Mercurial > repos > lecorguille > w4mclassfilter
changeset 0:8ad970e2c137 draft default tip
planemo upload
| author | lecorguille |
|---|---|
| date | Wed, 10 May 2017 11:28:01 -0400 |
| parents | |
| children | |
| files | LICENSE README README.md 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_log.txt w4mclassfilter.xml w4mclassfilter_wrapper.R |
| diffstat | 12 files changed, 984 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/LICENSE Wed May 10 11:28:01 2017 -0400 @@ -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.
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/README Wed May 10 11:28:01 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/>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/README.md Wed May 10 11:28:01 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/)
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/expected_dataMatrix.tsv Wed May 10 11:28:01 2017 -0400 @@ -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
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/expected_sampleMetadata.tsv Wed May 10 11:28:01 2017 -0400 @@ -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
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/expected_variableMetadata.tsv Wed May 10 11:28:01 2017 -0400 @@ -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
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/input_dataMatrix.tsv Wed May 10 11:28:01 2017 -0400 @@ -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
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/input_sampleMetadata.tsv Wed May 10 11:28:01 2017 -0400 @@ -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
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/input_variableMetadata.tsv Wed May 10 11:28:01 2017 -0400 @@ -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
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test_log.txt Wed May 10 11:28:01 2017 -0400 @@ -0,0 +1,334 @@ +git --git-dir /home/backdoor/.planemo/gx_repo fetch >/dev/null 2>&1 +cd /tmp/tmpBnX6kx; 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} +Cloning into 'galaxy-dev'... +done. +Set COMMON_STARTUP_ARGS to --dev-wheels +Initializing config/migrated_tools_conf.xml from migrated_tools_conf.xml.sample +Initializing config/shed_tool_conf.xml from shed_tool_conf.xml.sample +Initializing config/shed_tool_data_table_conf.xml from shed_tool_data_table_conf.xml.sample +Initializing config/shed_data_manager_conf.xml from shed_data_manager_conf.xml.sample +Initializing tool-data/shared/ucsc/builds.txt from builds.txt.sample +Initializing tool-data/shared/ucsc/manual_builds.txt from manual_builds.txt.sample +Initializing tool-data/shared/ucsc/ucsc_build_sites.txt from ucsc_build_sites.txt.sample +Initializing tool-data/shared/igv/igv_build_sites.txt from igv_build_sites.txt.sample +Initializing tool-data/shared/rviewer/rviewer_build_sites.txt from rviewer_build_sites.txt.sample +Initializing static/welcome.html from welcome.html.sample +Activating virtualenv at /home/backdoor/.planemo/gx_venv +Requirement already satisfied: pip>=8.1 in /home/backdoor/.planemo/gx_venv/lib/python2.7/site-packages +Requirement already satisfied: bx-python==0.7.3 in /home/backdoor/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 2)) +Requirement already satisfied: MarkupSafe==0.23 in /home/backdoor/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 3)) +Requirement already satisfied: PyYAML==3.11 in /home/backdoor/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 4)) +Requirement already satisfied: SQLAlchemy==1.0.15 in /home/backdoor/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 5)) +Requirement already satisfied: mercurial==3.7.3 in /home/backdoor/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 6)) +Requirement already satisfied: numpy==1.9.2 in /home/backdoor/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 7)) +Requirement already satisfied: pycrypto==2.6.1 in /home/backdoor/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 8)) +Requirement already satisfied: Paste==2.0.2 in /home/backdoor/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 15)) +Requirement already satisfied: PasteDeploy==1.5.2 in /home/backdoor/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 16)) +Requirement already satisfied: docutils==0.12 in /home/backdoor/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 17)) +Requirement already satisfied: wchartype==0.1 in /home/backdoor/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 18)) +Requirement already satisfied: repoze.lru==0.6 in /home/backdoor/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 19)) +Requirement already satisfied: Routes==2.2 in /home/backdoor/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 20)) +Requirement already satisfied: WebOb==1.4.1 in /home/backdoor/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 21)) +Requirement already satisfied: WebHelpers==1.3 in /home/backdoor/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 22)) +Requirement already satisfied: Mako==1.0.2 in /home/backdoor/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 23)) +Requirement already satisfied: pytz==2015.4 in /home/backdoor/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 24)) +Requirement already satisfied: Babel==2.0 in /home/backdoor/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 25)) +Requirement already satisfied: Beaker==1.7.0 in /home/backdoor/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 26)) +Requirement already satisfied: dictobj==0.3.1 in /home/backdoor/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 27)) +Requirement already satisfied: nose==1.3.7 in /home/backdoor/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 28)) +Requirement already satisfied: Parsley==1.3 in /home/backdoor/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 29)) +Requirement already satisfied: six==1.10.0 in /home/backdoor/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 30)) +Requirement already satisfied: Whoosh==2.7.4 in /home/backdoor/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 31)) +Requirement already satisfied: testfixtures==4.10.0 in /home/backdoor/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 32)) +Requirement already satisfied: galaxy_sequence_utils==1.0.2 in /home/backdoor/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 33)) +Requirement already satisfied: Cheetah==2.4.4 in /home/backdoor/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 36)) +Requirement already satisfied: Markdown==2.6.3 in /home/backdoor/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 37)) +Requirement already satisfied: bioblend==0.7.0 in /home/backdoor/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 40)) +Requirement already satisfied: boto==2.38.0 in /home/backdoor/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 41)) +Requirement already satisfied: requests==2.8.1 in /home/backdoor/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 42)) +Requirement already satisfied: requests-toolbelt==0.4.0 in /home/backdoor/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 43)) +Requirement already satisfied: kombu==3.0.30 in /home/backdoor/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 46)) +Requirement already satisfied: amqp==1.4.8 in /home/backdoor/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 47)) +Requirement already satisfied: anyjson==0.3.3 in /home/backdoor/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 48)) +Requirement already satisfied: psutil==4.1.0 in /home/backdoor/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 51)) +Requirement already satisfied: pulsar-galaxy-lib==0.7.0.dev5 in /home/backdoor/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 52)) +Requirement already satisfied: sqlalchemy-migrate==0.10.0 in /home/backdoor/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 55)) +Requirement already satisfied: decorator==4.0.2 in /home/backdoor/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 56)) +Requirement already satisfied: Tempita==0.5.3dev in /home/backdoor/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 57)) +Requirement already satisfied: sqlparse==0.1.16 in /home/backdoor/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 58)) +Requirement already satisfied: pbr==1.8.0 in /home/backdoor/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 59)) +Requirement already satisfied: svgwrite==1.1.6 in /home/backdoor/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 62)) +Requirement already satisfied: pyparsing==2.1.1 in /home/backdoor/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 63)) +Requirement already satisfied: Fabric==1.10.2 in /home/backdoor/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 66)) +Requirement already satisfied: paramiko==1.15.2 in /home/backdoor/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 67)) +Requirement already satisfied: ecdsa==0.13 in /home/backdoor/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 68)) +Requirement already satisfied: pysam==0.8.4+gx5 in /home/backdoor/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 71)) +Requirement already satisfied: PasteScript in /home/backdoor/.planemo/gx_venv/lib/python2.7/site-packages (from pulsar-galaxy-lib==0.7.0.dev5->-r requirements.txt (line 52)) +Requirement already satisfied: nose in /home/backdoor/.planemo/gx_venv/lib/python2.7/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 1)) +Requirement already satisfied: NoseHTML in /home/backdoor/.planemo/gx_venv/lib/python2.7/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 2)) +Requirement already satisfied: twill==0.9.1 in /home/backdoor/.planemo/gx_venv/lib/python2.7/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 3)) +Requirement already satisfied: mock in /home/backdoor/.planemo/gx_venv/lib/python2.7/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 4)) +Requirement already satisfied: selenium in /home/backdoor/.planemo/gx_venv/lib/python2.7/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 5)) +Requirement already satisfied: pbr>=0.11 in /home/backdoor/.planemo/gx_venv/lib/python2.7/site-packages (from mock->-r ./lib/galaxy/dependencies/dev-requirements.txt (line 4)) +Requirement already satisfied: funcsigs>=1; python_version < "3.3" in /home/backdoor/.planemo/gx_venv/lib/python2.7/site-packages (from mock->-r ./lib/galaxy/dependencies/dev-requirements.txt (line 4)) +Requirement already satisfied: six>=1.9 in /home/backdoor/.planemo/gx_venv/lib/python2.7/site-packages (from mock->-r ./lib/galaxy/dependencies/dev-requirements.txt (line 4)) +Testing using galaxy_root /tmp/tmpBnX6kx/galaxy-dev +Testing tools with command [cd /tmp/tmpBnX6kx/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; sh run_tests.sh $COMMON_STARTUP_ARGS --report_file /home/backdoor/toolshed_test/w4mclassfilter/tool_test_output.html --xunit_report_file /tmp/tmpBnX6kx/xunit.xml --structured_data_report_file /home/backdoor/toolshed_test/w4mclassfilter/tool_test_output.json functional.test_toolbox] +Activating virtualenv at /home/backdoor/.planemo/gx_venv +Requirement already satisfied: pip>=8.1 in /home/backdoor/.planemo/gx_venv/lib/python2.7/site-packages +Requirement already satisfied: bx-python==0.7.3 in /home/backdoor/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 2)) +Requirement already satisfied: MarkupSafe==0.23 in /home/backdoor/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 3)) +Requirement already satisfied: PyYAML==3.11 in /home/backdoor/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 4)) +Requirement already satisfied: SQLAlchemy==1.0.15 in /home/backdoor/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 5)) +Requirement already satisfied: mercurial==3.7.3 in /home/backdoor/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 6)) +Requirement already satisfied: numpy==1.9.2 in /home/backdoor/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 7)) +Requirement already satisfied: pycrypto==2.6.1 in /home/backdoor/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 8)) +Requirement already satisfied: Paste==2.0.2 in /home/backdoor/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 15)) +Requirement already satisfied: PasteDeploy==1.5.2 in /home/backdoor/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 16)) +Requirement already satisfied: docutils==0.12 in /home/backdoor/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 17)) +Requirement already satisfied: wchartype==0.1 in /home/backdoor/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 18)) +Requirement already satisfied: repoze.lru==0.6 in /home/backdoor/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 19)) +Requirement already satisfied: Routes==2.2 in /home/backdoor/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 20)) +Requirement already satisfied: WebOb==1.4.1 in /home/backdoor/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 21)) +Requirement already satisfied: WebHelpers==1.3 in /home/backdoor/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 22)) +Requirement already satisfied: Mako==1.0.2 in /home/backdoor/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 23)) +Requirement already satisfied: pytz==2015.4 in /home/backdoor/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 24)) +Requirement already satisfied: Babel==2.0 in /home/backdoor/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 25)) +Requirement already satisfied: Beaker==1.7.0 in /home/backdoor/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 26)) +Requirement already satisfied: dictobj==0.3.1 in /home/backdoor/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 27)) +Requirement already satisfied: nose==1.3.7 in /home/backdoor/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 28)) +Requirement already satisfied: Parsley==1.3 in /home/backdoor/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 29)) +Requirement already satisfied: six==1.10.0 in /home/backdoor/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 30)) +Requirement already satisfied: Whoosh==2.7.4 in /home/backdoor/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 31)) +Requirement already satisfied: testfixtures==4.10.0 in /home/backdoor/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 32)) +Requirement already satisfied: galaxy_sequence_utils==1.0.2 in /home/backdoor/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 33)) +Requirement already satisfied: Cheetah==2.4.4 in /home/backdoor/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 36)) +Requirement already satisfied: Markdown==2.6.3 in /home/backdoor/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 37)) +Requirement already satisfied: bioblend==0.7.0 in /home/backdoor/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 40)) +Requirement already satisfied: boto==2.38.0 in /home/backdoor/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 41)) +Requirement already satisfied: requests==2.8.1 in /home/backdoor/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 42)) +Requirement already satisfied: requests-toolbelt==0.4.0 in /home/backdoor/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 43)) +Requirement already satisfied: kombu==3.0.30 in /home/backdoor/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 46)) +Requirement already satisfied: amqp==1.4.8 in /home/backdoor/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 47)) +Requirement already satisfied: anyjson==0.3.3 in /home/backdoor/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 48)) +Requirement already satisfied: psutil==4.1.0 in /home/backdoor/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 51)) +Requirement already satisfied: pulsar-galaxy-lib==0.7.0.dev5 in /home/backdoor/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 52)) +Requirement already satisfied: sqlalchemy-migrate==0.10.0 in /home/backdoor/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 55)) +Requirement already satisfied: decorator==4.0.2 in /home/backdoor/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 56)) +Requirement already satisfied: Tempita==0.5.3dev in /home/backdoor/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 57)) +Requirement already satisfied: sqlparse==0.1.16 in /home/backdoor/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 58)) +Requirement already satisfied: pbr==1.8.0 in /home/backdoor/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 59)) +Requirement already satisfied: svgwrite==1.1.6 in /home/backdoor/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 62)) +Requirement already satisfied: pyparsing==2.1.1 in /home/backdoor/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 63)) +Requirement already satisfied: Fabric==1.10.2 in /home/backdoor/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 66)) +Requirement already satisfied: paramiko==1.15.2 in /home/backdoor/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 67)) +Requirement already satisfied: ecdsa==0.13 in /home/backdoor/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 68)) +Requirement already satisfied: pysam==0.8.4+gx5 in /home/backdoor/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 71)) +Requirement already satisfied: PasteScript in /home/backdoor/.planemo/gx_venv/lib/python2.7/site-packages (from pulsar-galaxy-lib==0.7.0.dev5->-r requirements.txt (line 52)) +Requirement already satisfied: nose in /home/backdoor/.planemo/gx_venv/lib/python2.7/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 1)) +Requirement already satisfied: NoseHTML in /home/backdoor/.planemo/gx_venv/lib/python2.7/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 2)) +Requirement already satisfied: twill==0.9.1 in /home/backdoor/.planemo/gx_venv/lib/python2.7/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 3)) +Requirement already satisfied: mock in /home/backdoor/.planemo/gx_venv/lib/python2.7/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 4)) +Requirement already satisfied: selenium in /home/backdoor/.planemo/gx_venv/lib/python2.7/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 5)) +Requirement already satisfied: pbr>=0.11 in /home/backdoor/.planemo/gx_venv/lib/python2.7/site-packages (from mock->-r ./lib/galaxy/dependencies/dev-requirements.txt (line 4)) +Requirement already satisfied: funcsigs>=1; python_version < "3.3" in /home/backdoor/.planemo/gx_venv/lib/python2.7/site-packages (from mock->-r ./lib/galaxy/dependencies/dev-requirements.txt (line 4)) +Requirement already satisfied: six>=1.9 in /home/backdoor/.planemo/gx_venv/lib/python2.7/site-packages (from mock->-r ./lib/galaxy/dependencies/dev-requirements.txt (line 4)) +Activating virtualenv at /home/backdoor/.planemo/gx_venv +2017-05-09 17:41:18,784 INFO [galaxy.queue_worker] Initializing main Galaxy Queue Worker on sqlalchemy+sqlite:// +2017-05-09 17:41:18,932 INFO [galaxy.model.migrate.check] Migrating 127 -> 128... +2017-05-09 17:41:19,345 INFO [galaxy.model.migrate.check] +2017-05-09 17:41:19,345 INFO [galaxy.model.migrate.check] Migration script to add session update time (used for timeouts) +2017-05-09 17:41:19,345 INFO [galaxy.model.migrate.check] +2017-05-09 17:41:19,345 INFO [galaxy.model.migrate.check] +2017-05-09 17:41:19,345 INFO [galaxy.model.migrate.check] Migrating 128 -> 129... +2017-05-09 17:41:19,750 INFO [galaxy.model.migrate.check] +2017-05-09 17:41:19,750 INFO [galaxy.model.migrate.check] Migration script to allow invalidation of job external output metadata temp files +2017-05-09 17:41:19,750 INFO [galaxy.model.migrate.check] +2017-05-09 17:41:19,750 INFO [galaxy.model.migrate.check] +2017-05-09 17:41:19,750 INFO [galaxy.model.migrate.check] Migrating 129 -> 130... +2017-05-09 17:41:20,242 INFO [galaxy.model.migrate.check] +2017-05-09 17:41:20,243 INFO [galaxy.model.migrate.check] Migration script to change the value column of user_preference from varchar to text. +2017-05-09 17:41:20,243 INFO [galaxy.model.migrate.check] +2017-05-09 17:41:20,243 INFO [galaxy.model.migrate.check] +2017-05-09 17:41:20,243 INFO [galaxy.model.migrate.check] Migrating 130 -> 131... +2017-05-09 17:41:20,998 INFO [galaxy.model.migrate.check] +2017-05-09 17:41:20,998 INFO [galaxy.model.migrate.check] Migration script to support subworkflows and workflow request input parameters +2017-05-09 17:41:20,998 INFO [galaxy.model.migrate.check] +2017-05-09 17:41:20,998 INFO [galaxy.model.migrate.check] +2017-05-09 17:41:20,998 INFO [galaxy.model.migrate.check] Migrating 131 -> 132... +2017-05-09 17:41:21,054 INFO [galaxy.model.migrate.check] +2017-05-09 17:41:21,055 INFO [galaxy.model.migrate.check] Migrating 132 -> 133... +2017-05-09 17:41:21,452 INFO [galaxy.model.migrate.check] +2017-05-09 17:41:21,452 INFO [galaxy.model.migrate.check] Add dependencies column to jobs table +2017-05-09 17:41:21,452 INFO [galaxy.model.migrate.check] +2017-05-09 17:41:21,452 INFO [galaxy.model.migrate.check] +2017-05-09 17:41:21,467 INFO [galaxy.config] Install database targetting Galaxy's database configuration. +2017-05-09 17:41:22,106 ERROR [galaxy.visualization.genomes] Error reading twobit.loc: [Errno 2] No such file or directory: '/tmp/tmpBnX6kx/galaxy-dev/tool-data/twobit.loc' +Traceback (most recent call last): + File "/tmp/tmpBnX6kx/galaxy-dev/lib/galaxy/visualization/genomes.py", line 210, in reload_genomes + for line in open( os.path.join( self.app.config.tool_data_path, "twobit.loc" ) ): +IOError: [Errno 2] No such file or directory: '/tmp/tmpBnX6kx/galaxy-dev/tool-data/twobit.loc' +2017-05-09 17:41:22,117 INFO [galaxy.jobs] Setting <handlers> default to child with id 'main' +2017-05-09 17:41:22,135 INFO [galaxy.tools.toolbox.watcher] Watchdog library unavailable, cannot monitor tools. +2017-05-09 17:41:22,135 INFO [galaxy.tools.toolbox.base] Parsing the tool configuration /tmp/tmpBnX6kx/tool_conf.xml +2017-05-09 17:41:22,146 INFO [galaxy.tools.toolbox.base] Parsing the tool configuration /tmp/tmpBnX6kx/shed_tools_conf.xml +2017-05-09 17:41:22,146 INFO [galaxy.tools.toolbox.base] Parsing the tool configuration /tmp/tmpBnX6kx/empty_tool_conf.xml +No handlers could be found for logger "galaxy.datatypes.display_applications.application" +2017-05-09 17:41:22,482 WARNI [galaxy.webhooks] directory not found: /tmp/tmpBnX6kx/galaxy-dev/lib/galaxy/util/../../.././config/plugins/webhooks/demo/config +2017-05-09 17:41:22,492 INFO [galaxy.jobs] Handler 'main' will load all configured runner plugins +2017-05-09 17:41:22,497 INFO [galaxy.jobs.handler] job handler stop queue started +2017-05-09 17:41:22,505 INFO [galaxy.jobs.handler] job handler queue started +2017-05-09 17:41:23,279 INFO [galaxy.queue_worker] Binding and starting galaxy control worker for main +/home/backdoor/.planemo/gx_venv/lib/python2.7/site-packages/sqlalchemy/sql/sqltypes.py:562: SAWarning: Dialect sqlite+pysqlite does *not* support Decimal objects natively, and SQLAlchemy must convert from floating point - rounding errors and other issues may occur. Please consider storing Decimal numbers as strings or integers on this platform for lossless storage. + 'storage.' % (dialect.name, dialect.driver)) +/home/backdoor/.planemo/gx_venv/lib/python2.7/site-packages/sqlalchemy/sql/default_comparator.py:153: SAWarning: The IN-predicate on "request_type.id" was invoked with an empty sequence. This results in a contradiction, which nonetheless can be expensive to evaluate. Consider alternative strategies for improved performance. + 'strategies for improved performance.' % expr) +W4MClassFilter ( W4MClassFilter ) > Test-1 ... 2017-05-09 17:41:24,463 INFO [galaxy.tools.actions.upload_common] tool upload1 created job id 1 +2017-05-09 17:41:24,891 INFO [galaxy.jobs.handler] (1) Job dispatched +2017-05-09 17:41:25,164 DEBUG [galaxy.tools.deps] Using dependency samtools version None of type conda +2017-05-09 17:41:25,165 DEBUG [galaxy.tools.deps] Using dependency samtools version None of type conda +2017-05-09 17:41:25,198 INFO [galaxy.jobs.command_factory] Built script [/tmp/tmpBnX6kx/job_working_directory/000/1/tool_script.sh] for tool command [export PATH=$PATH:'/home/backdoor/miniconda2/envs/__samtools@1.3.1/bin' ; python /tmp/tmpBnX6kx/galaxy-dev/tools/data_source/upload.py /tmp/tmpBnX6kx/galaxy-dev /tmp/tmpafqPoR /tmp/tmpFEU_uZ 1:/tmp/tmpBnX6kx/job_working_directory/000/1/dataset_1_files:/tmp/tmpBnX6kx/files/000/dataset_1.dat] +2017-05-09 17:41:25,365 DEBUG [galaxy.tools.deps] Using dependency samtools version None of type conda +2017-05-09 17:41:25,366 DEBUG [galaxy.tools.deps] Using dependency samtools version None of type conda +2017-05-09 17:41:29,174 INFO [galaxy.tools.actions.upload_common] tool upload1 created job id 2 +2017-05-09 17:41:30,112 INFO [galaxy.jobs.handler] (2) Job dispatched +2017-05-09 17:41:30,372 DEBUG [galaxy.tools.deps] Using dependency samtools version None of type conda +2017-05-09 17:41:30,377 DEBUG [galaxy.tools.deps] Using dependency samtools version None of type conda +2017-05-09 17:41:30,415 INFO [galaxy.jobs.command_factory] Built script [/tmp/tmpBnX6kx/job_working_directory/000/2/tool_script.sh] for tool command [export PATH=$PATH:'/home/backdoor/miniconda2/envs/__samtools@1.3.1/bin' ; python /tmp/tmpBnX6kx/galaxy-dev/tools/data_source/upload.py /tmp/tmpBnX6kx/galaxy-dev /tmp/tmpafqPoR /tmp/tmp819dTL 2:/tmp/tmpBnX6kx/job_working_directory/000/2/dataset_2_files:/tmp/tmpBnX6kx/files/000/dataset_2.dat] +2017-05-09 17:41:30,642 DEBUG [galaxy.tools.deps] Using dependency samtools version None of type conda +2017-05-09 17:41:30,642 DEBUG [galaxy.tools.deps] Using dependency samtools version None of type conda +2017-05-09 17:41:34,617 INFO [galaxy.tools.actions.upload_common] tool upload1 created job id 3 +2017-05-09 17:41:35,397 INFO [galaxy.jobs.handler] (3) Job dispatched +2017-05-09 17:41:35,661 DEBUG [galaxy.tools.deps] Using dependency samtools version None of type conda +2017-05-09 17:41:35,661 DEBUG [galaxy.tools.deps] Using dependency samtools version None of type conda +2017-05-09 17:41:35,707 INFO [galaxy.jobs.command_factory] Built script [/tmp/tmpBnX6kx/job_working_directory/000/3/tool_script.sh] for tool command [export PATH=$PATH:'/home/backdoor/miniconda2/envs/__samtools@1.3.1/bin' ; python /tmp/tmpBnX6kx/galaxy-dev/tools/data_source/upload.py /tmp/tmpBnX6kx/galaxy-dev /tmp/tmpafqPoR /tmp/tmpOXdXDH 3:/tmp/tmpBnX6kx/job_working_directory/000/3/dataset_3_files:/tmp/tmpBnX6kx/files/000/dataset_3.dat] +2017-05-09 17:41:35,889 DEBUG [galaxy.tools.deps] Using dependency samtools version None of type conda +2017-05-09 17:41:35,890 DEBUG [galaxy.tools.deps] Using dependency samtools version None of type conda +2017-05-09 17:41:39,590 INFO [galaxy.tools.actions] Handled output named dataMatrix_out for tool W4MClassFilter (102.610 ms) +2017-05-09 17:41:39,630 INFO [galaxy.tools.actions] Handled output named sampleMetadata_out for tool W4MClassFilter (39.109 ms) +2017-05-09 17:41:39,662 INFO [galaxy.tools.actions] Handled output named variableMetadata_out for tool W4MClassFilter (32.632 ms) +2017-05-09 17:41:39,694 INFO [galaxy.tools.actions] Handled output named information for tool W4MClassFilter (31.837 ms) +2017-05-09 17:41:39,716 INFO [galaxy.tools.actions] Added output datasets to history (21.785 ms) +2017-05-09 17:41:39,760 INFO [galaxy.tools.actions] Verified access to datasets for Job[unflushed,tool_id=W4MClassFilter] (23.849 ms) +2017-05-09 17:41:39,761 INFO [galaxy.tools.actions] Setup for job Job[unflushed,tool_id=W4MClassFilter] complete, ready to flush (44.332 ms) +2017-05-09 17:41:39,795 INFO [galaxy.tools.actions] Flushed transaction for job Job[id=4,tool_id=W4MClassFilter] (34.570 ms) +2017-05-09 17:41:40,615 INFO [galaxy.jobs.handler] (4) Job dispatched +2017-05-09 17:41:40,918 DEBUG [galaxy.tools.deps] Using dependency r-base version 3.3.1 of type conda +2017-05-09 17:41:40,918 DEBUG [galaxy.tools.deps] Using dependency r-batch version 1.1_4 of type conda +2017-05-09 17:41:40,918 DEBUG [galaxy.tools.deps] Using dependency w4mclassfilter version 0.98.1 of type conda +2017-05-09 17:41:40,919 DEBUG [galaxy.tools.deps] Using dependency r-base version 3.3.1 of type conda +2017-05-09 17:41:40,919 DEBUG [galaxy.tools.deps] Using dependency r-batch version 1.1_4 of type conda +2017-05-09 17:41:40,919 DEBUG [galaxy.tools.deps] Using dependency w4mclassfilter version 0.98.1 of type conda +2017-05-09 17:41:40,951 INFO [galaxy.jobs.command_factory] Built script [/tmp/tmpBnX6kx/job_working_directory/000/4/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 ; [ "$CONDA_DEFAULT_ENV" = "/home/backdoor/miniconda2/envs/mulled-v1-e6b0d2ef4e5cf48144629c11c5bc66b43fc076b336419c5c00247560d01a3bc4" ] || . /home/backdoor/miniconda2/bin/activate '/home/backdoor/miniconda2/envs/mulled-v1-e6b0d2ef4e5cf48144629c11c5bc66b43fc076b336419c5c00247560d01a3bc4' > conda_activate.log 2>&1 ; Rscript /home/backdoor/toolshed_test/w4mclassfilter/w4mclassfilter_wrapper.R dataMatrix_in "/tmp/tmpBnX6kx/files/000/dataset_1.dat" sampleMetadata_in "/tmp/tmpBnX6kx/files/000/dataset_2.dat" variableMetadata_in "/tmp/tmpBnX6kx/files/000/dataset_3.dat" sampleclassNames "M" inclusive "TRUE" classnameColumn "gender" samplenameColumn "sampleMetadata" dataMatrix_out "/tmp/tmpBnX6kx/files/000/dataset_4.dat" sampleMetadata_out "/tmp/tmpBnX6kx/files/000/dataset_5.dat" variableMetadata_out "/tmp/tmpBnX6kx/files/000/dataset_6.dat" information "/tmp/tmpBnX6kx/files/000/dataset_7.dat"] +2017-05-09 17:41:41,340 DEBUG [galaxy.tools.deps] Using dependency samtools version None of type conda +2017-05-09 17:41:41,341 DEBUG [galaxy.tools.deps] Using dependency samtools version None of type conda +ok +W4MClassFilter ( W4MClassFilter ) > Test-2 ... 2017-05-09 17:41:47,453 INFO [galaxy.tools.actions.upload_common] tool upload1 created job id 5 +2017-05-09 17:41:47,929 INFO [galaxy.jobs.handler] (5) Job dispatched +2017-05-09 17:41:48,185 DEBUG [galaxy.tools.deps] Using dependency samtools version None of type conda +2017-05-09 17:41:48,185 DEBUG [galaxy.tools.deps] Using dependency samtools version None of type conda +2017-05-09 17:41:48,246 INFO [galaxy.jobs.command_factory] Built script [/tmp/tmpBnX6kx/job_working_directory/000/5/tool_script.sh] for tool command [export PATH=$PATH:'/home/backdoor/miniconda2/envs/__samtools@1.3.1/bin' ; python /tmp/tmpBnX6kx/galaxy-dev/tools/data_source/upload.py /tmp/tmpBnX6kx/galaxy-dev /tmp/tmpafqPoR /tmp/tmpCJ6i2V 8:/tmp/tmpBnX6kx/job_working_directory/000/5/dataset_8_files:/tmp/tmpBnX6kx/files/000/dataset_8.dat] +2017-05-09 17:41:48,468 DEBUG [galaxy.tools.deps] Using dependency samtools version None of type conda +2017-05-09 17:41:48,469 DEBUG [galaxy.tools.deps] Using dependency samtools version None of type conda +2017-05-09 17:41:52,575 INFO [galaxy.tools.actions.upload_common] tool upload1 created job id 6 +2017-05-09 17:41:53,192 INFO [galaxy.jobs.handler] (6) Job dispatched +2017-05-09 17:41:53,442 DEBUG [galaxy.tools.deps] Using dependency samtools version None of type conda +2017-05-09 17:41:53,444 DEBUG [galaxy.tools.deps] Using dependency samtools version None of type conda +2017-05-09 17:41:53,484 INFO [galaxy.jobs.command_factory] Built script [/tmp/tmpBnX6kx/job_working_directory/000/6/tool_script.sh] for tool command [export PATH=$PATH:'/home/backdoor/miniconda2/envs/__samtools@1.3.1/bin' ; python /tmp/tmpBnX6kx/galaxy-dev/tools/data_source/upload.py /tmp/tmpBnX6kx/galaxy-dev /tmp/tmpafqPoR /tmp/tmpTkRIU7 9:/tmp/tmpBnX6kx/job_working_directory/000/6/dataset_9_files:/tmp/tmpBnX6kx/files/000/dataset_9.dat] +2017-05-09 17:41:53,711 DEBUG [galaxy.tools.deps] Using dependency samtools version None of type conda +2017-05-09 17:41:53,712 DEBUG [galaxy.tools.deps] Using dependency samtools version None of type conda +2017-05-09 17:41:57,685 INFO [galaxy.tools.actions.upload_common] tool upload1 created job id 7 +2017-05-09 17:41:58,415 INFO [galaxy.jobs.handler] (7) Job dispatched +2017-05-09 17:41:58,668 DEBUG [galaxy.tools.deps] Using dependency samtools version None of type conda +2017-05-09 17:41:58,669 DEBUG [galaxy.tools.deps] Using dependency samtools version None of type conda +2017-05-09 17:41:58,718 INFO [galaxy.jobs.command_factory] Built script [/tmp/tmpBnX6kx/job_working_directory/000/7/tool_script.sh] for tool command [export PATH=$PATH:'/home/backdoor/miniconda2/envs/__samtools@1.3.1/bin' ; python /tmp/tmpBnX6kx/galaxy-dev/tools/data_source/upload.py /tmp/tmpBnX6kx/galaxy-dev /tmp/tmpafqPoR /tmp/tmppTa3ww 10:/tmp/tmpBnX6kx/job_working_directory/000/7/dataset_10_files:/tmp/tmpBnX6kx/files/000/dataset_10.dat] +2017-05-09 17:41:58,874 DEBUG [galaxy.tools.deps] Using dependency samtools version None of type conda +2017-05-09 17:41:58,874 DEBUG [galaxy.tools.deps] Using dependency samtools version None of type conda +2017-05-09 17:42:02,544 INFO [galaxy.tools.actions] Handled output named dataMatrix_out for tool W4MClassFilter (54.150 ms) +2017-05-09 17:42:02,576 INFO [galaxy.tools.actions] Handled output named sampleMetadata_out for tool W4MClassFilter (32.411 ms) +2017-05-09 17:42:02,613 INFO [galaxy.tools.actions] Handled output named variableMetadata_out for tool W4MClassFilter (36.563 ms) +2017-05-09 17:42:02,660 INFO [galaxy.tools.actions] Handled output named information for tool W4MClassFilter (46.442 ms) +2017-05-09 17:42:02,682 INFO [galaxy.tools.actions] Added output datasets to history (21.663 ms) +2017-05-09 17:42:02,732 INFO [galaxy.tools.actions] Verified access to datasets for Job[unflushed,tool_id=W4MClassFilter] (25.405 ms) +2017-05-09 17:42:02,732 INFO [galaxy.tools.actions] Setup for job Job[unflushed,tool_id=W4MClassFilter] complete, ready to flush (50.729 ms) +2017-05-09 17:42:02,766 INFO [galaxy.tools.actions] Flushed transaction for job Job[id=8,tool_id=W4MClassFilter] (33.131 ms) +2017-05-09 17:42:03,604 INFO [galaxy.jobs.handler] (8) Job dispatched +2017-05-09 17:42:03,920 DEBUG [galaxy.tools.deps] Using dependency r-base version 3.3.1 of type conda +2017-05-09 17:42:03,921 DEBUG [galaxy.tools.deps] Using dependency r-batch version 1.1_4 of type conda +2017-05-09 17:42:03,921 DEBUG [galaxy.tools.deps] Using dependency w4mclassfilter version 0.98.1 of type conda +2017-05-09 17:42:03,921 DEBUG [galaxy.tools.deps] Using dependency r-base version 3.3.1 of type conda +2017-05-09 17:42:03,921 DEBUG [galaxy.tools.deps] Using dependency r-batch version 1.1_4 of type conda +2017-05-09 17:42:03,921 DEBUG [galaxy.tools.deps] Using dependency w4mclassfilter version 0.98.1 of type conda +2017-05-09 17:42:03,960 INFO [galaxy.jobs.command_factory] Built script [/tmp/tmpBnX6kx/job_working_directory/000/8/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 ; [ "$CONDA_DEFAULT_ENV" = "/home/backdoor/miniconda2/envs/mulled-v1-e6b0d2ef4e5cf48144629c11c5bc66b43fc076b336419c5c00247560d01a3bc4" ] || . /home/backdoor/miniconda2/bin/activate '/home/backdoor/miniconda2/envs/mulled-v1-e6b0d2ef4e5cf48144629c11c5bc66b43fc076b336419c5c00247560d01a3bc4' > conda_activate.log 2>&1 ; Rscript /home/backdoor/toolshed_test/w4mclassfilter/w4mclassfilter_wrapper.R dataMatrix_in "/tmp/tmpBnX6kx/files/000/dataset_8.dat" sampleMetadata_in "/tmp/tmpBnX6kx/files/000/dataset_9.dat" variableMetadata_in "/tmp/tmpBnX6kx/files/000/dataset_10.dat" sampleclassNames "M" inclusive "TRUE" classnameColumn "gender" samplenameColumn "sampleMetadata" dataMatrix_out "/tmp/tmpBnX6kx/files/000/dataset_11.dat" sampleMetadata_out "/tmp/tmpBnX6kx/files/000/dataset_12.dat" variableMetadata_out "/tmp/tmpBnX6kx/files/000/dataset_13.dat" information "/tmp/tmpBnX6kx/files/000/dataset_14.dat"] +2017-05-09 17:42:04,366 DEBUG [galaxy.tools.deps] Using dependency samtools version None of type conda +2017-05-09 17:42:04,366 DEBUG [galaxy.tools.deps] Using dependency samtools version None of type conda +ok +W4MClassFilter ( W4MClassFilter ) > Test-3 ... 2017-05-09 17:42:10,658 INFO [galaxy.tools.actions.upload_common] tool upload1 created job id 9 +2017-05-09 17:42:10,906 INFO [galaxy.jobs.handler] (9) Job dispatched +2017-05-09 17:42:11,150 DEBUG [galaxy.tools.deps] Using dependency samtools version None of type conda +2017-05-09 17:42:11,151 DEBUG [galaxy.tools.deps] Using dependency samtools version None of type conda +2017-05-09 17:42:11,233 INFO [galaxy.jobs.command_factory] Built script [/tmp/tmpBnX6kx/job_working_directory/000/9/tool_script.sh] for tool command [export PATH=$PATH:'/home/backdoor/miniconda2/envs/__samtools@1.3.1/bin' ; python /tmp/tmpBnX6kx/galaxy-dev/tools/data_source/upload.py /tmp/tmpBnX6kx/galaxy-dev /tmp/tmpafqPoR /tmp/tmp0F7oAs 15:/tmp/tmpBnX6kx/job_working_directory/000/9/dataset_15_files:/tmp/tmpBnX6kx/files/000/dataset_15.dat] +2017-05-09 17:42:11,471 DEBUG [galaxy.tools.deps] Using dependency samtools version None of type conda +2017-05-09 17:42:11,472 DEBUG [galaxy.tools.deps] Using dependency samtools version None of type conda +2017-05-09 17:42:15,491 INFO [galaxy.tools.actions.upload_common] tool upload1 created job id 10 +2017-05-09 17:42:16,194 INFO [galaxy.jobs.handler] (10) Job dispatched +2017-05-09 17:42:16,447 DEBUG [galaxy.tools.deps] Using dependency samtools version None of type conda +2017-05-09 17:42:16,448 DEBUG [galaxy.tools.deps] Using dependency samtools version None of type conda +2017-05-09 17:42:16,485 INFO [galaxy.jobs.command_factory] Built script [/tmp/tmpBnX6kx/job_working_directory/000/10/tool_script.sh] for tool command [export PATH=$PATH:'/home/backdoor/miniconda2/envs/__samtools@1.3.1/bin' ; python /tmp/tmpBnX6kx/galaxy-dev/tools/data_source/upload.py /tmp/tmpBnX6kx/galaxy-dev /tmp/tmpafqPoR /tmp/tmpmkABaW 16:/tmp/tmpBnX6kx/job_working_directory/000/10/dataset_16_files:/tmp/tmpBnX6kx/files/000/dataset_16.dat] +2017-05-09 17:42:16,649 DEBUG [galaxy.tools.deps] Using dependency samtools version None of type conda +2017-05-09 17:42:16,650 DEBUG [galaxy.tools.deps] Using dependency samtools version None of type conda +2017-05-09 17:42:20,509 INFO [galaxy.tools.actions.upload_common] tool upload1 created job id 11 +2017-05-09 17:42:21,426 INFO [galaxy.jobs.handler] (11) Job dispatched +2017-05-09 17:42:21,680 DEBUG [galaxy.tools.deps] Using dependency samtools version None of type conda +2017-05-09 17:42:21,681 DEBUG [galaxy.tools.deps] Using dependency samtools version None of type conda +2017-05-09 17:42:21,764 INFO [galaxy.jobs.command_factory] Built script [/tmp/tmpBnX6kx/job_working_directory/000/11/tool_script.sh] for tool command [export PATH=$PATH:'/home/backdoor/miniconda2/envs/__samtools@1.3.1/bin' ; python /tmp/tmpBnX6kx/galaxy-dev/tools/data_source/upload.py /tmp/tmpBnX6kx/galaxy-dev /tmp/tmpafqPoR /tmp/tmpfEj6tV 17:/tmp/tmpBnX6kx/job_working_directory/000/11/dataset_17_files:/tmp/tmpBnX6kx/files/000/dataset_17.dat] +2017-05-09 17:42:21,991 DEBUG [galaxy.tools.deps] Using dependency samtools version None of type conda +2017-05-09 17:42:21,991 DEBUG [galaxy.tools.deps] Using dependency samtools version None of type conda +2017-05-09 17:42:25,709 INFO [galaxy.tools.actions] Handled output named dataMatrix_out for tool W4MClassFilter (34.677 ms) +2017-05-09 17:42:25,751 INFO [galaxy.tools.actions] Handled output named sampleMetadata_out for tool W4MClassFilter (41.778 ms) +2017-05-09 17:42:25,784 INFO [galaxy.tools.actions] Handled output named variableMetadata_out for tool W4MClassFilter (32.888 ms) +2017-05-09 17:42:25,815 INFO [galaxy.tools.actions] Handled output named information for tool W4MClassFilter (30.527 ms) +2017-05-09 17:42:25,838 INFO [galaxy.tools.actions] Added output datasets to history (22.886 ms) +2017-05-09 17:42:25,886 INFO [galaxy.tools.actions] Verified access to datasets for Job[unflushed,tool_id=W4MClassFilter] (26.826 ms) +2017-05-09 17:42:25,887 INFO [galaxy.tools.actions] Setup for job Job[unflushed,tool_id=W4MClassFilter] complete, ready to flush (48.981 ms) +2017-05-09 17:42:25,936 INFO [galaxy.tools.actions] Flushed transaction for job Job[id=12,tool_id=W4MClassFilter] (48.570 ms) +2017-05-09 17:42:26,617 INFO [galaxy.jobs.handler] (12) Job dispatched +2017-05-09 17:42:26,893 DEBUG [galaxy.tools.deps] Using dependency r-base version 3.3.1 of type conda +2017-05-09 17:42:26,900 DEBUG [galaxy.tools.deps] Using dependency r-batch version 1.1_4 of type conda +2017-05-09 17:42:26,902 DEBUG [galaxy.tools.deps] Using dependency w4mclassfilter version 0.98.1 of type conda +2017-05-09 17:42:26,903 DEBUG [galaxy.tools.deps] Using dependency r-base version 3.3.1 of type conda +2017-05-09 17:42:26,903 DEBUG [galaxy.tools.deps] Using dependency r-batch version 1.1_4 of type conda +2017-05-09 17:42:26,903 DEBUG [galaxy.tools.deps] Using dependency w4mclassfilter version 0.98.1 of type conda +2017-05-09 17:42:26,955 INFO [galaxy.jobs.command_factory] Built script [/tmp/tmpBnX6kx/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/toolshed_test/w4mclassfilter/w4mclassfilter_wrapper.R dataMatrix_in "/tmp/tmpBnX6kx/files/000/dataset_15.dat" sampleMetadata_in "/tmp/tmpBnX6kx/files/000/dataset_16.dat" variableMetadata_in "/tmp/tmpBnX6kx/files/000/dataset_17.dat" sampleclassNames "M" inclusive "TRUE" classnameColumn "gender" samplenameColumn "sampleMetadata" dataMatrix_out "/tmp/tmpBnX6kx/files/000/dataset_18.dat" sampleMetadata_out "/tmp/tmpBnX6kx/files/000/dataset_19.dat" variableMetadata_out "/tmp/tmpBnX6kx/files/000/dataset_20.dat" information "/tmp/tmpBnX6kx/files/000/dataset_21.dat"] +2017-05-09 17:42:27,374 DEBUG [galaxy.tools.deps] Using dependency samtools version None of type conda +2017-05-09 17:42:27,375 DEBUG [galaxy.tools.deps] Using dependency samtools version None of type conda +ok + +---------------------------------------------------------------------- +XML: /tmp/tmpBnX6kx/xunit.xml +---------------------------------------------------------------------- +Ran 3 tests in 69.356s + +OK +2017-05-09 17:42:33,110 INFO [test_driver] Shutting down +2017-05-09 17:42:33,110 INFO [test_driver] Shutting down embedded galaxy web server +2017-05-09 17:42:33,112 INFO [test_driver] Embedded web server galaxy stopped +2017-05-09 17:42:33,112 INFO [test_driver] Stopping application galaxy +2017-05-09 17:42:33,112 INFO [galaxy.jobs.handler] sending stop signal to worker thread +2017-05-09 17:42:33,112 INFO [galaxy.jobs.handler] job handler queue stopped +2017-05-09 17:42:33,112 INFO [galaxy.jobs.runners] TaskRunner: Sending stop signal to 2 worker threads +2017-05-09 17:42:33,112 INFO [galaxy.jobs.runners] LocalRunner: Sending stop signal to 4 worker threads +2017-05-09 17:42:33,112 INFO [galaxy.jobs.handler] sending stop signal to worker thread +2017-05-09 17:42:33,112 INFO [galaxy.jobs.handler] job handler stop queue stopped +2017-05-09 17:42:33,113 INFO [test_driver] Application galaxy stopped. +2017-05-09 17:42:34,087 INFO [galaxy.jobs.handler] sending stop signal to worker thread +2017-05-09 17:42:34,088 INFO [galaxy.jobs.handler] job handler queue stopped +2017-05-09 17:42:34,088 INFO [galaxy.jobs.runners] TaskRunner: Sending stop signal to 2 worker threads +2017-05-09 17:42:34,089 INFO [galaxy.jobs.runners] LocalRunner: Sending stop signal to 4 worker threads +2017-05-09 17:42:34,089 INFO [galaxy.jobs.handler] sending stop signal to worker thread +2017-05-09 17:42:34,089 INFO [galaxy.jobs.handler] job handler stop queue stopped +Testing complete. HTML report is in "/home/backdoor/toolshed_test/w4mclassfilter/tool_test_output.html". +All 3 test(s) executed passed. +W4MClassFilter[0]: passed +W4MClassFilter[1]: passed +W4MClassFilter[2]: passed
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/w4mclassfilter.xml Wed May 10 11:28:01 2017 -0400 @@ -0,0 +1,374 @@ +<tool id="w4mclassfilter" name="Sample_Subset" version="0.98.1"> + <description>Filter W4M data by sample class</description> + + <requirements> + <requirement type="package" version="3.3.1">r-base</requirement> + <requirement type="package" version="1.1_4">r-batch</requirement> + <requirement type="package" version="0.98.1">w4mclassfilter</requirement> + </requirements> + + <stdio> + <exit_code range="1:" level="fatal" /> + </stdio> + + + <command detect_errors="aggressive"><![CDATA[ + Rscript $__tool_directory__/w4mclassfilter_wrapper.R + dataMatrix_in "$dataMatrix_in" + sampleMetadata_in "$sampleMetadata_in" + variableMetadata_in "$variableMetadata_in" + sampleclassNames "$sampleclassNames" + inclusive "$inclusive" + classnameColumn "$classnameColumn" + samplenameColumn "$samplenameColumn" + dataMatrix_out "$dataMatrix_out" + sampleMetadata_out "$sampleMetadata_out" + variableMetadata_out "$variableMetadata_out" + ]]></command> + + <inputs> + <param name="dataMatrix_in" label="Data matrix file" type="data" format="tabular" help="variable x sample, decimal: '.', missing: NA, mode: numerical, separator: tab" /> + <param name="sampleMetadata_in" label="Sample metadata file" type="data" format="tabular" help="sample x metadata columns, separator: tab" /> + <param name="variableMetadata_in" label="Variable metadata file" type="data" format="tabular" help="variable x metadata columns, separator: tab" /> + <param name="sampleclassNames" label="Names of sample classes" type="text" value = "" help="comma-separated names of sample classes to filter in or out; defaults to no names" /> + <param name="inclusive" label="Include named classes" type="select" help="filter-in - include only the named sample classes; filter-out (the default) - exclude only the named sample classes"> + <option value="TRUE">filter-in</option> + <option value="FALSE" selected="true">filter-out</option> + </param> + <param name="classnameColumn" label="Column that names the sample-class" type="text" value = "class" help="name of the column in sample metadata that has the values to be tested against the 'classes' input parameter - defaults to 'class'" /> + <param name="samplenameColumn" label="Column that names the sample" type="text" value = "sampleMetadata" help="name of the column in sample metadata that has the name of the sample - defaults to 'sampleMetadata'" /> + </inputs> + <outputs> + <data name="dataMatrix_out" label="${tool.name}_${dataMatrix_in.name}" format="tabular" ></data> + <data name="sampleMetadata_out" label="${tool.name}_${sampleMetadata_in.name}" format="tabular" ></data> + <data name="variableMetadata_out" label="${tool.name}_${variableMetadata_in.name}" format="tabular" ></data> + </outputs> + + <tests> + <test> + <param name="dataMatrix_in" value="input_dataMatrix.tsv"/> + <param name="sampleMetadata_in" value="input_sampleMetadata.tsv"/> + <param name="variableMetadata_in" value="input_variableMetadata.tsv"/> + <param name="classnameColumn" value="gender"/> + <param name="sampleclassNames" value="M"/> + <param name="samplenameColumn" value="sampleMetadata"/> + <param name="inclusive" value="filter-in"/> + <output name="dataMatrix_out"> + <assert_contents> + <not_has_text text="HU_028" /> + <not_has_text text="HU_051" /> + <not_has_text text="HU_060" /> + <not_has_text text="HU_110" /> + <not_has_text text="HU_149" /> + <not_has_text text="HU_152" /> + <not_has_text text="HU_175" /> + <not_has_text text="HU_178" /> + <not_has_text text="HU_185" /> + <not_has_text text="HU_204" /> + <not_has_text text="HU_208" /> + <has_text text="HU_017" /> + <has_text text="HU_034" /> + <has_text text="HU_078" /> + <has_text text="HU_091" /> + <has_text text="HU_093" /> + <has_text text="HU_099" /> + <has_text text="HU_130" /> + <has_text text="HU_134" /> + <has_text text="HU_138" /> + <has_text text="HMDB03193" /> + <not_has_text text="HMDB00822" /> + <has_text text="HMDB01101" /> + <has_text text="HMDB01101.1" /> + <has_text text="HMDB10348" /> + <has_text text="HMDB59717" /> + <has_text text="HMDB13189" /> + <has_text text="HMDB00299" /> + <has_text text="HMDB00191" /> + <has_text text="HMDB00518" /> + <has_text text="HMDB00715" /> + <has_text text="HMDB01032" /> + <has_text text="HMDB00208" /> + <has_text text="HMDB04824" /> + <has_text text="HMDB00512" /> + <has_text text="HMDB00251" /> + </assert_contents> + </output> + </test> + <test> + <param name="dataMatrix_in" value="input_dataMatrix.tsv"/> + <param name="sampleMetadata_in" value="input_sampleMetadata.tsv"/> + <param name="variableMetadata_in" value="input_variableMetadata.tsv"/> + <param name="classnameColumn" value="gender"/> + <param name="sampleclassNames" value="M"/> + <param name="samplenameColumn" value="sampleMetadata"/> + <param name="inclusive" value="filter-in"/> + <output name="sampleMetadata_out"> + <assert_contents> + <not_has_text text="HU_028" /> + <not_has_text text="HU_051" /> + <not_has_text text="HU_060" /> + <not_has_text text="HU_110" /> + <not_has_text text="HU_149" /> + <not_has_text text="HU_152" /> + <not_has_text text="HU_175" /> + <not_has_text text="HU_178" /> + <not_has_text text="HU_185" /> + <not_has_text text="HU_204" /> + <not_has_text text="HU_208" /> + <has_text text="HU_017" /> + <has_text text="HU_034" /> + <has_text text="HU_078" /> + <has_text text="HU_091" /> + <has_text text="HU_093" /> + <has_text text="HU_099" /> + <has_text text="HU_130" /> + <has_text text="HU_134" /> + <has_text text="HU_138" /> + </assert_contents> + </output> + </test> + <test> + <param name="dataMatrix_in" value="input_dataMatrix.tsv"/> + <param name="sampleMetadata_in" value="input_sampleMetadata.tsv"/> + <param name="variableMetadata_in" value="input_variableMetadata.tsv"/> + <param name="classnameColumn" value="gender"/> + <param name="sampleclassNames" value="M"/> + <param name="samplenameColumn" value="sampleMetadata"/> + <param name="inclusive" value="filter-in"/> + <output name="variableMetadata_out"> + <assert_contents> + <has_text text="HMDB03193" /> + <not_has_text text="HMDB00822" /> + <has_text text="HMDB01101" /> + <has_text text="HMDB01101.1" /> + <has_text text="HMDB10348" /> + <has_text text="HMDB59717" /> + <has_text text="HMDB13189" /> + <has_text text="HMDB00299" /> + <has_text text="HMDB00191" /> + <has_text text="HMDB00518" /> + <has_text text="HMDB00715" /> + <has_text text="HMDB01032" /> + <has_text text="HMDB00208" /> + <has_text text="HMDB04824" /> + <has_text text="HMDB00512" /> + <has_text text="HMDB00251" /> + </assert_contents> + </output> + </test> + </tests> + + + + <help> + <![CDATA[ + +.. class:: infomark + +**Author** Arthur Eschenlauer (University of Minnesota, esch0041@umn.edu) + +-------------------------------------------------------------------------- + +.. class:: infomark + +**R package** + +The *w4mclassfilter* package is available from the Hegeman lab github repository (https://github.com/HegemanLab/w4mclassfilter/releases). + +----------------------------------------------------------------------------------------------------------------------------------------- + +.. class:: infomark + +**Tool updates** + +See the **NEWS** section at the bottom of this page + +--------------------------------------------------- + +============================================== +Filter Workflow4Metabolomics data matrix files +============================================== + +----------- +Description +----------- + +Filter a set of retention-corrected W4M files (dataMatrix, sampleMetadata, variableMetadata) by sample-class + +----------------- +Workflow Position +----------------- + + - Upstream tool category: Preprocessing + - Downstream tool categories: Normalisation, Statistical Analysis, Quality Control + +---------- +Motivation +---------- + +GC-MS1 and LC-MS1 experiments seek to resolve chemicals as features that have distinct chromatographic behavior and (after ionization) mass-to-charge ratio. +Data for a sample are collected as MS intensities, each of which is associated with a position on a 2D plane with dimensions of m/z ratio and chromatographic retention time. +Ideally, features would be sufficiently reproducible from sample-run to sample-run to identify features that are commmon among samples and those that differ. +However, the chromatographic retention time for a chemical can vary from one run to another. +In the Workflow4Metabolomics (W4M, [Giacomoni *et al.*, 2014]) "flavor" of Galaxy, the XCMS [Smith *et al.*, 2006] preprocessing tools provide for "retention time correction" to align features among samples, but features may be better aligned if pooled samples and blanks are included. + +Multivariate statistical techniques may be used to discover clusters of similar samples, and sometimes it is desirable to apply clustering iteratively to smaller and smaller subsets of samples until observable separation of clusters is no longer significant. +Once feature-alignment has been achieved among samples in GC-MS and LC-MS datasets, however, the presence of pools and blanks may confound identification and separation of clusters. +Multivariate statistical algorithms also may be impacted by missing values or dimensions that have zero variance. + +The w4mclassfilter tool provides a way to choose subsets of samples for further analysis. +The tool takes as input the data matrix, sample metadata, and variable metadata Galaxy datasets produced by W4M and produces the same trio of datasets with data only for the selected samples. +The tool uses a "sample-class" column in the sample metadata as the basis for including or eliminating samples for further analysis. +Class-values to be considered are provided by the user as a comma-separated list. +The user also provides an indication whether the list specifies classes to be included in further analysis ("filter-in") or rather to be excluded from it ("filter-out"). +Next, missing and negative intensites for features of the remaining samples are imputed to zero. +Finally, samples or features with zero variance are eliminated. + + +----------- +Input files +----------- + ++---------------------------+------------+ +| File | Format | ++===========================+============+ +| Data matrix | tabular | ++---------------------------+------------+ +| Sample metadata | tabular | ++---------------------------+------------+ +| Variable metadata | tabular | ++---------------------------+------------+ + + +---------- +Parameters +---------- + +Data matrix file + | variable x sample **dataMatrix** (tabular separated values) 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) + | + +Sample metadata file + | sample x metadata **sampleMetadata** (tabular separated values) file of the numeric and/or character sample metadata, with . as decimal and NA for missing values + | + +Variable metadata file + | variable x metadata **variableMetadata** (tabular separated values) file of the numeric and/or character variable metadata, with . as decimal and NA for missing values + | + +Names of sample classes (default = no names) + | comma-separated names of sample classes to include or exclude + | + +Include named classes (default = filter-out) + | *filter-in* - include only the named sample classes + | *filter-out* - exclude only the named sample classes + | + + +Column that names the sample-class (default = 'class') + | name of the column in sample metadata that has the values to be tested against the 'classes' input parameter + | + +Column that names the sample (default = 'sampleMetadata') + | name of the column in sample metadata that has the name of the sample + | + + +------------ +Output files +------------ + + +sampleMetadata + | (tabular separated values) file identical to the **sampleMetadata** file given as an input argument, excepting lacking rows for samples (xC-MS features) that have been filtered out (by the sample-class filter or because of zero variance) + | + +variableMetadata + | (tabular separated values) file identical to the **variableMetadata** file given as an input argument, excepting lacking rows for variables (xC-MS features) that have been filtered out (because of zero variance) + | + +dataMatrix + | (tabular separated values) file identical to the **dataMatrix** file given as an input argument, excepting lacking rows for variables (xC-MS features) that have been filtered out (because of zero variance) and columns that have been filtered out (by the sample-class filter or because of zero variance) + | + + +--------------- +Working example +--------------- + +.. class:: infomark + +**Input files** + ++-------------------+--------------------------------------------------------------------------------------------------------------+ +| Input File | Download from URL | ++===================+==============================================================================================================+ +| Data matrix | https://raw.githubusercontent.com/HegemanLab/w4mclassfilter/master/tests/testthat/input_dataMatrix.tsv | ++-------------------+--------------------------------------------------------------------------------------------------------------+ +| Sample metadata | https://raw.githubusercontent.com/HegemanLab/w4mclassfilter/master/tests/testthat/input_sampleMetadata.tsv | ++-------------------+--------------------------------------------------------------------------------------------------------------+ +| Variable metadata | https://raw.githubusercontent.com/HegemanLab/w4mclassfilter/master/tests/testthat/input_variableMetadata.tsv | ++-------------------+--------------------------------------------------------------------------------------------------------------+ + +.. class:: infomark + +**Other input parameters** + ++------------------------------------+-----------------+ +| Input Parameter | Value | ++====================================+=================+ +| Names of sample classes | M | ++------------------------------------+-----------------+ +| Include named classes | filter-in | ++------------------------------------+-----------------+ +| Column that names the sample-class | gender | ++------------------------------------+-----------------+ +| Column that names the sample | sampleMetadata | ++------------------------------------+-----------------+ + +.. class:: infomark + +**Expected outputs** + ++-------------------+-----------------------------------------------------------------------------------------------------------------+ +| Expected Output | Download from URL | ++===================+=================================================================================================================+ +| Data matrix | https://raw.githubusercontent.com/HegemanLab/w4mclassfilter/master/tests/testthat/expected_dataMatrix.tsv | ++-------------------+-----------------------------------------------------------------------------------------------------------------+ +| Sample metadata | https://raw.githubusercontent.com/HegemanLab/w4mclassfilter/master/tests/testthat/expected_sampleMetadata.tsv | ++-------------------+-----------------------------------------------------------------------------------------------------------------+ +| Variable metadata | https://raw.githubusercontent.com/HegemanLab/w4mclassfilter/master/tests/testthat/expected_variableMetadata.tsv | ++-------------------+-----------------------------------------------------------------------------------------------------------------+ + + +----------------------------------------------------------------------------- + +---- +NEWS +---- + +CHANGES IN VERSION 0.98.1 +========================= + +NEW FEATURES + +First release - Wrap the w4mclassfilter R package that implements filtering of W4M data matrix, variable metadata, and sample metadata by class of sample. + +*dataMatrix* *is* modified by the tool, so it *does* appear as an output file +*sampleMetadata* *is* modified by the tool, so it *does* appear as an output file +*variableMetadata* *is* modified by the tool, so it *does* appear as an output file + +INTERNAL MODIFICATIONS + +none + + ]]> + </help> + <citations> + <citation type="doi">10.1021/ac051437y</citation> + <citation type="doi">10.1093/bioinformatics/btu813</citation> + </citations> +</tool> +<!-- vim: noet sw=4 ts=4 : +-->
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/w4mclassfilter_wrapper.R Wed May 10 11:28:01 2017 -0400 @@ -0,0 +1,144 @@ +#!/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 + +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())