| Next changeset 1:371741d19743 (2017-05-09) |
|
Commit message:
planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79 |
|
added:
LICENSE README README.md planemo_install_history.txt planemo_shed_init.sh run_test.sh test-data/expected_dataMatrix.tsv test-data/expected_sampleMetadata.tsv test-data/expected_variableMetadata.tsv test-data/input_dataMatrix.tsv test-data/input_sampleMetadata.tsv test-data/input_variableMetadata.tsv test-data/output_dataMatrix.tsv test-data/output_sampleMetadata.tsv test-data/output_variableMetadata.tsv test_log.txt w4mclassfilter.xml w4mclassfilter_wrapper.R |
| b |
| diff -r 000000000000 -r bab3a658f74e LICENSE --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/LICENSE Tue May 09 18:34:35 2017 -0400 |
| b |
| @@ -0,0 +1,21 @@ +MIT License + +Copyright (c) 2017 Hegeman Lab + +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 000000000000 -r bab3a658f74e README --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/README Tue May 09 18:34:35 2017 -0400 |
| b |
| @@ -0,0 +1,7 @@ +# w4mclassfilter_galaxy_wrapper + +planemo <http://planemo.readthedocs.io/en/latest/> +oriented 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/> |
| b |
| diff -r 000000000000 -r bab3a658f74e README.md --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/README.md Tue May 09 18:34:35 2017 -0400 |
| [ |
| @@ -0,0 +1,7 @@ +# w4mclassfilter_galaxy_wrapper + +[planemo](http://planemo.readthedocs.io/en/latest/)-oriented +[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/) |
| b |
| diff -r 000000000000 -r bab3a658f74e planemo_install_history.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/planemo_install_history.txt Tue May 09 18:34:35 2017 -0400 |
| b |
| @@ -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 |
| b |
| diff -r 000000000000 -r bab3a658f74e planemo_shed_init.sh --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/planemo_shed_init.sh Tue May 09 18:34:35 2017 -0400 |
| [ |
| @@ -0,0 +1,10 @@ +#!/bin/bash +planemo shed_init --name=w4mclassfilter \ + --owner=eschen42 \ + --description="Filter W4M data files by class" \ + --homepage_url=https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper \ + --long_description="Filter Workflow4Metabolomics data matrix and metadata by sample-class" \ + --remote_repository_url="https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper" \ + --category="Metabolomics" + +# [--remote_repository_url=<URL to .shed.yml on github>] \ |
| b |
| diff -r 000000000000 -r bab3a658f74e run_test.sh --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/run_test.sh Tue May 09 18:34:35 2017 -0400 |
| [ |
| @@ -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 000000000000 -r bab3a658f74e test-data/expected_dataMatrix.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/expected_dataMatrix.tsv Tue May 09 18:34:35 2017 -0400 |
| b |
| @@ -0,0 +1,16 @@ + HU_017 HU_034 HU_078 HU_091 HU_093 HU_099 HU_130 HU_134 HU_138 +HMDB03193 76043 44943 173175 242549 57066 559869 339188 471368 262271 +HMDB01101 30689 52217 229568 4763576 3878773 976436 608298 1605075 72021 +HMDB01101.1 6877586 3158 4763576 3878773 976436 831937 1605075 72021 442510 +HMDB10348 47259 60885 168264 176500 76457 610110 279156 524468 451573 +HMDB59717 357351 301983 1028110 1530493 270027 1378535 808334 1132813 871209 +HMDB13189 2644620 1661412 2755434 593863 837865 3526136 1608814 3446611 1941527 +HMDB00299 250551 456162 808657 614370 250403 768004 504108 1014041 1362408 +HMDB00191 560002 575790 785428 645785 591569 960658 639437 1092885 1409045 +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 +HMDB00208 747080 595872 3143654 4059767 1433702 5593888 2477288 3346077 4230072 +HMDB04824 374028 539206 959381 605191 310260 1253319 477995 825691 1157093 +HMDB00512 0 280560 556003 590779 209285 342532 569970 525240 246282 +HMDB00251 368600 94936 293988 352855 767894 268331 310918 1248919 577184 |
| b |
| diff -r 000000000000 -r bab3a658f74e test-data/expected_sampleMetadata.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/expected_sampleMetadata.tsv Tue May 09 18:34:35 2017 -0400 |
| 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 000000000000 -r bab3a658f74e test-data/expected_variableMetadata.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/expected_variableMetadata.tsv Tue May 09 18:34:35 2017 -0400 |
| b |
| @@ -0,0 +1,16 @@ +variableMetadata name +HMDB03193 Testosterone_glucuronide +HMDB01101 p-Anisic_acid +HMDB01101.1 p-Anisic_acid_2 +HMDB10348 Dehydroepiandrosterone_3-glucuronide +HMDB59717 Glu-Val +HMDB13189 3-Indole_carboxylic_acid_glucuronide +HMDB00299 Xanthosine +HMDB00191 L-Aspartic_acid +HMDB00518 Chenodeoxycholic_acid +HMDB00715 Kynurenic_acid +HMDB01032 Dehydroepiandrosterone_sulfate +HMDB00208 Oxoglutaric_acid +HMDB04824 N2,N2-Dimethylguanosine +HMDB00512 N-Acetyl-L-phenylalanine +HMDB00251 Taurine |
| b |
| diff -r 000000000000 -r bab3a658f74e test-data/input_dataMatrix.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/input_dataMatrix.tsv Tue May 09 18:34:35 2017 -0400 |
| 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 000000000000 -r bab3a658f74e test-data/input_sampleMetadata.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/input_sampleMetadata.tsv Tue May 09 18:34:35 2017 -0400 |
| 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 000000000000 -r bab3a658f74e test-data/input_variableMetadata.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/input_variableMetadata.tsv Tue May 09 18:34:35 2017 -0400 |
| b |
| @@ -0,0 +1,17 @@ +variableMetadata name +HMDB03193 Testosterone_glucuronide +HMDB01101 p-Anisic_acid +HMDB01101 p-Anisic_acid_2 +HMDB10348 Dehydroepiandrosterone_3-glucuronide +HMDB59717 Glu-Val +HMDB00822 p-Hydroxymandelic_acid +HMDB13189 3-Indole_carboxylic_acid_glucuronide +HMDB00299 Xanthosine +HMDB00191 L-Aspartic_acid +HMDB00518 Chenodeoxycholic_acid +HMDB00715 Kynurenic_acid +HMDB01032 Dehydroepiandrosterone_sulfate +HMDB00208 Oxoglutaric_acid +HMDB04824 N2,N2-Dimethylguanosine +HMDB00512 N-Acetyl-L-phenylalanine +HMDB00251 Taurine |
| b |
| diff -r 000000000000 -r bab3a658f74e test-data/output_dataMatrix.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/output_dataMatrix.tsv Tue May 09 18:34:35 2017 -0400 |
| b |
| @@ -0,0 +1,16 @@ + HU_017 HU_034 HU_078 HU_091 HU_093 HU_099 HU_130 HU_134 HU_138 +HMDB03193 76043 44943 173175 242549 57066 559869 339188 471368 262271 +HMDB01101 30689 52217 229568 4763576 3878773 976436 608298 1605075 72021 +HMDB01101.1 6877586 3158 4763576 3878773 976436 831937 1605075 72021 442510 +HMDB10348 47259 60885 168264 176500 76457 610110 279156 524468 451573 +HMDB59717 357351 301983 1028110 1530493 270027 1378535 808334 1132813 871209 +HMDB13189 2644620 1661412 2755434 593863 837865 3526136 1608814 3446611 1941527 +HMDB00299 250551 456162 808657 614370 250403 768004 504108 1014041 1362408 +HMDB00191 560002 575790 785428 645785 591569 960658 639437 1092885 1409045 +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 +HMDB00208 747080 595872 3143654 4059767 1433702 5593888 2477288 3346077 4230072 +HMDB04824 374028 539206 959381 605191 310260 1253319 477995 825691 1157093 +HMDB00512 0 280560 556003 590779 209285 342532 569970 525240 246282 +HMDB00251 368600 94936 293988 352855 767894 268331 310918 1248919 577184 |
| b |
| diff -r 000000000000 -r bab3a658f74e test-data/output_sampleMetadata.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/output_sampleMetadata.tsv Tue May 09 18:34:35 2017 -0400 |
| 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 000000000000 -r bab3a658f74e test-data/output_variableMetadata.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/output_variableMetadata.tsv Tue May 09 18:34:35 2017 -0400 |
| b |
| @@ -0,0 +1,16 @@ +variableMetadata name +HMDB03193 Testosterone_glucuronide +HMDB01101 p-Anisic_acid +HMDB01101.1 p-Anisic_acid_2 +HMDB10348 Dehydroepiandrosterone_3-glucuronide +HMDB59717 Glu-Val +HMDB13189 3-Indole_carboxylic_acid_glucuronide +HMDB00299 Xanthosine +HMDB00191 L-Aspartic_acid +HMDB00518 Chenodeoxycholic_acid +HMDB00715 Kynurenic_acid +HMDB01032 Dehydroepiandrosterone_sulfate +HMDB00208 Oxoglutaric_acid +HMDB04824 N2,N2-Dimethylguanosine +HMDB00512 N-Acetyl-L-phenylalanine +HMDB00251 Taurine |
| b |
| diff -r 000000000000 -r bab3a658f74e test_log.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test_log.txt Tue May 09 18:34:35 2017 -0400 |
| [ |
| b'@@ -0,0 +1,410 @@\n+git clone --bare \'https://github.com/galaxyproject/galaxy\' \'/home/backdoor/.planemo/gx_repo\'\n+Cloning into bare repository \'/home/backdoor/.planemo/gx_repo\'...\n+cd /tmp/tmp4Jz5Zv; git clone --branch \'master\' \'/home/backdoor/.planemo/gx_repo\' \'galaxy-dev\'; cd galaxy-dev; if [ -d .venv ] || [ -f dist-eggs.ini ]; then GALAXY_VIRTUAL_ENV=.venv; else GALAXY_VIRTUAL_ENV=/home/backdoor/.planemo/gx_venv; fi; export GALAXY_VIRTUAL_ENV; if [ ! -e $GALAXY_VIRTUAL_ENV ]; then /home/backdoor/.linuxbrew/bin/virtualenv -p /home/backdoor/.linuxbrew/bin/python2.7 $GALAXY_VIRTUAL_ENV; fi; [ -e $GALAXY_VIRTUAL_ENV ] && . $GALAXY_VIRTUAL_ENV/bin/activate; 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+Cloning into \'galaxy-dev\'...\n+done.\n+New python executable in /home/backdoor/.planemo/gx_venv/bin/python2.7\n+Also creating executable in /home/backdoor/.planemo/gx_venv/bin/python\n+Installing setuptools, pip, wheel...done.\n+Running virtualenv with interpreter /home/backdoor/.linuxbrew/bin/python2.7\n+Set COMMON_STARTUP_ARGS to --dev-wheels\n+Initializing config/migrated_tools_conf.xml from migrated_tools_conf.xml.sample\n+Initializing config/shed_tool_conf.xml from shed_tool_conf.xml.sample\n+Initializing config/shed_tool_data_table_conf.xml from shed_tool_data_table_conf.xml.sample\n+Initializing config/shed_data_manager_conf.xml from shed_data_manager_conf.xml.sample\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 tool-data/shared/ucsc/ucsc_build_sites.txt from ucsc_build_sites.txt.sample\n+Initializing tool-data/shared/igv/igv_build_sites.txt from igv_build_sites.txt.sample\n+Initializing tool-data/shared/rviewer/rviewer_build_sites.txt from rviewer_build_sites.txt.sample\n+Initializing static/welcome.html from welcome.html.sample\n+Activating virtualenv at /home/backdoor/.planemo/gx_venv\n+Collecting pip>=8.1\n+ Downloading pip-9.0.1-py2.py3-none-any.whl (1.3MB)\n+Installing collected packages: pip\n+ Found existing installation: pip 7.1.2\n+ Uninstalling pip-7.1.2:\n+ Successfully uninstalled pip-7.1.2\n+Successfully installed pip-9.0.1\n+Collecting bx-python==0.7.3 (from -r requirements.txt (line 2))\n+ Downloading https://wheels.galaxyproject.org/packages/bx_python-0.7.3-cp27-cp27m-manylinux1_x86_64.whl (2.1MB)\n+Collecting MarkupSafe==0.23 (from -r requirements.txt (line 3))\n+ Downloading https://wheels.galaxyproject.org/packages/MarkupSafe-0.23-cp27-cp27m-manylinux1_x86_64.whl\n+Collecting PyYAML==3.11 (from -r requirements.txt (line 4))\n+ Downloading https://wheels.galaxyproject.org/packages/PyYAML-3.11-cp27-cp27m-manylinux1_x86_64.whl (367kB)\n+Collecting SQLAlchemy==1.0.15 (from -r requirements.txt (line 5))\n+ Downloading https://wheels.galaxyproject.org/packages/SQLAlchemy-1.0.15-cp27-cp27m-manylinux1_x86_64.whl (1.0MB)\n+Collecting mercurial==3.7.3 (from -r requirements.txt (line 6))\n+ Downloading https://wheels.galaxyproject.org/packages/mercurial-3.7.3-cp27-cp27m-manylinux1_x86_64.whl (1.5MB)\n+Collecting numpy==1.9.2 (from -r requirements.txt (line 7))\n+ Downloading https://wheels.galaxyproject.org/packages/numpy-1.9.2-cp27-cp27m-manylinux1_x86_64.whl (10.2MB)\n+Collecting pycrypto==2.6.1 (from -r requirements.txt (line 8))\n+ Downloading https://wheels.galaxyproject.org/packages/pycrypto-2.6.1-cp27-cp27m-manylinux1_x86_64.whl (492kB)\n+Collecting Paste==2.0.2 (from -r requirements.txt (line 15))\n+ Downloading https://wheels.galaxyproject.org/packages/Paste-2.0.2-py2-none-any.whl (610kB)\n+Collecting PasteDeploy==1.5.2 (from -r requirements.txt (line 16))\n+ Downloading https://wheels.galaxyproject.org/packages/PasteDeploy-1.5.2-py2.py3-none-any.whl\n+Collecting docutils==0.12 (from -r requirements.txt (line 17))\n+ D'..b'61 DEBUG [galaxy.tools.deps] Using dependency r-batch version 1.1_4 of type conda\n+2017-05-09 15:54:20,961 DEBUG [galaxy.tools.deps] Using dependency w4mclassfilter version 0.98.1 of type conda\n+2017-05-09 15:54:21,013 INFO [galaxy.jobs.command_factory] Built script [/tmp/tmp4Jz5Zv/job_working_directory/000/12/tool_script.sh] for tool command [[ "$CONDA_DEFAULT_ENV" = "/home/backdoor/miniconda2/envs/mulled-v1-e6b0d2ef4e5cf48144629c11c5bc66b43fc076b336419c5c00247560d01a3bc4" ] || . /home/backdoor/miniconda2/bin/activate \'/home/backdoor/miniconda2/envs/mulled-v1-e6b0d2ef4e5cf48144629c11c5bc66b43fc076b336419c5c00247560d01a3bc4\' > conda_activate.log 2>&1 ; [ "$CONDA_DEFAULT_ENV" = "/home/backdoor/miniconda2/envs/mulled-v1-e6b0d2ef4e5cf48144629c11c5bc66b43fc076b336419c5c00247560d01a3bc4" ] || . /home/backdoor/miniconda2/bin/activate \'/home/backdoor/miniconda2/envs/mulled-v1-e6b0d2ef4e5cf48144629c11c5bc66b43fc076b336419c5c00247560d01a3bc4\' > conda_activate.log 2>&1 ; [ "$CONDA_DEFAULT_ENV" = "/home/backdoor/miniconda2/envs/mulled-v1-e6b0d2ef4e5cf48144629c11c5bc66b43fc076b336419c5c00247560d01a3bc4" ] || . /home/backdoor/miniconda2/bin/activate \'/home/backdoor/miniconda2/envs/mulled-v1-e6b0d2ef4e5cf48144629c11c5bc66b43fc076b336419c5c00247560d01a3bc4\' > conda_activate.log 2>&1 ; Rscript /home/backdoor/w4mclassfilter_galaxy_wrapper/w4mclassfilter_wrapper.R dataMatrix_in "/tmp/tmp4Jz5Zv/files/000/dataset_15.dat" sampleMetadata_in "/tmp/tmp4Jz5Zv/files/000/dataset_16.dat" variableMetadata_in "/tmp/tmp4Jz5Zv/files/000/dataset_17.dat" sampleclassNames "M" inclusive "TRUE" classnameColumn "gender" samplenameColumn "sampleMetadata" dataMatrix_out "/tmp/tmp4Jz5Zv/files/000/dataset_18.dat" sampleMetadata_out "/tmp/tmp4Jz5Zv/files/000/dataset_19.dat" variableMetadata_out "/tmp/tmp4Jz5Zv/files/000/dataset_20.dat" information "/tmp/tmp4Jz5Zv/files/000/dataset_21.dat"]\n+2017-05-09 15:54:21,503 DEBUG [galaxy.tools.deps] Using dependency samtools version None of type conda\n+2017-05-09 15:54:21,503 DEBUG [galaxy.tools.deps] Using dependency samtools version None of type conda\n+ok\n+\n+----------------------------------------------------------------------\n+XML: /tmp/tmp4Jz5Zv/xunit.xml\n+----------------------------------------------------------------------\n+Ran 3 tests in 83.693s\n+\n+OK\n+2017-05-09 15:54:27,359 INFO [test_driver] Shutting down\n+2017-05-09 15:54:27,359 INFO [test_driver] Shutting down embedded galaxy web server\n+2017-05-09 15:54:27,361 INFO [test_driver] Embedded web server galaxy stopped\n+2017-05-09 15:54:27,361 INFO [test_driver] Stopping application galaxy\n+2017-05-09 15:54:27,361 INFO [galaxy.jobs.handler] sending stop signal to worker thread\n+2017-05-09 15:54:27,361 INFO [galaxy.jobs.handler] job handler queue stopped\n+2017-05-09 15:54:27,361 INFO [galaxy.jobs.runners] TaskRunner: Sending stop signal to 2 worker threads\n+2017-05-09 15:54:27,361 INFO [galaxy.jobs.runners] LocalRunner: Sending stop signal to 4 worker threads\n+2017-05-09 15:54:27,361 INFO [galaxy.jobs.handler] sending stop signal to worker thread\n+2017-05-09 15:54:27,361 INFO [galaxy.jobs.handler] job handler stop queue stopped\n+2017-05-09 15:54:27,362 INFO [test_driver] Application galaxy stopped.\n+2017-05-09 15:54:28,335 INFO [galaxy.jobs.handler] sending stop signal to worker thread\n+2017-05-09 15:54:28,335 INFO [galaxy.jobs.handler] job handler queue stopped\n+2017-05-09 15:54:28,335 INFO [galaxy.jobs.runners] TaskRunner: Sending stop signal to 2 worker threads\n+2017-05-09 15:54:28,335 INFO [galaxy.jobs.runners] LocalRunner: Sending stop signal to 4 worker threads\n+2017-05-09 15:54:28,335 INFO [galaxy.jobs.handler] sending stop signal to worker thread\n+2017-05-09 15:54:28,335 INFO [galaxy.jobs.handler] job handler stop queue stopped\n+Testing complete. HTML report is in "/home/backdoor/w4mclassfilter_galaxy_wrapper/tool_test_output.html".\n+All 3 test(s) executed passed.\n+W4MClassFilter[0]: passed\n+W4MClassFilter[1]: passed\n+W4MClassFilter[2]: passed\n' |
| b |
| diff -r 000000000000 -r bab3a658f74e w4mclassfilter.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/w4mclassfilter.xml Tue May 09 18:34:35 2017 -0400 |
| [ |
| b'@@ -0,0 +1,304 @@\n+<tool id="W4MClassFilter" name="W4MClassFilter" version="0.98.1">\n+ <description>Filter W4M data by sample class</description>\n+\n+ <requirements>\n+ <requirement type="package" version="3.3.1">r-base</requirement>\n+ <requirement type="package" version="1.1_4">r-batch</requirement>\n+ <requirement type="package" version="0.98.1">w4mclassfilter</requirement>\n+ </requirements>\n+\n+ <stdio>\n+ <exit_code range="1:" level="fatal" />\n+ </stdio>\n+\n+\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+ classnameColumn "$classnameColumn"\n+ samplenameColumn "$samplenameColumn"\n+ dataMatrix_out "$dataMatrix_out"\n+ sampleMetadata_out "$sampleMetadata_out"\n+ variableMetadata_out "$variableMetadata_out"\n+ information "$information"\n+ ]]></command>\n+\n+ <inputs>\n+ <param name="dataMatrix_in" label="Data matrix file" type="data" format="tabular" help="variable x sample, decimal: \'.\', missing: NA, mode: numerical, sep: tabular" />\n+ <param name="sampleMetadata_in" label="Sample metadata file" type="data" format="tabular" help="sample x metadata, decimal: \'.\', missing: NA, mode: character and numerical, sep: tabular" />\n+ <param name="variableMetadata_in" label="Variable metadata file" type="data" format="tabular" help="variable x metadata, decimal: \'.\', missing: NA, mode: character and numerical, sep: tabular" />\n+ <param name="sampleclassNames" label="Names of sample classes" type="text" value = "" help="comma-separated names of sample classes to filter in or out; defaults to no names" />\n+ <param name="inclusive" label="Include named classes" type="select" help="filter-in - include only the named sample classes; filter-out (the default) - exclude only the named sample classes">\n+ <option value="TRUE">filter-in</option>\n+ <option value="FALSE" selected="true">filter-out</option>\n+ </param>\n+ <param name="classnameColumn" label="Column that names the sample-class" type="text" value = "class" help="name of the column in sample metadata that has the values to be tested against the \'classes\' input parameter - defaults to \'class\'" />\n+ <param name="samplenameColumn" label="Column that names the sample" type="text" value = "sampleMetadata" help="name of the column in sample metadata that has the name of the sample - defaults to \'sampleMetadata\'" />\n+ </inputs>\n+ <outputs>\n+ <data name="dataMatrix_out" label="${tool.name}_${dataMatrix_in.name}" format="tabular" ></data>\n+ <data name="sampleMetadata_out" label="${tool.name}_${sampleMetadata_in.name}" format="tabular" ></data>\n+ <data name="variableMetadata_out" label="${tool.name}_${variableMetadata_in.name}" format="tabular" ></data>\n+ <data name="information" label="${tool.name}__information.txt" format="txt"/>\n+ </outputs>\n+\n+ <tests>\n+ <test>\n+ <param name="dataMatrix_in" value="input_dataMatrix.tsv"/>\n+ <param name="sampleMetadata_in" value="input_sampleMetadata.tsv"/>\n+ <param name="variableMetadata_in" value="input_variableMetadata.tsv"/>\n+ <param name="classnameColumn" value="gender"/>\n+ <param name="sampleclassNames" value="M"/>\n+ <param name="samplenameColumn" value="sampleMetadata"/>\n+ <param name="inclusive" value="filter-in"/>\n+ <param name="information" value="test-information.txt"/>\n+ <output name="dataMatrix_out">\n+ <assert_contents>\n+ <not_has_text text="HU_028" />\n+ <not_has_text text="HU_051" />\n+ <not_has_text text="HU_060" />\n+ <not_has_text text="HU_110" />\n+ <not_has_text text="HU_149" />\n+ <not_has_text text="HU_152" />\n+ <not_has_text text="HU_175" />\n+ <not_has_text text="HU_178" />\n+ <not_has_text text="HU_185" />\n'..b"--------------------------------------------------------------------------------\n+\n+.. class:: infomark\n+\n+**Tool updates**\n+\n+See the **NEWS** section at the bottom of this page\n+\n+---------------------------------------------------\n+\n+==============================================\n+Filter Workflow4Metabolomics data matrix files\n+==============================================\n+\n+-----------\n+Description\n+-----------\n+\n+Filter set of retention-corrected W4M files (dataMatrix, sampleMetadata, variableMetadata) by sample class\n+\n+--------\n+Comments\n+--------\n+\n+The *inclusive* parameter indicates:\n+ - when 'filter-in', that only the sample-classes named should be included\n+ - when 'filter-out', that all sample-classes should be included excepting the sample-classes named\n+\n+-----------\n+Input files\n+-----------\n+\n++---------------------------+------------+\n+| File | Format |\n++===========================+============+\n+| 1) Data matrix | tabular |\n++---------------------------+------------+\n+| 2) Sample metadata | tabular |\n++---------------------------+------------+\n+| 3) Variable metadata | tabular |\n++---------------------------+------------+\n+\n+\n+----------\n+Parameters\n+----------\n+\n+Data matrix file\n+\t| variable x sample **dataMatrix** tabular separated file of the numeric data matrix, with . as decimal, and NA for missing values; the table must not contain metadata apart from row and column names; the row and column names must be identical to the rownames of the sample and variable metadata, respectively (see below)\n+\t|\n+\n+Sample metadata file\n+\t| sample x metadata **sampleMetadata** tabular separated file of the numeric and/or character sample metadata, with . as decimal and NA for missing values\n+\t|\n+\n+Variable metadata file\n+\t| variable x metadata **variableMetadata** tabular separated file of the numeric and/or character variable metadata, with . as decimal and NA for missing values\n+\t|\n+\n+Names of sample classes (default = no names)\n+\t| comma-separated names of sample classes to include or exclude\n+\t|\n+\n+Include named classes (default = filter-out)\n+ | *filter-in* - include only the named sample classes\n+ | *filter-out* - exclude only the named sample classes\n+\t|\n+\n+Column that names the sample-class (default = 'class')\n+\t| name of the column in sample metadata that has the values to be tested against the 'classes' input parameter\n+\t|\n+\n+Column that names the sample (default = 'sampleMetadata')\n+\t| name of the column in sample metadata that has the name of the sample\n+\t|\n+\n+\n+------------\n+Output files\n+------------\n+\n+\n+sampleMetadata_out.tabular\n+\t| **sampleMetadata** tabular separated file identical to the file given as argument, excepting lacking rows for samples that have been filtered out\n+\t|\n+\n+variableMetadata_out.tabular\n+\t| **variableMetadata** tabular separated file identical to the file given as argument, excepting lacking rows for variables (xC-MS features) that have been filtered out (because of zero variance)\n+\t|\n+\n+dataMatrix_out.tabular\n+\t| **dataMatrix** tabular separated file identical to the file given as argument, excepting lacking columns for samples that have been filtered out (because of the sample-classes specified in the input parameters) and rows for variables (xC-MS features) that have been filtered out (because of zero variance)\n+\t|\n+\n+information.txt\n+\t| Text file with all messages and warnings generated during the computation\n+\t|\n+\n+-----------------------------------------------------------------------------\n+\n+----\n+NEWS\n+----\n+\n+CHANGES IN VERSION 0.98.1\n+=========================\n+\n+NEW FEATURES\n+\n+First release - R package that implements filtering of W4M data matrix, variable metadata, and sample metadata by class of sample.\n+\n+*dataMatrix* *is* modified by the tool, so it *does* appear as an output file\n+\n+INTERNAL MODIFICATIONS\n+\n+none\n+\n+ </help>\n+ <citations>\n+ </citations>\n+</tool>\n+<!-- vim: et sw=2 ts=2 :\n+-->\n" |
| b |
| diff -r 000000000000 -r bab3a658f74e w4mclassfilter_wrapper.R --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/w4mclassfilter_wrapper.R Tue May 09 18:34:35 2017 -0400 |
| [ |
| @@ -0,0 +1,148 @@ +#!/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 +##--------- + +information <- as.character(argVc["information"]) + +#sink(information) + +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 + +sampleclassNames <- as.character(argVc["sampleclassNames"]) +# if (sampleclassNames == "NONE_SPECIFIED") { +# sampleclassNames <- as.character(c()) +# +# } else { +# sampleclassNames <- strsplit(x = sampleclassNames, split = ",", fixed = TRUE)[[1]] +# } +sampleclassNames <- strsplit(x = sampleclassNames, split = ",", fixed = TRUE)[[1]] +inclusive <- as.logical(argVc["inclusive"]) +# print(sprintf("inclusive = '%s'", as.character(inclusive))) +classnameColumn <- as.character(argVc["classnameColumn"]) +samplenameColumn <- as.character(argVc["samplenameColumn"]) + +##------------------------------ +## 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 +, failure_action = my_print +) + +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()) |