 21.3 M -HU_110 53 pos 50 20.9 F -HU_130 63 pos 33 26.06 M -HU_134 67 pos 48 22.89 M -HU_138 68 pos 42 21.88 M -HU_149 72 pos 35 19.49 F -HU_152 75 pos 26 17.58 F -HU_175 87 pos 35 21.26 F -HU_178 88 pos 60 32.87 F -HU_185 95 pos 42 21.09 F -HU_208 106 pos 27 18.61 F |
| b |
| diff -r b24ca78a425b -r 1d36ecf93e67 test-data/rangefilter_variableMetadata.tsv --- a/test-data/rangefilter_variableMetadata.tsv Mon Sep 03 22:28:03 2018 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,6 +0,0 @@ -variableMetadata name mz rt -HMDB00191 loquor 650 600 -HMDB00208 loquimini 873 476 -HMDB01032 loquimur 550 425 -HMDB01101.1 baz 200 225 -HMDB13189 baris 800 325 |
| b |
| diff -r b24ca78a425b -r 1d36ecf93e67 test_repositories.list --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test_repositories.list Thu Mar 11 20:44:23 2021 +0000 |
| b |
| @@ -0,0 +1,1 @@ +tools/w4mclassfilter |
| b |
| diff -r b24ca78a425b -r 1d36ecf93e67 tools/old_w4mclassfilter.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tools/old_w4mclassfilter.xml Thu Mar 11 20:44:23 2021 +0000 |
| [ |
| b'@@ -0,0 +1,1146 @@\n+<tool id="w4mclassfilter" name="W4m Data Subset" version="0.98.19">\n+ <description>Filter W4M data by values or metadata</description>\n+ <requirements>\n+ <requirement type="package" version="4.0.3">r-base</requirement>\n+ <requirement type="package" version="1.1_5">r-batch</requirement>\n+ <requirement type="package" version="0.98.19">w4mclassfilter</requirement>\n+ </requirements>\n+ <command detect_errors="aggressive"><![CDATA[\n+ unset R_HOME;\n+ if [ \'$centering\' == \'medoid\' -a \'$imputation\' == \'none\' ]; then\n+ (echo \'medoid\' centering may not be chosen with imputation \'none\' 1>&2);\n+ [ ! 1 ];\n+ else\n+ Rscript\n+ $__tool_directory__/w4mclassfilter_wrapper.R\n+ dataMatrix_in \'$dataMatrix_in\'\n+ sampleMetadata_in \'$sampleMetadata_in\'\n+ variableMetadata_in \'$variableMetadata_in\'\n+ sampleclassNames \'$sampleclassNames\'\n+ inclusive \'$inclusive\'\n+ wildcards \'$wildcards\'\n+ classnameColumn \'$classnameColumn\'\n+ samplenameColumn \'sampleMetadata\'\n+ variable_range_filter \'$variableRangeFilter\'\n+ transformation \'$transformation\'\n+ imputation \'$imputation\'\n+ dataMatrix_out \'$dataMatrix_out\'\n+ sampleMetadata_out \'$sampleMetadata_out\'\n+ variableMetadata_out \'$variableMetadata_out\'\n+ order_vrbl \'$order_vrbl\'\n+ order_smpl \'$order_smpl\'\n+ centering \'$centering\';\n+ fi\n+ ]]></command>\n+ <inputs>\n+ <param name="dataMatrix_in" format="tabular" label="Data matrix" type="data"\n+ help="Choose data-matrix file (tab-separated values with sample names in first row and feature names in first column)." />\n+ <param name="sampleMetadata_in" format="tabular" label="Sample metadata" type="data"\n+ help="Choose sample-metadata file (tab-separated values with one row per sample, sample name in first column)." />\n+ <param name="variableMetadata_in" format="tabular" label="Variable metadata" type="data"\n+ help="Choose variable-metadata file (tab-separated values with one row per feature, feature name in first column)." />\n+ <param name="classnameColumn" label="Column containing the sample-class names (or treatment names)" type="text" value = "class"\n+ help="Name the column in \'Sample metadata\' that has the values to be referenced by \'Sample-class names\' and \'Compute centers for classes\'. [default: \'class\']">\n+ <sanitizer>\n+ <valid initial="string.letters">\n+ <add preset="string.digits"/>\n+ <add value="." /> <!-- dot, period -->\n+ <add value="_" /> <!-- underscore -->\n+ </valid>\n+ </sanitizer>\n+ </param>\n+ <param name="sampleclassNames" label="Sample-class names (or patterns)" type="text" value = ""\n+ help="List of names (or patterns to match names) of sample classes to include or exclude. List should be comma-separated with no stray space characters. (Leave this empty to match no names.) [default: empty]">\n+ <sanitizer>\n+ <valid initial="string.letters">\n+ <add preset="string.digits"/>\n+ <add value="{" /> <!-- l-curb, left-curly-bracket -->\n+ <add value="|" /> <!-- pipe -->\n+ <add value="}" /> <!-- r-curb, right-curly-bracket -->\n+ <add value="$" /> <!-- dollar, dollar-sign -->\n+ <add value="(" /> <!-- left-paren -->\n+ <add value=")" /> <!-- right-paren -->\n+ <add value="*" /> <!-- splat, asterisk -->\n+ <add value="+" /> <!-- plus -->\n+ <add value="-" /> <'..b'+\n+\n+--------------------------------\n+Example with Treatment-Centering\n+--------------------------------\n+\n+This example retains only the samples that are medoids for their gender.\n+\n+**Input parameters**\n+\n++---------------------------------------------+-----------------------------------+\n+| Input Parameter | Value |\n++=============================================+===================================+\n+| Column that names the sample class | gender |\n++---------------------------------------------+-----------------------------------+\n+| Sample-class names | (Leave this field empty.) |\n++---------------------------------------------+-----------------------------------+\n+| Exclude/include named classes | filter-out |\n++---------------------------------------------+-----------------------------------+\n+| Use \'wild-cards\' or \'regular expressions\' | wild-cards |\n++---------------------------------------------+-----------------------------------+\n+| Variable range-filters | (Leave this field empty.) |\n++---------------------------------------------+-----------------------------------+\n+| Data transformation | none |\n++---------------------------------------------+-----------------------------------+\n+| Missing-value imputation | zero |\n++---------------------------------------------+-----------------------------------+\n+| Sample-sort column | gender |\n++---------------------------------------------+-----------------------------------+\n+| Feature-sort column | rt |\n++---------------------------------------------+-----------------------------------+\n+| Compute centers for classes | medoid |\n++---------------------------------------------+-----------------------------------+\n+\n+**Expected outputs**\n+\n++-------------------+----------------------------------------------------------------------------------------------------------+\n+| Expected Output | Download from URL |\n++===================+==========================================================================================================+\n+| Data matrix | https://raw.githubusercontent.com/HegemanLab/w4mclassfilter/master/tests/testthat/exp_cent_medoid_dm.tsv |\n++-------------------+----------------------------------------------------------------------------------------------------------+\n+| Sample metadata | https://raw.githubusercontent.com/HegemanLab/w4mclassfilter/master/tests/testthat/exp_cent_medoid_sm.tsv |\n++-------------------+----------------------------------------------------------------------------------------------------------+\n+| Variable metadata | https://raw.githubusercontent.com/HegemanLab/w4mclassfilter/master/tests/testthat/exp_cent_medoid_vm.tsv |\n++-------------------+----------------------------------------------------------------------------------------------------------+\n+ ]]></help>\n+ <citations>\n+ <!-- Giacomoni_2014 W4M 2.5 -->\n+ <citation type="doi">10.1093/bioinformatics/btu813</citation>\n+ <!-- Guitton_2017 W4M 3.0 -->\n+ <citation type="doi">10.1016/j.biocel.2017.07.002</citation>\n+ <!-- Kuhl_2012 CAMERA -->\n+ <citation type="doi">10.1021/ac202450g</citation>\n+ <!-- Smith_2006 XCMS -->\n+ <citation type="doi">10.1021/ac051437y</citation>\n+ <!-- Thevenot_2015 Urinary metabolome statistics -->\n+ <citation type="doi">10.1021/acs.jproteome.5b00354</citation>\n+ </citations>\n+ <!--\n+ vim:noet:sw=4:ts=4\n+--> </tool>\n' |
| b |
| diff -r b24ca78a425b -r 1d36ecf93e67 tools/w4mclassfilter/LICENSE --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tools/w4mclassfilter/LICENSE Thu Mar 11 20:44:23 2021 +0000 |
| b |
| @@ -0,0 +1,21 @@ +MIT License + +Copyright (c) 2017-2020 Adrian D. Hegeman's Laboratory + +Permission is hereby granted, free of charge, to any person obtaining a copy +of this software and associated documentation files (the "Software"), to deal +in the Software without restriction, including without limitation the rights +to use, copy, modify, merge, publish, distribute, sublicense, and/or sell +copies of the Software, and to permit persons to whom the Software is +furnished to do so, subject to the following conditions: + +The above copyright notice and this permission notice shall be included in all +copies or substantial portions of the Software. + +THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR +IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, +FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE +AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER +LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, +OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE +SOFTWARE. |
| b |
| diff -r b24ca78a425b -r 1d36ecf93e67 tools/w4mclassfilter/README --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tools/w4mclassfilter/README Thu Mar 11 20:44:23 2021 +0000 |
| b |
| @@ -0,0 +1,17 @@ +Galaxy Wrapper for the w4mclassfilter R Package +https://doi.org/10.5281/zenodo.1034793 + +This is a Galaxy tool-wrapper +https://docs.galaxyproject.org/en/latest/dev/schema.htm + +to wrap the w4mclassfilter R package +https://github.com/HegemanLab/w4mclassfilter + +for use with the Workflow4Metabolomics +https://workflow4metabolomics.org + +flavor of Galaxy +https://galaxyproject.org + +The tool is tested and deployed with Planemo +https://planemo.readthedocs.io/en/latest |
| b |
| diff -r b24ca78a425b -r 1d36ecf93e67 tools/w4mclassfilter/quick_test.sh --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tools/w4mclassfilter/quick_test.sh Thu Mar 11 20:44:23 2021 +0000 |
| [ |
| @@ -0,0 +1,13 @@ +#!/bin/bash + +# purge old output files +if [ -f test_log.txt ]; then rm test_log.txt; fi +if [ -f tool_test_output.html ]; then rm tool_test_output.html; fi +if [ -f tool_test_output.json ]; then rm tool_test_output.json; fi + +# run test and write new output files, showing progress to command line output +# planemo conda_install . +planemo test --conda_dependency_resolution w4mclassfilter.xml 2>&1 | grep -v -i observer | tee test_log.txt + +# summarize warnings and errors to command line output +grep -E "(ERROR)|(WARNING)" test_log.txt | grep -v samtools | grep -v "Dynamic Display Application links" | grep -v "twobit.loc" |
| b |
| diff -r b24ca78a425b -r 1d36ecf93e67 tools/w4mclassfilter/run_serve.sh --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tools/w4mclassfilter/run_serve.sh Thu Mar 11 20:44:23 2021 +0000 |
| b |
| @@ -0,0 +1,8 @@ +#!/bin/bash + +# run test and write new output files, showing progress to command line output +planemo conda_install . + +#planemo serve --host 0.0.0.0 --port 8389 --galaxy_root ~/planemo-dev/galaxy-dev . +planemo serve --host 0.0.0.0 . + |
| b |
| diff -r b24ca78a425b -r 1d36ecf93e67 tools/w4mclassfilter/run_test.sh --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tools/w4mclassfilter/run_test.sh Thu Mar 11 20:44:23 2021 +0000 |
| [ |
| @@ -0,0 +1,13 @@ +#!/bin/bash + +# purge old output files +if [ -f test_log.txt ]; then rm test_log.txt; fi +if [ -f tool_test_output.html ]; then rm tool_test_output.html; fi +if [ -f tool_test_output.json ]; then rm tool_test_output.json; fi + +# run test and write new output files, showing progress to command line output +planemo conda_install . +planemo test --conda_dependency_resolution w4mclassfilter.xml 2>&1 | grep -v -i observer | tee test_log.txt + +# summarize warnings and errors to command line output +grep -E "(ERROR)|(WARNING)" test_log.txt | grep -v samtools | grep -v "Dynamic Display Application links" | grep -v "twobit.loc" |
| b |
| diff -r b24ca78a425b -r 1d36ecf93e67 tools/w4mclassfilter/test-data/exp_med1_medoid_dm.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tools/w4mclassfilter/test-data/exp_med1_medoid_dm.tsv Thu Mar 11 20:44:23 2021 +0000 |
| b |
| @@ -0,0 +1,10 @@ + X1 X8 X10 X26 X27 X28 X29 X35 X37 X44 X45 X50 X80 X85 X89 X134 X160 X183 X231 X345 X353 +trtA_1 0 0.00180737321564983 0 0 0 0 0 0 0 0 0.09826970333995 0.502704391270598 0 0 0 0.103676462792297 0 0 0.219609447733449 0 0.0303803032193031 +trtA_2 0 0 0.1499611203546 0 0.171306020866901 0.7407933477417 0 0.0317311746973008 1.0677832262992 0.4890197262973 0 0.251352195635299 0 0.0285671029685997 0.04320144565955 0 0.0256247716491007 0.243708505613103 0 0.0398841868243505 0.00253982134690034 +trtA_3 0 0.0300457862235994 0.0424174908139001 0 0.342612041733801 0 0.528508602842599 0.1222967572165 0.0147975909652498 3.869505334958 0.849339292282099 0 0.1934182113026 0.6387333497781 0.0864028913191 0.0518382313961485 0.411653240176999 0.121854252806552 0.439218895466897 0.183561229851001 0 +trtB_1 0 0 0 0 1.5113745967984 0 0 0 0.0295951819304996 0 0.1965394066799 0.251352195635299 0 0 0 0 0.0256247716491007 0 0.219609447733449 0.2933301023069 0.00507964269380068 +trtB_2 0 0.220593700553497 0.124637442941602 1.086467693902 0 0 0 0.0634623493946016 0 0.978039452594601 0 0.580225894218799 0 0.0571342059371993 0.357735292121102 0.140388243320103 0.0815161028168028 0.414790130357598 0.761398854361399 0.0398841868243505 0 +trtB_3 0 0.00180737321564983 0.0424174908139001 0 0.171306020866901 0 0 0.0317311746973008 0.0147975909652498 0.4890197262973 0.09826970333995 0 0 0.0285671029685997 0.04320144565955 0.0518382313961485 0 0.121854252806552 0 0 0.00253982134690034 +trtC_1 0 0 0 0 1.8589982127458 0.268514070203597 0.0667424385274984 1.9883459973714 0.269349110340201 1.2385296023128 1.1443146127588 0.754715219586299 0.752261526391599 0.125735401747001 0.7011594009854 0.0518382313961485 0.0512495432982014 0.320143072543999 0.679179854411199 0 0.730941378584301 +trtC_2 1.900985710853 0.00180737321564983 0.0848349816278002 0 0 0 0 0 0 0.4890197262973 0 0.251352195635299 0 0.0285671029685997 0 0.244624610443701 0.0256247716491007 0.121854252806552 0 0.0797683736487009 0 +trtC_3 0 0.00361474643129966 0.0424174908139001 0 0.171306020866901 0 0 0.0317311746973008 0.0147975909652498 0 0.09826970333995 0 0 0 0.04320144565955 0 0 0 0.219609447733449 0.0398841868243505 0.00253982134690034 |
| b |
| diff -r b24ca78a425b -r 1d36ecf93e67 tools/w4mclassfilter/test-data/exp_med1_medoid_sm.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tools/w4mclassfilter/test-data/exp_med1_medoid_sm.tsv Thu Mar 11 20:44:23 2021 +0000 |
| b |
| @@ -0,0 +1,22 @@ +sampleMetadata medoid pcgroup mz rt +X1 M75T431 1 75.0246219750883 431.003601360729 +X8 M73T1061 8 72.9367161649113 1060.80034606296 +X10 M70T1043 10 70.0122929793033 1042.83709612962 +X26 M75T505 26 74.5552304268754 505.059650753422 +X27 M71T369 27 71.0488456490549 368.759546615083 +X28 M74T876_2 28 73.7524067558588 876.27549665073 +X29 M74T871 29 73.7524028205993 871.313876430572 +X35 M71T377 35 71.0488173286188 376.931518857336 +X37 M71T555 37 71.0489644640144 555.004553220191 +X44 M71T581 44 71.0490430805114 581.198136872667 +X45 M71T364 45 71.0488487473802 364.081506343325 +X50 M77T537 50 76.9819350151329 536.652145428441 +X80 M74T858 80 73.7524235616046 858.00252803859 +X85 M73T32_1 85 72.9368652358215 31.7025769021219 +X89 M71T1041 89 70.9909558511769 1041.40508992281 +X134 M71T138 134 70.7378907468715 137.798948287145 +X160 M73T1096 160 72.936874804031 1095.52504027727 +X183 M70T61 183 70.0651210994061 61.3905354181062 +X231 M74T1033 231 74.0963050198453 1033.01869720333 +X345 M74T33 345 73.5315669737491 33.3902011282139 +X353 M72T54 353 72.0807228513553 54.4048259006589 |
| b |
| diff -r b24ca78a425b -r 1d36ecf93e67 tools/w4mclassfilter/test-data/exp_med1_medoid_vm.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tools/w4mclassfilter/test-data/exp_med1_medoid_vm.tsv Thu Mar 11 20:44:23 2021 +0000 |
| b |
| @@ -0,0 +1,10 @@ +variableMetadata sample trt +trtA_1 trtA_1 A +trtA_2 trtA_2 A +trtA_3 trtA_3 A +trtB_1 trtB_1 B +trtB_2 trtB_2 B +trtB_3 trtB_3 B +trtC_1 trtC_1 C +trtC_2 trtC_2 C +trtC_3 trtC_3 C |
| b |
| diff -r b24ca78a425b -r 1d36ecf93e67 tools/w4mclassfilter/test-data/expected_dataMatrix.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tools/w4mclassfilter/test-data/expected_dataMatrix.tsv Thu Mar 11 20:44:23 2021 +0000 |
| b |
| @@ -0,0 +1,16 @@ + HU_017 HU_034 HU_078 HU_091 HU_093 HU_099 HU_130 HU_134 HU_138 +HMDB00191 560002 575790 785428 645785 591569 960658 639437 1092885 1409045 +HMDB00208 747080 595872 3143654 4059767 1433702 5593888 2477288 3346077 4230072 +HMDB00251 368600 94936 293988 352855 767894 268331 310918 1248919 577184 +HMDB00299 250551 456162 808657 614370 250403 768004 504108 1014041 1362408 +HMDB00512 525240 280560 556003 590779 209285 342532 569970 525240 246282 +HMDB00518 0 85944 129886 175800 13154 230242 440223 315368 10657 +HMDB00715 1252089 905408 5140022 2658555 814523 2558923 4184204 3865723 3236644 +HMDB01032 2569205 1604999 26222916 257139 675754 59906109 31151730 18648127 14989438 +HMDB01101 30689 52217 229568 4763576 3878773 976436 608298 1605075 72021 +HMDB01101.1 6877586 3158 4763576 3878773 976436 831937 1605075 72021 442510 +HMDB03193 76043 44943 173175 242549 57066 559869 339188 471368 262271 +HMDB04824 374028 539206 959381 605191 310260 1253319 477995 825691 1157093 +HMDB10348 47259 60885 168264 176500 76457 610110 279156 524468 451573 +HMDB13189 2644620 1661412 2755434 593863 837865 3526136 1608814 3446611 1941527 +HMDB59717 357351 301983 1028110 1530493 270027 1378535 808334 1132813 871209 |
| b |
| diff -r b24ca78a425b -r 1d36ecf93e67 tools/w4mclassfilter/test-data/expected_sampleMetadata.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tools/w4mclassfilter/test-data/expected_sampleMetadata.tsv Thu Mar 11 20:44:23 2021 +0000 |
| b |
| @@ -0,0 +1,10 @@ +sampleMetadata injectionOrder mode age bmi gender +HU_017 2 pos 41 23.03 M +HU_034 9 pos 52 23.37 M +HU_078 34 pos 46 25.18 M +HU_091 42 pos 61 26.12 M +HU_093 43 pos 53 21.71 M +HU_099 46 pos 23 21.3 M +HU_130 63 pos 33 26.06 M +HU_134 67 pos 48 22.89 M +HU_138 68 pos 42 21.88 M |
| b |
| diff -r b24ca78a425b -r 1d36ecf93e67 tools/w4mclassfilter/test-data/expected_variableMetadata.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tools/w4mclassfilter/test-data/expected_variableMetadata.tsv Thu Mar 11 20:44:23 2021 +0000 |
| b |
| @@ -0,0 +1,16 @@ +variableMetadata name mz rt +HMDB00191 loquor 650 600 +HMDB00208 loquimini 873 476 +HMDB00251 pasamur 500 423 +HMDB00299 bantur 700 500 +HMDB00512 pantur 900 543 +HMDB00518 loquoris 870 250 +HMDB00715 loquitur 725 900 +HMDB01032 loquimur 550 425 +HMDB01101 bar 150 300 +HMDB01101.1 baz 200 225 +HMDB03193 foo 100 200 +HMDB04824 loquantur 950 522 +HMDB10348 batur 300 275 +HMDB13189 baris 800 325 +HMDB59717 bamur 125 400 |
| b |
| diff -r b24ca78a425b -r 1d36ecf93e67 tools/w4mclassfilter/test-data/input_dataMatrix.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tools/w4mclassfilter/test-data/input_dataMatrix.tsv Thu Mar 11 20:44:23 2021 +0000 |
| b |
| @@ -0,0 +1,17 @@ +dataMatrix HU_017 HU_028 HU_034 HU_051 HU_060 HU_078 HU_091 HU_093 HU_099 HU_110 HU_130 HU_134 HU_138 HU_149 HU_152 HU_175 HU_178 HU_185 HU_204 HU_208 +HMDB03193 76043 412165 44943 27242 436566 173175 242549 57066 559869 3732 339188 471368 262271 127285 451270 212500 79673 NA 891129 43907 +HMDB01101 30689 6877586 52217 3158 10789748 229568 4763576 3878773 976436 831937 608298 1605075 72021 442510 1107705 1464339 31250 2724553 891129 32742 +HMDB01101 6877586 52217 3158 10789748 229568 4763576 3878773 976436 831937 608298 1605075 72021 442510 1107705 1464339 31250 2724553 72900 891129 30689 +HMDB10348 47259 544877 60885 34582 529874 168264 176500 76457 610110 16262 279156 524468 451573 591487 433529 161069 214392 13781 891129 39315 +HMDB59717 357351 1030464 301983 67604 306862 1028110 1530493 270027 1378535 289677 808334 1132813 871209 895435 715190 1563158 784738 146195 891129 239030 +HMDB00822 14627 14627 14627 14627 14627 14627 14627 14627 14627 14627 14627 14627 14627 14627 14627 14627 14627 14627 14627 14627 +HMDB13189 2644620 727587 1661412 619181 136278 2755434 593863 837865 3526136 2003278 1608814 3446611 1941527 113937 3132404 2893445 2092753 1034666 891129 841661 +HMDB00299 250551 1046138 456162 159386 1013302 808657 614370 250403 768004 242085 504108 1014041 1362408 1057660 1110050 566050 411886 142233 891129 284775 +HMDB00191 560002 771533 575790 392284 888498 785428 645785 591569 960658 910201 639437 1092885 1409045 2292023 1246459 1945577 710519 773384 891129 622898 +HMDB00518 -34236 58249 85944 NA 342102 129886 175800 13154 230242 NA 440223 315368 10657 419508 48673 28361 514579 23108 891129 73831 +HMDB00715 1252089 2547452 905408 371059 4983588 5140022 2658555 814523 2558923 859466 4184204 3865723 3236644 2615560 3820724 3577833 2295288 625924 891129 1341900 +HMDB01032 2569205 26023086 1604999 430453 8103558 26222916 257139 675754 59906109 263055 31151730 18648127 14989438 1554658 20249262 5588731 871010 15920 891129 44276 +HMDB00208 747080 13420742 595872 1172376 7172632 3143654 4059767 1433702 5593888 5402629 2477288 3346077 4230072 7621236 8960828 10335722 7037373 1574738 891129 2540044 +HMDB04824 374028 1144386 539206 178517 1046190 959381 605191 310260 1253319 477259 477995 825691 1157093 1089284 1411802 1020206 782673 346761 891129 387811 +HMDB00512 NA 319783 280560 85009 1333877 556003 590779 209285 342532 198512 569970 525240 246282 1140422 542345 1171008 827723 222953 891129 85554 +HMDB00251 368600 616555 94936 622468 180988 293988 352855 767894 268331 167246 310918 1248919 577184 10985 335711 403815 80614 63393 891129 616061 |
| b |
| diff -r b24ca78a425b -r 1d36ecf93e67 tools/w4mclassfilter/test-data/input_med1_dm.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tools/w4mclassfilter/test-data/input_med1_dm.tsv Thu Mar 11 20:44:23 2021 +0000 |
| b |
| @@ -0,0 +1,10 @@ +X M70T1043 M70T61 M71T138 M71T1041 M71T377 M71T369 M71T364 M71T555 M71T581 M72T34_1 M72T54 M72T34_3 M73T1061 M73T1044 M73T32_1 M73T1096 M73T32_2 M73T1043 M74T1042_1 M74T33 M74T871 M74T876_2 M74T858 M74T34 M74T1033 M75T34 M75T505 M75T431 M76T1040 M77T537 +trtA_1 0 0 0.103676462792297 0 0 0 0.09826970333995 0 0 0 0.0303803032193031 0 0.00180737321564983 0.174619941309 0 0 0 0 0 0 0 0 0 0 0.219609447733449 0 0 0 0.0151151439275008 0.502704391270598 +trtA_2 0.1499611203546 0.243708505613103 0 0.04320144565955 0.0317311746973008 0.171306020866901 0 1.0677832262992 0.4890197262973 0.140208039060401 0.00253982134690034 0.0563798353136988 0 0.00346576229545015 0.0285671029685997 0.0256247716491007 0.818318427514498 0.2150061358386 0.1234949545399 0.0398841868243505 0 0.7407933477417 0 0.0476545410972502 0 0.112811564993098 0 0 0 0.251352195635299 +trtA_3 0.0424174908139001 0.121854252806552 0.0518382313961485 0.0864028913191 0.1222967572165 0.342612041733801 0.849339292282099 0.0147975909652498 3.869505334958 0.285443289823299 0 0.112759670627398 0.0300457862235994 0 0.6387333497781 0.411653240176999 0.0933267742982 0.0514902142761002 0.0463451483315485 0.183561229851001 0.528508602842599 0 0.1934182113026 0.420661197739499 0.439218895466897 0.0175408561815491 0 0 0.1265423906184 0 +trtB_1 0 0 0 0 0 1.5113745967984 0.1965394066799 0.0295951819304996 0 0.280416078120801 0.00507964269380068 0 0 0.00346576229545015 0 0.0256247716491007 0.0933267742982 0 0.0463451483315485 0.2933301023069 0 0 0 0.935782704287199 0.219609447733449 0.0175408561815491 0 0 0.0151151439275008 0.251352195635299 +trtB_2 0.124637442941602 0.414790130357598 0.140388243320103 0.357735292121102 0.0634623493946016 0 0 0 0.978039452594601 0.140208039060401 0 0.0563798353136988 0.220593700553497 0.0767204072380991 0.0571342059371993 0.0815161028168028 0.446741706469403 0.0514902142761002 0 0.0398841868243505 0 0 0 0.0476545410972502 0.761398854361399 0 1.086467693902 0 0 0.580225894218799 +trtB_3 0.0424174908139001 0.121854252806552 0.0518382313961485 0.04320144565955 0.0317311746973008 0.171306020866901 0.09826970333995 0.0147975909652498 0.4890197262973 0 0.00253982134690034 0.2357122484906 0.00180737321564983 0 0.0285671029685997 0 0 0.1029804285522 0.204744259308601 0 0 0 0 0 0 0.0422615246151992 0 0 0.2218306650343 0 +trtC_1 0 0.320143072543999 0.0518382313961485 0.7011594009854 1.9883459973714 1.8589982127458 1.1443146127588 0.269349110340201 1.2385296023128 0 0.730941378584301 0.640778164724498 0 0.0069315245909003 0.125735401747001 0.0512495432982014 0 0 0 0 0.0667424385274984 0.268514070203597 0.752261526391599 0 0.679179854411199 0.0175408561815491 0 0 0.0302302878550016 0.754715219586299 +trtC_2 0.0848349816278002 0.121854252806552 0.244624610443701 0 0 0 0 0 0.4890197262973 0.513858474098299 0 0.0563798353136988 0.00180737321564983 0.00346576229545015 0.0285671029685997 0.0256247716491007 0.1866535485964 0.3576876580278 0.0926902966630969 0.0797683736487009 0 0 0 0.0953090821945004 0 0.0350817123630982 0 1.900985710853 0.0151151439275008 0.251352195635299 +trtC_3 0.0424174908139001 0 0 0.04320144565955 0.0317311746973008 0.171306020866901 0.09826970333995 0.0147975909652498 0 0.140208039060401 0.00253982134690034 0 0.00361474643129966 0 0 0 0.0933267742982 0.0514902142761002 0.0463451483315485 0.0398841868243505 0 0 0 0.0476545410972502 0.219609447733449 0 0 0 0 0 |
| b |
| diff -r b24ca78a425b -r 1d36ecf93e67 tools/w4mclassfilter/test-data/input_med1_sm.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tools/w4mclassfilter/test-data/input_med1_sm.tsv Thu Mar 11 20:44:23 2021 +0000 |
| b |
| @@ -0,0 +1,31 @@ +sampleMetadata pcgroup mz rt +M70T1043 10 70.0122929793033 1042.83709612962 +M70T61 183 70.0651210994061 61.3905354181062 +M71T138 134 70.7378907468715 137.798948287145 +M71T1041 89 70.9909558511769 1041.40508992281 +M71T377 35 71.0488173286188 376.931518857336 +M71T369 27 71.0488456490549 368.759546615083 +M71T364 45 71.0488487473802 364.081506343325 +M71T555 37 71.0489644640144 555.004553220191 +M71T581 44 71.0490430805114 581.198136872667 +M72T34_1 345 71.529455784918 33.7387759459325 +M72T54 353 72.0807228513553 54.4048259006589 +M72T34_3 345 72.0807426611777 33.8672738618788 +M73T1061 8 72.9367161649113 1060.80034606296 +M73T1044 10 72.9367229345106 1043.98726790638 +M73T32_1 85 72.9368652358215 31.7025769021219 +M73T1096 160 72.936874804031 1095.52504027727 +M73T32_2 85 73.0647299005977 32.166230277174 +M73T1043 10 73.1056566280053 1042.8817438948 +M74T1042_1 10 73.531470577532 1042.13833094273 +M74T33 345 73.5315669737491 33.3902011282139 +M74T871 29 73.7524028205993 871.313876430572 +M74T876_2 28 73.7524067558588 876.27549665073 +M74T858 80 73.7524235616046 858.00252803859 +M74T34 345 74.0319853847452 33.6736778224506 +M74T1033 231 74.0963050198453 1033.01869720333 +M75T34 345 74.5303776078914 33.8541677395798 +M75T505 26 74.5552304268754 505.059650753422 +M75T431 1 75.0246219750883 431.003601360729 +M76T1040 89 76.0391694122706 1039.93848585356 +M77T537 50 76.9819350151329 536.652145428441 |
| b |
| diff -r b24ca78a425b -r 1d36ecf93e67 tools/w4mclassfilter/test-data/input_med1_vm.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tools/w4mclassfilter/test-data/input_med1_vm.tsv Thu Mar 11 20:44:23 2021 +0000 |
| b |
| @@ -0,0 +1,10 @@ +variableMetadata sample trt +trtA_1 trtA_1 A +trtA_2 trtA_2 A +trtA_3 trtA_3 A +trtB_1 trtB_1 B +trtB_2 trtB_2 B +trtB_3 trtB_3 B +trtC_1 trtC_1 C +trtC_2 trtC_2 C +trtC_3 trtC_3 C |
| b |
| diff -r b24ca78a425b -r 1d36ecf93e67 tools/w4mclassfilter/test-data/input_nofilter_dataMatrix.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tools/w4mclassfilter/test-data/input_nofilter_dataMatrix.tsv Thu Mar 11 20:44:23 2021 +0000 |
| b |
| @@ -0,0 +1,16 @@ +dataMatrix HU_017 HU_028 HU_034 HU_051 HU_060 HU_078 HU_091 HU_093 HU_099 HU_110 HU_130 HU_134 HU_138 HU_149 HU_152 HU_175 HU_178 HU_185 HU_204 HU_208 +HMDB03193 76043 412165 44943 27242 436566 173175 242549 57066 559869 3732 339188 471368 262271 127285 451270 212500 79673 NA 891129 43907 +HMDB01101 30689 6877586 52217 3158 10789748 229568 4763576 3878773 976436 831937 608298 1605075 72021 442510 1107705 1464339 31250 2724553 891129 32742 +HMDB01101 6877586 52217 3158 10789748 229568 4763576 3878773 976436 831937 608298 1605075 72021 442510 1107705 1464339 31250 2724553 72900 891129 30689 +HMDB10348 47259 544877 60885 34582 529874 168264 176500 76457 610110 16262 279156 524468 451573 591487 433529 161069 214392 13781 891129 39315 +HMDB59717 357351 1030464 301983 67604 306862 1028110 1530493 270027 1378535 289677 808334 1132813 871209 895435 715190 1563158 784738 146195 891129 239030 +HMDB00822 14627 14627 14627 14627 14627 14627 14627 14627 14627 14627 14627 14627 14627 14627 14627 14627 14627 14627 14627 14627 +HMDB00299 250551 1046138 456162 159386 1013302 808657 614370 250403 768004 242085 504108 1014041 1362408 1057660 1110050 566050 411886 142233 891129 284775 +HMDB00191 560002 771533 575790 392284 888498 785428 645785 591569 960658 910201 639437 1092885 1409045 2292023 1246459 1945577 710519 773384 891129 622898 +HMDB00518 -34236 58249 85944 NA 342102 129886 175800 13154 230242 NA 440223 315368 10657 419508 48673 28361 514579 23108 891129 73831 +HMDB00715 1252089 2547452 905408 371059 4983588 5140022 2658555 814523 2558923 859466 4184204 3865723 3236644 2615560 3820724 3577833 2295288 625924 891129 1341900 +HMDB01032 2569205 26023086 1604999 430453 8103558 26222916 257139 675754 59906109 263055 31151730 18648127 14989438 1554658 20249262 5588731 871010 15920 891129 44276 +HMDB00208 747080 13420742 595872 1172376 7172632 3143654 4059767 1433702 5593888 5402629 2477288 3346077 4230072 7621236 8960828 10335722 7037373 1574738 891129 2540044 +HMDB04824 374028 1144386 539206 178517 1046190 959381 605191 310260 1253319 477259 477995 825691 1157093 1089284 1411802 1020206 782673 346761 891129 387811 +HMDB00512 NA 319783 280560 85009 1333877 556003 590779 209285 342532 198512 569970 525240 246282 1140422 542345 1171008 827723 222953 891129 85554 +HMDB00251 368600 616555 94936 622468 180988 293988 352855 767894 268331 167246 310918 1248919 577184 10985 335711 403815 80614 63393 891129 616061 |
| b |
| diff -r b24ca78a425b -r 1d36ecf93e67 tools/w4mclassfilter/test-data/input_sampleMetadata.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tools/w4mclassfilter/test-data/input_sampleMetadata.tsv Thu Mar 11 20:44:23 2021 +0000 |
| b |
| @@ -0,0 +1,21 @@ +sampleMetadata injectionOrder mode age bmi gender +HU_017 2 pos 41 23.03 M +HU_028 7 pos 41 23.92 F +HU_034 9 pos 52 23.37 M +HU_051 20 pos 24 23.23 F +HU_060 24 pos 55 28.72 F +HU_078 34 pos 46 25.18 M +HU_091 42 pos 61 26.12 M +HU_093 43 pos 53 21.71 M +HU_099 46 pos 23 21.3 M +HU_110 53 pos 50 20.9 F +HU_130 63 pos 33 26.06 M +HU_134 67 pos 48 22.89 M +HU_138 68 pos 42 21.88 M +HU_149 72 pos 35 19.49 F +HU_152 75 pos 26 17.58 F +HU_175 87 pos 35 21.26 F +HU_178 88 pos 60 32.87 F +HU_185 95 pos 42 21.09 F +HU_204 104 pos 31 29.06 M +HU_208 106 pos 27 18.61 F |
| b |
| diff -r b24ca78a425b -r 1d36ecf93e67 tools/w4mclassfilter/test-data/input_variableMetadata.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tools/w4mclassfilter/test-data/input_variableMetadata.tsv Thu Mar 11 20:44:23 2021 +0000 |
| b |
| @@ -0,0 +1,17 @@ +variable name mz rt +HMDB03193 foo 100 200 +HMDB01101 bar 150 300 +HMDB01101 baz 200 225 +HMDB00208 loquimini 873 476 +HMDB10348 batur 300 275 +HMDB00299 bantur 700 500 +HMDB00191 loquor 650 600 +HMDB00518 loquoris 870 250 +HMDB59717 bamur 125 400 +HMDB00822 bamini 300 199 +HMDB13189 baris 800 325 +HMDB00715 loquitur 725 900 +HMDB01032 loquimur 550 425 +HMDB04824 loquantur 950 522 +HMDB00512 pantur 900 543 +HMDB00251 pasamur 500 423 |
| b |
| diff -r b24ca78a425b -r 1d36ecf93e67 tools/w4mclassfilter/test-data/rangefilter_dataMatrix.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tools/w4mclassfilter/test-data/rangefilter_dataMatrix.tsv Thu Mar 11 20:44:23 2021 +0000 |
| b |
| @@ -0,0 +1,6 @@ + HU_017 HU_028 HU_034 HU_051 HU_060 HU_078 HU_091 HU_093 HU_099 HU_110 HU_130 HU_149 HU_152 HU_175 HU_178 HU_185 HU_208 +HMDB00191 19.0950724540801 19.5573683394871 19.1351832076319 18.581538968171 19.7610090032025 19.5831195045026 19.3006944055142 19.1741869272827 19.8736633887651 19.7958256457729 19.2864427002132 21.1281900906526 20.2494039981067 20.8917666482316 19.438513703552 19.5608253922588 19.2486364146654 +HMDB00208 19.5109032146715 23.6779611010349 19.1846429313023 20.1610039089984 22.7740711828923 21.5840110083096 21.9529654992985 20.451313755289 22.4154199380002 22.3652301844309 21.2403301698498 22.8615935600174 23.0952006159265 23.3011358356974 22.746605551146 20.5866803867983 21.2764220576728 +HMDB01032 21.2928905785523 24.6332887213057 20.6141409677961 18.7154961966847 22.9501240553341 24.6443247870262 17.9721889132336 19.3661386209868 25.8361997953493 18.0050049466979 24.8928089492302 20.5681658146509 24.2713659930314 22.4140893053724 19.7323297568288 13.958552715431 15.4342372710269 +HMDB01101.1 22.7134708439962 15.6722319530667 11.6247954558602 23.3631578345615 17.8085620299575 22.183613575742 21.8871689158671 19.8971659609365 19.6661147561338 19.214418735272 20.6142092807528 20.079142288524 20.4818181509538 14.9315685693242 21.3775881248719 16.1536311941017 14.9054340159519 +HMDB13189 21.3346290086766 19.4727602406215 20.6639784491577 19.2400016764968 17.0561931543153 21.3938481405109 19.1797706242895 19.6763582845664 21.7496566885488 20.9339312108399 20.6175661105571 16.7978767996065 21.5788388647145 21.4643567902489 20.9969706149343 19.9807336965562 19.6828797432404 |
| b |
| diff -r b24ca78a425b -r 1d36ecf93e67 tools/w4mclassfilter/test-data/rangefilter_sampleMetadata.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tools/w4mclassfilter/test-data/rangefilter_sampleMetadata.tsv Thu Mar 11 20:44:23 2021 +0000 |
| b |
| @@ -0,0 +1,18 @@ +sampleMetadata injectionOrder mode age bmi gender +HU_017 2 pos 41 23.03 M +HU_028 7 pos 41 23.92 F +HU_034 9 pos 52 23.37 M +HU_051 20 pos 24 23.23 F +HU_060 24 pos 55 28.72 F +HU_078 34 pos 46 25.18 M +HU_091 42 pos 61 26.12 M +HU_093 43 pos 53 21.71 M +HU_099 46 pos 23 21.3 M +HU_110 53 pos 50 20.9 F +HU_130 63 pos 33 26.06 M +HU_149 72 pos 35 19.49 F +HU_152 75 pos 26 17.58 F +HU_175 87 pos 35 21.26 F +HU_178 88 pos 60 32.87 F +HU_185 95 pos 42 21.09 F +HU_208 106 pos 27 18.61 F |
| b |
| diff -r b24ca78a425b -r 1d36ecf93e67 tools/w4mclassfilter/test-data/rangefilter_variableMetadata.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tools/w4mclassfilter/test-data/rangefilter_variableMetadata.tsv Thu Mar 11 20:44:23 2021 +0000 |
| b |
| @@ -0,0 +1,6 @@ +variableMetadata name mz rt +HMDB00191 loquor 650 600 +HMDB00208 loquimini 873 476 +HMDB01032 loquimur 550 425 +HMDB01101.1 baz 200 225 +HMDB13189 baris 800 325 |
| b |
| diff -r b24ca78a425b -r 1d36ecf93e67 tools/w4mclassfilter/test_log.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tools/w4mclassfilter/test_log.txt Thu Mar 11 20:44:23 2021 +0000 |
| [ |
| b'@@ -0,0 +1,1670 @@\n+git --git-dir /home/rstudio/.planemo/gx_repo config remote.origin.fetch \'+refs/*:refs/*\'\n+git --git-dir /home/rstudio/.planemo/gx_repo config remote.origin.mirror true\n+git --git-dir /home/rstudio/.planemo/gx_repo remote update >/dev/null 2>&1\n+galaxy.util.commands WARNING: Passing program arguments as a string may be a security hazard if combined with untrusted input\n+git clone --branch master /home/rstudio/.planemo/gx_repo /tmp/tmp0krucrv3/galaxy-dev\n+Cloning into \'/tmp/tmp0krucrv3/galaxy-dev\'...\n+done.\n+Updating files: 39% (2112/5412)\rUpdating files: 40% (2165/5412)\rUpdating files: 41% (2219/5412)\rUpdating files: 42% (2274/5412)\rUpdating files: 43% (2328/5412)\rUpdating files: 44% (2382/5412)\rUpdating files: 45% (2436/5412)\rUpdating files: 46% (2490/5412)\rUpdating files: 47% (2544/5412)\rUpdating files: 48% (2598/5412)\rUpdating files: 49% (2652/5412)\rUpdating files: 50% (2706/5412)\rUpdating files: 51% (2761/5412)\rUpdating files: 52% (2815/5412)\rUpdating files: 53% (2869/5412)\rUpdating files: 54% (2923/5412)\rUpdating files: 55% (2977/5412)\rUpdating files: 56% (3031/5412)\rUpdating files: 57% (3085/5412)\rUpdating files: 57% (3097/5412)\rUpdating files: 58% (3139/5412)\rUpdating files: 59% (3194/5412)\rUpdating files: 60% (3248/5412)\rUpdating files: 61% (3302/5412)\rUpdating files: 62% (3356/5412)\rUpdating files: 63% (3410/5412)\rUpdating files: 64% (3464/5412)\rUpdating files: 65% (3518/5412)\rUpdating files: 66% (3572/5412)\rUpdating files: 67% (3627/5412)\rUpdating files: 68% (3681/5412)\rUpdating files: 69% (3735/5412)\rUpdating files: 70% (3789/5412)\rUpdating files: 71% (3843/5412)\rUpdating files: 72% (3897/5412)\rUpdating files: 73% (3951/5412)\rUpdating files: 74% (4005/5412)\rUpdating files: 75% (4059/5412)\rUpdating files: 76% (4114/5412)\rUpdating files: 77% (4168/5412)\rUpdating files: 78% (4222/5412)\rUpdating files: 79% (4276/5412)\rUpdating files: 80% (4330/5412)\rUpdating files: 81% (4384/5412)\rUpdating files: 82% (4438/5412)\rUpdating files: 83% (4492/5412)\rUpdating files: 84% (4547/5412)\rUpdating files: 85% (4601/5412)\rUpdating files: 86% (4655/5412)\rUpdating files: 87% (4709/5412)\rUpdating files: 88% (4763/5412)\rUpdating files: 89% (4817/5412)\rUpdating files: 90% (4871/5412)\rUpdating files: 91% (4925/5412)\rUpdating files: 92% (4980/5412)\rUpdating files: 93% (5034/5412)\rUpdating files: 94% (5088/5412)\rUpdating files: 95% (5142/5412)\rUpdating files: 96% (5196/5412)\rUpdating files: 97% (5250/5412)\rUpdating files: 98% (5304/5412)\rUpdating files: 99% (5358/5412)\rUpdating files: 100% (5412/5412)\rUpdating files: 100% (5412/5412), done.\n+if [ -d .venv ] || [ -f dist-eggs.ini ]; then GALAXY_VIRTUAL_ENV=.venv; else GALAXY_VIRTUAL_ENV=/home/rstudio/.planemo/gx_venv_3; fi && export GALAXY_VIRTUAL_ENV && if [ ! -e "$GALAXY_VIRTUAL_ENV" ]; then /home/rstudio/venv/bin/virtualenv -p /home/rstudio/venv/bin/python3 $GALAXY_VIRTUAL_ENV; echo "Created virtualenv"; fi && if [ -e "$GALAXY_VIRTUAL_ENV" ]; then . "$GALAXY_VIRTUAL_ENV"/bin/activate; echo "Activated a virtualenv for Galaxy"; echo "$VIRTUAL_ENV"; else echo "Failed to activate virtualenv."; fi && COMMON_STARTUP_ARGS=; $(grep -q \'skip-venv\' run_tests.sh) && COMMON_STARTUP_ARGS="--dev-wheels"; export COMMON_STARTUP_ARGS; echo "Set COMMON_STARTUP_ARGS to ${COMMON_STARTUP_ARGS}" && ./scripts/common_startup.sh ${COMMON_STARTUP_ARGS}\n+galaxy.util.commands WARNING: Passing program arguments as a string may be a security hazard if combined with untrusted input\n+Activated a virtualenv for Galaxy\n+/home/rstudio/.planemo/gx_venv_3\n+Set COMMON_STARTUP_ARGS to --dev-wheels\n+Initializing tool-data/shared/ucsc/builds.txt from builds.txt.sample\n+Initializing tool-data/shared/ucsc/manual_builds.txt from manual_builds.txt.sample\n+Initializing static/welcome.html from welcome.html.sample\n+Activating virtualenv at /home/rstudio/.planemo/gx_venv_3\n+Requirement already satisfied: pip>=8.1 in /home/rstudio/.planemo/gx_venv_3/lib/pytho'..b'521\')" ] || {\n+MAX_TRIES=3\n+COUNT=0\n+while [ $COUNT -lt $MAX_TRIES ]; do\n+ . \'/home/rstudio/miniconda3/bin/activate\' \'/home/rstudio/miniconda3/envs/mulled-v1-132b61d9c88900ff975b44a9aad2b439393214f7dc447ec92cf134b55ae57521\' > conda_activate.log 2>&1\n+ if [ $? -eq 0 ];then\n+ break\n+ else\n+ let COUNT=COUNT+1\n+ if [ $COUNT -eq $MAX_TRIES ];then\n+ echo "Failed to activate conda environment! Error was:"\n+ cat conda_activate.log\n+ exit 1\n+ fi\n+ sleep 10s\n+ fi\n+done\n+} ; unset R_HOME; if [ \'medoid\' == \'medoid\' -a \'zero\' == \'none\' ]; then (echo \'medoid\' centering may not be chosen with imputation \'none\' 1>&2); [ ! 1 ]; else Rscript /home/rstudio/.planemo/planemo_tmp_ahme9v2m/w4mclassfilter_wrapper.R dataMatrix_in \'/tmp/tmp0krucrv3/files/d/e/b/dataset_deb04e85-d7f8-481d-b03c-5189ce9b2a9f.dat\' sampleMetadata_in \'/tmp/tmp0krucrv3/files/c/7/7/dataset_c772a3d6-a6ef-49e0-a8f7-d3dc057cdba4.dat\' variableMetadata_in \'/tmp/tmp0krucrv3/files/a/f/a/dataset_afad8efa-19e8-47e7-a6bd-6d55e0539a44.dat\' sampleclassNames \'\' inclusive \'FALSE\' wildcards \'TRUE\' classnameColumn \'pcgroup\' samplenameColumn \'sampleMetadata\' variable_range_filter \'\' transformation \'none\' imputation \'zero\' dataMatrix_out \'/tmp/tmp0krucrv3/files/7/1/1/dataset_711ba603-0791-41a7-ac7d-6bc401054381.dat\' sampleMetadata_out \'/tmp/tmp0krucrv3/files/e/7/3/dataset_e73aa99b-e412-4c7f-acd6-808e6f83e083.dat\' variableMetadata_out \'/tmp/tmp0krucrv3/files/d/b/f/dataset_dbf8bc47-81f4-4c87-8511-0bc876a46927.dat\' order_vrbl \'sample\' order_smpl \'pcgroup\' centering \'medoid\'; fi]\n+ok\n+\n+----------------------------------------------------------------------\n+XML: /tmp/tmp0krucrv3/xunit.xml\n+----------------------------------------------------------------------\n+Ran 13 tests in 363.871s\n+\n+OK\n+2021-03-11 20:18:22,641 INFO [test_driver] Shutting down\n+2021-03-11 20:18:22,642 INFO [test_driver] Shutting down embedded galaxy web server\n+2021-03-11 20:18:22,644 INFO [test_driver] Embedded web server galaxy stopped\n+2021-03-11 20:18:22,644 INFO [test_driver] Stopping application galaxy\n+2021-03-11 20:18:23,634 INFO [galaxy.queue_worker] Sending reconfigure_watcher control task.\n+2021-03-11 20:18:23,679 INFO [galaxy.jobs.handler] sending stop signal to worker thread\n+2021-03-11 20:18:23,680 INFO [galaxy.jobs.handler] job handler queue stopped\n+2021-03-11 20:18:23,680 INFO [galaxy.jobs.runners] LocalRunner: Sending stop signal to 4 job worker threads\n+2021-03-11 20:18:23,680 INFO [galaxy.jobs.runners] Waiting up to 5 seconds for job worker threads to shutdown...\n+2021-03-11 20:18:23,681 INFO [galaxy.jobs.runners] All job worker threads shutdown cleanly\n+2021-03-11 20:18:23,681 INFO [galaxy.jobs.runners] TaskRunner: Sending stop signal to 2 job worker threads\n+2021-03-11 20:18:23,681 INFO [galaxy.jobs.runners] Waiting up to 5 seconds for job worker threads to shutdown...\n+2021-03-11 20:18:23,681 INFO [galaxy.jobs.runners] All job worker threads shutdown cleanly\n+2021-03-11 20:18:23,681 INFO [galaxy.jobs.handler] sending stop signal to worker thread\n+2021-03-11 20:18:23,682 INFO [galaxy.jobs.handler] job handler stop queue stopped\n+2021-03-11 20:18:23,682 INFO [test_driver] Application galaxy stopped.\n+Testing complete. HTML report is in "/home/rstudio/src/w4mclassfilter_galaxy_wrapper/tools/w4mclassfilter/tool_test_output.html".\n+All 13 test(s) executed passed.\n+w4mclassfilter (Test #1): passed\n+w4mclassfilter (Test #2): passed\n+w4mclassfilter (Test #3): passed\n+w4mclassfilter (Test #4): passed\n+w4mclassfilter (Test #5): passed\n+w4mclassfilter (Test #6): passed\n+w4mclassfilter (Test #7): passed\n+w4mclassfilter (Test #8): passed\n+w4mclassfilter (Test #9): passed\n+w4mclassfilter (Test #10): passed\n+w4mclassfilter (Test #11): passed\n+w4mclassfilter (Test #12): passed\n+w4mclassfilter (Test #13): passed\n' |
| b |
| diff -r b24ca78a425b -r 1d36ecf93e67 tools/w4mclassfilter/w4mclassfilter.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tools/w4mclassfilter/w4mclassfilter.xml Thu Mar 11 20:44:23 2021 +0000 |
| [ |
| b'@@ -0,0 +1,1114 @@\n+<tool id="w4mclassfilter" name="W4m Data Subset" version="0.98.19">\n+ <description>Filter W4M data by values or metadata</description>\n+ <requirements>\n+ <requirement type="package" version="4.0.3">r-base</requirement>\n+ <requirement type="package" version="1.1_5">r-batch</requirement>\n+ <requirement type="package" version="0.98.19">w4mclassfilter</requirement>\n+ </requirements>\n+ <command detect_errors="aggressive"><![CDATA[\n+ unset R_HOME;\n+ if [ \'$centering\' == \'medoid\' -a \'$imputation\' == \'none\' ]; then\n+ (echo \'medoid\' centering may not be chosen with imputation \'none\' 1>&2);\n+ [ ! 1 ];\n+ else\n+ Rscript\n+ $__tool_directory__/w4mclassfilter_wrapper.R\n+ dataMatrix_in \'$dataMatrix_in\'\n+ sampleMetadata_in \'$sampleMetadata_in\'\n+ variableMetadata_in \'$variableMetadata_in\'\n+ sampleclassNames \'$sampleclassNames\'\n+ inclusive \'$inclusive\'\n+ wildcards \'$wildcards\'\n+ classnameColumn \'$classnameColumn\'\n+ samplenameColumn \'sampleMetadata\'\n+ variable_range_filter \'$variableRangeFilter\'\n+ transformation \'$transformation\'\n+ imputation \'$imputation\'\n+ dataMatrix_out \'$dataMatrix_out\'\n+ sampleMetadata_out \'$sampleMetadata_out\'\n+ variableMetadata_out \'$variableMetadata_out\'\n+ order_vrbl \'$order_vrbl\'\n+ order_smpl \'$order_smpl\'\n+ centering \'$centering\';\n+ fi\n+ ]]></command>\n+ <inputs>\n+ <param name="dataMatrix_in" format="tabular" label="Data matrix" type="data"\n+ help="Choose data-matrix file (tab-separated values with sample names in first row and feature names in first column)." />\n+ <param name="sampleMetadata_in" format="tabular" label="Sample metadata" type="data"\n+ help="Choose sample-metadata file (tab-separated values with one row per sample, sample name in first column)." />\n+ <param name="variableMetadata_in" format="tabular" label="Variable metadata" type="data"\n+ help="Choose variable-metadata file (tab-separated values with one row per feature, feature name in first column)." />\n+ <param name="classnameColumn" label="Column containing the sample-class names (or treatment names)" type="text" value = "class"\n+ help="Name the column in \'Sample metadata\' that has the values to be referenced by \'Sample-class names\' and \'Compute centers for classes\'. [default: \'class\']">\n+ <sanitizer>\n+ <valid initial="string.letters">\n+ <add preset="string.digits"/>\n+ <add value="." /> <!-- dot, period -->\n+ <add value="_" /> <!-- underscore -->\n+ </valid>\n+ </sanitizer>\n+ </param>\n+ <param name="sampleclassNames" label="Sample-class names (or patterns)" type="text" value = ""\n+ help="List of names (or patterns to match names) of sample classes to include or exclude. List should be comma-separated with no stray space characters. (Leave this empty to match no names.) [default: empty]">\n+ <sanitizer>\n+ <valid initial="string.letters">\n+ <add preset="string.digits"/>\n+ <add value="{" /> <!-- l-curb, left-curly-bracket -->\n+ <add value="|" /> <!-- pipe -->\n+ <add value="}" /> <!-- r-curb, right-curly-bracket -->\n+ <add value="$" /> <!-- dollar, dollar-sign -->\n+ <add value="(" /> <!-- left-paren -->\n+ <add value=")" /> <!-- right-paren -->\n+ <add value="*" /> <!-- splat, asterisk -->\n+ <add value="+" /> <!-- plus -->\n+ <add value="-" /> <'..b'+\n+\n+--------------------------------\n+Example with Treatment-Centering\n+--------------------------------\n+\n+This example retains only the samples that are medoids for their gender.\n+\n+**Input parameters**\n+\n++---------------------------------------------+-----------------------------------+\n+| Input Parameter | Value |\n++=============================================+===================================+\n+| Column that names the sample class | gender |\n++---------------------------------------------+-----------------------------------+\n+| Sample-class names | (Leave this field empty.) |\n++---------------------------------------------+-----------------------------------+\n+| Exclude/include named classes | filter-out |\n++---------------------------------------------+-----------------------------------+\n+| Use \'wild-cards\' or \'regular expressions\' | wild-cards |\n++---------------------------------------------+-----------------------------------+\n+| Variable range-filters | (Leave this field empty.) |\n++---------------------------------------------+-----------------------------------+\n+| Data transformation | none |\n++---------------------------------------------+-----------------------------------+\n+| Missing-value imputation | zero |\n++---------------------------------------------+-----------------------------------+\n+| Sample-sort column | gender |\n++---------------------------------------------+-----------------------------------+\n+| Feature-sort column | rt |\n++---------------------------------------------+-----------------------------------+\n+| Compute centers for classes | medoid |\n++---------------------------------------------+-----------------------------------+\n+\n+**Expected outputs**\n+\n++-------------------+----------------------------------------------------------------------------------------------------------+\n+| Expected Output | Download from URL |\n++===================+==========================================================================================================+\n+| Data matrix | https://raw.githubusercontent.com/HegemanLab/w4mclassfilter/master/tests/testthat/exp_cent_medoid_dm.tsv |\n++-------------------+----------------------------------------------------------------------------------------------------------+\n+| Sample metadata | https://raw.githubusercontent.com/HegemanLab/w4mclassfilter/master/tests/testthat/exp_cent_medoid_sm.tsv |\n++-------------------+----------------------------------------------------------------------------------------------------------+\n+| Variable metadata | https://raw.githubusercontent.com/HegemanLab/w4mclassfilter/master/tests/testthat/exp_cent_medoid_vm.tsv |\n++-------------------+----------------------------------------------------------------------------------------------------------+\n+ ]]></help>\n+ <citations>\n+ <!-- Giacomoni_2014 W4M 2.5 -->\n+ <citation type="doi">10.1093/bioinformatics/btu813</citation>\n+ <!-- Guitton_2017 W4M 3.0 -->\n+ <citation type="doi">10.1016/j.biocel.2017.07.002</citation>\n+ <!-- Kuhl_2012 CAMERA -->\n+ <citation type="doi">10.1021/ac202450g</citation>\n+ <!-- Smith_2006 XCMS -->\n+ <citation type="doi">10.1021/ac051437y</citation>\n+ <!-- Thevenot_2015 Urinary metabolome statistics -->\n+ <citation type="doi">10.1021/acs.jproteome.5b00354</citation>\n+ </citations>\n+ <!--\n+ vim:noet:sw=4:ts=4\n+--> </tool>\n' |
| b |
| diff -r b24ca78a425b -r 1d36ecf93e67 tools/w4mclassfilter/w4mclassfilter_wrapper.R --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tools/w4mclassfilter/w4mclassfilter_wrapper.R Thu Mar 11 20:44:23 2021 +0000 |
| [ |
| @@ -0,0 +1,233 @@ +#!/usr/bin/env Rscript + +library(batch) ## parseCommandArgs + +######## +# MAIN # +######## + +argVc <- unlist(parseCommandArgs(evaluate=FALSE)) + +##------------------------------ +## Initializing +##------------------------------ + +## options +##-------- + +strAsFacL <- options()$stringsAsFactors +options(stringsAsFactors = FALSE) + +## libraries +##---------- + +suppressMessages(library(w4mclassfilter)) + +expected_version <- "0.98.18" +actual_version <- packageVersion("w4mclassfilter") +if(packageVersion("w4mclassfilter") < expected_version) { + stop( + sprintf( + "Unrecoverable error: Version %s of the 'w4mclassfilter' R package was loaded instead of expected version %s", + actual_version, expected_version + ) + ) +} + +## constants +##---------- + +modNamC <- "w4mclassfilter" ## module name + +topEnvC <- environment() +flgC <- "\n" + +## functions +##---------- + +flgF <- function(tesC, + envC = topEnvC, + txtC = NA) { ## management of warning and error messages + + tesL <- eval(parse(text = tesC), envir = envC) + + if(!tesL) { + + #sink(NULL) + stpTxtC <- ifelse(is.na(txtC), + paste0(tesC, " is FALSE"), + txtC) + + stop(stpTxtC, + call. = FALSE) + + } + +} ## flgF + + +## log file +##--------- + +my_print <- function(x, ...) { cat(c(x, ...))} + +my_print("\nStart of the '", modNamC, "' Galaxy module call: ", + format(Sys.time(), "%a %d %b %Y %X"), "\n", sep="") + +## arguments +##---------- + +# files + +dataMatrix_in <- as.character(argVc["dataMatrix_in"]) +dataMatrix_out <- as.character(argVc["dataMatrix_out"]) + +sampleMetadata_in <- as.character(argVc["sampleMetadata_in"]) +sampleMetadata_out <- as.character(argVc["sampleMetadata_out"]) + +variableMetadata_in <- as.character(argVc["variableMetadata_in"]) +variableMetadata_out <- as.character(argVc["variableMetadata_out"]) + +# other parameters + +transformation <- as.character(argVc["transformation"]) +my_imputation_label <- as.character(argVc["imputation"]) +my_imputation_function <- if (my_imputation_label == "zero") { + w4m_filter_zero_imputation +} else if (my_imputation_label == "center") { + w4m_filter_median_imputation +} else if (my_imputation_label == "none") { + w4m_filter_no_imputation +} else { + stop(sprintf("Unknown value %s supplied for 'imputation' parameter. Expected one of {zero,center,none}.")) +} +wildcards <- as.logical(argVc["wildcards"]) +sampleclassNames <- as.character(argVc["sampleclassNames"]) +sampleclassNames <- strsplit(x = sampleclassNames, split = ",", fixed = TRUE)[[1]] +if (wildcards) { + sampleclassNames <- gsub("[.]", "[.]", sampleclassNames) + sampleclassNames <- utils::glob2rx(sampleclassNames, trim.tail = FALSE) +} +inclusive <- as.logical(argVc["inclusive"]) +classnameColumn <- as.character(argVc["classnameColumn"]) +samplenameColumn <- as.character(argVc["samplenameColumn"]) + +order_vrbl <- as.character(argVc["order_vrbl"]) +centering <- as.character(argVc["centering"]) +order_smpl <- + if (centering == 'centroid' || centering == 'median') { + "sampleMetadata" + } else { + as.character(argVc["order_smpl"]) + } + +variable_range_filter <- as.character(argVc["variable_range_filter"]) +variable_range_filter <- strsplit(x = variable_range_filter, split = ",", fixed = TRUE)[[1]] + +## ----------------------------- +## Transformation and imputation +## ----------------------------- +my_transformation_and_imputation <- if (transformation == "log10") { + function(m) { + # convert negative intensities to missing values + m[m < 0] <- NA + if (!is.matrix(m)) + stop("Cannot transform and impute data - the supplied data is not in matrix form") + if (nrow(m) == 0) + stop("Cannot transform and impute data - data matrix has no rows") + if (ncol(m) == 0) + stop("Cannot transform and impute data - data matrix has no columns") + suppressWarnings({ + # suppress warnings here since non-positive values will produce NaN's that will be fixed in the next step + m <- log10(m) + m[is.na(m)] <- NA + }) + return ( my_imputation_function(m) ) + } +} else if (transformation == "log2") { + function(m) { + # convert negative intensities to missing values + m[m < 0] <- NA + if (!is.matrix(m)) + stop("Cannot transform and impute data - the supplied data is not in matrix form") + if (nrow(m) == 0) + stop("Cannot transform and impute data - data matrix has no rows") + if (ncol(m) == 0) + stop("Cannot transform and impute data - data matrix has no columns") + suppressWarnings({ + # suppress warnings here since non-positive values will produce NaN's that will be fixed in the next step + m <- log2(m) + m[is.na(m)] <- NA + }) + return ( my_imputation_function(m) ) + } +} else { + function(m) { + # convert negative intensities to missing values + m[m < 0] <- NA + if (!is.matrix(m)) + stop("Cannot transform and impute data - the supplied data is not in matrix form") + if (nrow(m) == 0) + stop("Cannot transform and impute data - data matrix has no rows") + if (ncol(m) == 0) + stop("Cannot transform and impute data - data matrix has no columns") + suppressWarnings({ + # suppress warnings here since non-positive values will produce NaN's that will be fixed in the next step + m[is.na(m)] <- NA + }) + return ( my_imputation_function(m) ) + } +} + +##------------------------------ +## Computation +##------------------------------ + +result <- w4m_filter_by_sample_class( + dataMatrix_in = dataMatrix_in +, sampleMetadata_in = sampleMetadata_in +, variableMetadata_in = variableMetadata_in +, dataMatrix_out = dataMatrix_out +, sampleMetadata_out = sampleMetadata_out +, variableMetadata_out = variableMetadata_out +, classes = sampleclassNames +, include = inclusive +, class_column = classnameColumn +, samplename_column = samplenameColumn +, order_vrbl = order_vrbl +, order_smpl = order_smpl +, centering = centering +, variable_range_filter = variable_range_filter +, failure_action = my_print +, data_imputation = my_transformation_and_imputation +) + +my_print("\nResult of '", modNamC, "' Galaxy module call to 'w4mclassfilter::w4m_filter_by_sample_class' R function: ", + as.character(result), "\n", sep = "") + +##-------- +## Closing +##-------- + +my_print("\nEnd of '", modNamC, "' Galaxy module call: ", + as.character(Sys.time()), "\n", sep = "") + +#sink() + +if (!file.exists(dataMatrix_out)) { + print(sprintf("ERROR %s::w4m_filter_by_sample_class - file '%s' was not created", modNamC, dataMatrix_out)) +}# else { print(sprintf("INFO %s::w4m_filter_by_sample_class - file '%s' was exists", modNamC, dataMatrix_out)) } + +if (!file.exists(variableMetadata_out)) { + print(sprintf("ERROR %s::w4m_filter_by_sample_class - file '%s' was not created", modNamC, variableMetadata_out)) +} # else { print(sprintf("INFO %s::w4m_filter_by_sample_class - file '%s' was exists", modNamC, variableMetadata_out)) } + +if (!file.exists(sampleMetadata_out)) { + print(sprintf("ERROR %s::w4m_filter_by_sample_class - file '%s' was not created", modNamC, sampleMetadata_out)) +} # else { print(sprintf("INFO %s::w4m_filter_by_sample_class - file '%s' was exists", modNamC, sampleMetadata_out)) } + +if( !result ) { + stop(sprintf("ERROR %s::w4m_filter_by_sample_class - method failed", modNamC)) +} + +rm(list = ls()) |
| b |
| diff -r b24ca78a425b -r 1d36ecf93e67 w4mclassfilter.xml --- a/w4mclassfilter.xml Mon Sep 03 22:28:03 2018 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| [ |
| b'@@ -1,820 +0,0 @@\n-<tool id="w4mclassfilter" name="W4m Data Subset" version="0.98.11">\n- <description>Filter W4m data by values or metadata</description>\n- <!-- Here is the hyphenation standard that I *try* to apply consistently in my documentation: http://www.sandranoonan.com/dont-let-hyphenation-drive-crazy/ -->\n- <requirements>\n- <!-- <requirement type="package" version="6.2">readline</requirement> -->\n- <requirement type="package" version="3.4.1">r-base</requirement>\n- <requirement type="package" version="1.1_4">r-batch</requirement>\n- <requirement type="package" version="0.98.8">w4mclassfilter</requirement>\n- </requirements>\n- <command detect_errors="aggressive"><![CDATA[\n- Rscript $__tool_directory__/w4mclassfilter_wrapper.R\n- dataMatrix_in \'$dataMatrix_in\'\n- sampleMetadata_in \'$sampleMetadata_in\'\n- variableMetadata_in \'$variableMetadata_in\'\n- sampleclassNames \'$sampleclassNames\'\n- inclusive \'$inclusive\'\n- wildcards \'$wildcards\'\n- classnameColumn \'$classnameColumn\'\n- samplenameColumn \'sampleMetadata\'\n- variable_range_filter \'$variableRangeFilter\'\n- transformation \'$transformation\'\n- dataMatrix_out \'$dataMatrix_out\'\n- sampleMetadata_out \'$sampleMetadata_out\'\n- variableMetadata_out \'$variableMetadata_out\'\n- ]]></command>\n- <inputs>\n- <param name="dataMatrix_in" format="tabular" label="Data matrix file" type="data"\n- help="variables ✖ samples" />\n- <param name="sampleMetadata_in" format="tabular" label="Sample metadata file" type="data"\n- help="sample metadata, one row per sample" />\n- <param name="variableMetadata_in" format="tabular" label="Variable metadata file" type="data"\n- help="variable metadata, one row per variable" />\n- <param name="classnameColumn" label="Column that names the sample-class" type="text" value = "class"\n- help="name of the column in sample metadata that has the values to be tested against the \'Names of sample-classes\' input parameter - defaults to \'class\'">\n- <sanitizer>\n- <valid initial="string.letters">\n- <add preset="string.digits"/>\n- <add value="." /> <!-- dot, period -->\n- <add value="_" /> <!-- underscore -->\n- </valid>\n- </sanitizer>\n- </param>\n- <param name="sampleclassNames" label="Names of sample-classes" type="text" value = ""\n- help="comma-separated names (or regular expressions to match names) of sample-classes to filter in or out; defaults to no names">\n- <sanitizer>\n- <valid initial="string.letters">\n- <add preset="string.digits"/>\n- <add value="{" /> <!-- l-cube, left-curly-bracket -->\n- <add value="|" /> <!-- pipe -->\n- <add value="}" /> <!-- r-cube, right-curly-bracket -->\n- <add value="$" /> <!-- dollar, dollar-sign -->\n- <add value="(" /> <!-- left-paren -->\n- <add value=")" /> <!-- right-paren -->\n- <add value="*" /> <!-- splat, asterisk -->\n- <add value="+" /> <!-- plus -->\n- <add value="-" /> <!-- dash, hyphen -->\n- <add value="," /> <!-- comma -->\n- <add value="." /> <!-- dot, period -->\n- <add value=":" /> <!-- colon -->\n- <add value=";" /> <!-- semi, semicolon -->\n- <add value="?" /> <!-- what, question mark -->\n- <add value="[" /> <!-- l-squib, left-squre-bracket -->\n- <add value="\" /> <!-- whack, backslash -->\n- <add value="]" /> <!-- r-squib, right-squre-bracket -->\n- '..b'---------+\n-| Variable metadata | https://raw.githubusercontent.com/HegemanLab/w4mclassfilter_galaxy_wrapper/master/tools/w4mclassfilter/test-data/expected_variableMetadata.tsv |\n-+-------------------+-------------------------------------------------------------------------------------------------------------------------------------------------+\n-\n-.. class:: infomark\n-\n-----------------------------\n-Running With Range-Filtering\n-----------------------------\n-\n-This example retains only features whose mz is greater than 200, whose rt is less than 800, and whose maximum intensity across all samples is 2,000,000.\n-This example retains all samples (except those having zero variance for all feature), although it would be possible to filter on samples as well.\n-\n-**Input parameters**\n-\n-+------------------------------------+------------------------------------+\n-| Input Parameter | Value |\n-+====================================+====================================+\n-| Names of sample-classes | (Leave this field empty.) |\n-+------------------------------------+------------------------------------+\n-| Include named classes | filter-out |\n-+------------------------------------+------------------------------------+\n-| Column that names the sample-class | gender |\n-+------------------------------------+------------------------------------+\n-| Variable range-filters | FEATMAX:20.93157:,mz:200:,rt::800 |\n-+------------------------------------+------------------------------------+\n-| Data transforamtion | log2 |\n-+------------------------------------+------------------------------------+\n-\n-**Expected outputs**\n-\n-+-------------------+---------------------------------------------------------------------------------------------------------------------------------------------------+\n-| Expected Output | Download from URL |\n-+===================+===================================================================================================================================================+\n-| Data matrix | https://raw.githubusercontent.com/HegemanLab/w4mclassfilter_galaxy_wrapper/master/tools/w4mclassfilter/test-data/rangefilter_dataMatrix.tsv |\n-+-------------------+---------------------------------------------------------------------------------------------------------------------------------------------------+\n-| Sample metadata | https://raw.githubusercontent.com/HegemanLab/w4mclassfilter_galaxy_wrapper/master/tools/w4mclassfilter/test-data/rangefilter_sampleMetadata.tsv |\n-+-------------------+---------------------------------------------------------------------------------------------------------------------------------------------------+\n-| Variable metadata | https://raw.githubusercontent.com/HegemanLab/w4mclassfilter_galaxy_wrapper/master/tools/w4mclassfilter/test-data/rangefilter_variableMetadata.tsv |\n-+-------------------+---------------------------------------------------------------------------------------------------------------------------------------------------+\n- ]]></help>\n- <citations>\n- <!-- Giacomoni_2014 W4m 2.5 -->\n- <citation type="doi">10.1093/bioinformatics/btu813</citation>\n- <!-- Guitton_2017 W4m 3.0 -->\n- <citation type="doi">10.1016/j.biocel.2017.07.002</citation>\n- <!-- Kuhl_2012 CAMERA -->\n- <citation type="doi">10.1021/ac202450g</citation>\n- <!-- Smith_2006 XCMS -->\n- <citation type="doi">10.1021/ac051437y</citation>\n- <!-- Thevenot_2015 Urinary metabolome statistics -->\n- <citation type="doi">10.1021/acs.jproteome.5b00354</citation>\n- </citations>\n- <!--\n- vim:noet:sw=4:ts=4\n---> </tool>\n' |
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| diff -r b24ca78a425b -r 1d36ecf93e67 w4mclassfilter_wrapper.R --- a/w4mclassfilter_wrapper.R Mon Sep 03 22:28:03 2018 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| [ |
| @@ -1,184 +0,0 @@ -#!/usr/bin/env Rscript - -library(batch) ## parseCommandArgs - -######## -# MAIN # -######## - -argVc <- unlist(parseCommandArgs(evaluate=FALSE)) - -##------------------------------ -## Initializing -##------------------------------ - -## options -##-------- - -strAsFacL <- options()$stringsAsFactors -options(stringsAsFactors = FALSE) - -## libraries -##---------- - -suppressMessages(library(w4mclassfilter)) - -if(packageVersion("w4mclassfilter") < "0.98.0") - stop("Please use 'w4mclassfilter' versions of 0.98.0 and above") - -## constants -##---------- - -modNamC <- "w4mclassfilter" ## module name - -topEnvC <- environment() -flgC <- "\n" - -## functions -##---------- - -flgF <- function(tesC, - envC = topEnvC, - txtC = NA) { ## management of warning and error messages - - tesL <- eval(parse(text = tesC), envir = envC) - - if(!tesL) { - - #sink(NULL) - stpTxtC <- ifelse(is.na(txtC), - paste0(tesC, " is FALSE"), - txtC) - - stop(stpTxtC, - call. = FALSE) - - } - -} ## flgF - - -## log file -##--------- - -my_print <- function(x, ...) { cat(c(x, ...))} - -my_print("\nStart of the '", modNamC, "' Galaxy module call: ", - format(Sys.time(), "%a %d %b %Y %X"), "\n", sep="") - -## arguments -##---------- - -# files - -dataMatrix_in <- as.character(argVc["dataMatrix_in"]) -dataMatrix_out <- as.character(argVc["dataMatrix_out"]) - -sampleMetadata_in <- as.character(argVc["sampleMetadata_in"]) -sampleMetadata_out <- as.character(argVc["sampleMetadata_out"]) - -variableMetadata_in <- as.character(argVc["variableMetadata_in"]) -variableMetadata_out <- as.character(argVc["variableMetadata_out"]) - -# other parameters - -transformation <- as.character(argVc["transformation"]) -wildcards <- as.logical(argVc["wildcards"]) -sampleclassNames <- as.character(argVc["sampleclassNames"]) -sampleclassNames <- strsplit(x = sampleclassNames, split = ",", fixed = TRUE)[[1]] -if (wildcards) { - sampleclassNames <- gsub("[.]", "[.]", sampleclassNames) - sampleclassNames <- utils::glob2rx(sampleclassNames, trim.tail = FALSE) -} -inclusive <- as.logical(argVc["inclusive"]) -classnameColumn <- as.character(argVc["classnameColumn"]) -samplenameColumn <- as.character(argVc["samplenameColumn"]) - -variable_range_filter <- as.character(argVc["variable_range_filter"]) -variable_range_filter <- strsplit(x = variable_range_filter, split = ",", fixed = TRUE)[[1]] - -## ----------------------------- -## Transformation and imputation -## ----------------------------- -my_w4m_filter_imputation <- if (transformation == "log10") { - function(m) { - if (!is.matrix(m)) - stop("Cannot impute and transform data - the supplied data is not in matrix form") - if (nrow(m) == 0) - stop("Cannot impute and transform data - data matrix has no rows") - if (ncol(m) == 0) - stop("Cannot impute and transform data - data matrix has no columns") - suppressWarnings( - # suppress warnings here since non-positive values will produce NaN's that will be fixed in the next step - m <- log10(m) - ) - return ( w4m_filter_imputation(m) ) - } -} else if (transformation == "log2") { - function(m) { - if (!is.matrix(m)) - stop("Cannot impute and transform data - the supplied data is not in matrix form") - if (nrow(m) == 0) - stop("Cannot impute and transform data - data matrix has no rows") - if (ncol(m) == 0) - stop("Cannot impute and transform data - data matrix has no columns") - suppressWarnings( - # suppress warnings here since non-positive values will produce NaN's that will be fixed in the next step - m <- log2(m) - ) - return ( w4m_filter_imputation(m) ) - } -} else { - # use the method from the w4mclassfilter class - w4m_filter_imputation -} - -##------------------------------ -## Computation -##------------------------------ - -result <- w4m_filter_by_sample_class( - dataMatrix_in = dataMatrix_in -, sampleMetadata_in = sampleMetadata_in -, variableMetadata_in = variableMetadata_in -, dataMatrix_out = dataMatrix_out -, sampleMetadata_out = sampleMetadata_out -, variableMetadata_out = variableMetadata_out -, classes = sampleclassNames -, include = inclusive -, class_column = classnameColumn -, samplename_column = samplenameColumn -, variable_range_filter = variable_range_filter -, failure_action = my_print -, data_imputation = my_w4m_filter_imputation -) - -my_print("\nResult of '", modNamC, "' Galaxy module call to 'w4mclassfilter::w4m_filter_by_sample_class' R function: ", - as.character(result), "\n", sep = "") - -##-------- -## Closing -##-------- - -my_print("\nEnd of '", modNamC, "' Galaxy module call: ", - as.character(Sys.time()), "\n", sep = "") - -#sink() - -if (!file.exists(dataMatrix_out)) { - print(sprintf("ERROR %s::w4m_filter_by_sample_class - file '%s' was not created", modNamC, dataMatrix_out)) -}# else { print(sprintf("INFO %s::w4m_filter_by_sample_class - file '%s' was exists", modNamC, dataMatrix_out)) } - -if (!file.exists(variableMetadata_out)) { - print(sprintf("ERROR %s::w4m_filter_by_sample_class - file '%s' was not created", modNamC, variableMetadata_out)) -} # else { print(sprintf("INFO %s::w4m_filter_by_sample_class - file '%s' was exists", modNamC, variableMetadata_out)) } - -if (!file.exists(sampleMetadata_out)) { - print(sprintf("ERROR %s::w4m_filter_by_sample_class - file '%s' was not created", modNamC, sampleMetadata_out)) -} # else { print(sprintf("INFO %s::w4m_filter_by_sample_class - file '%s' was exists", modNamC, sampleMetadata_out)) } - -if( !result ) { - stop(sprintf("ERROR %s::w4m_filter_by_sample_class - method failed", modNamC)) -} - -rm(list = ls()) |