# HG changeset patch
# User lecorguille
# Date 1494430081 14400
# Node ID 8ad970e2c137cddd884f4147cb6811f9d1af71fe
planemo upload
diff -r 000000000000 -r 8ad970e2c137 LICENSE
--- /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.
diff -r 000000000000 -r 8ad970e2c137 README
--- /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
+oriented galaxy-tool-wrapper
+to wrap the w4mclassfilter R package
+for use with the Workflow4Metabolomics
+flavor of Galaxy
diff -r 000000000000 -r 8ad970e2c137 README.md
--- /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/)
diff -r 000000000000 -r 8ad970e2c137 test-data/expected_dataMatrix.tsv
--- /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
diff -r 000000000000 -r 8ad970e2c137 test-data/expected_sampleMetadata.tsv
--- /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
diff -r 000000000000 -r 8ad970e2c137 test-data/expected_variableMetadata.tsv
--- /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
diff -r 000000000000 -r 8ad970e2c137 test-data/input_dataMatrix.tsv
--- /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
diff -r 000000000000 -r 8ad970e2c137 test-data/input_sampleMetadata.tsv
--- /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
diff -r 000000000000 -r 8ad970e2c137 test-data/input_variableMetadata.tsv
--- /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
diff -r 000000000000 -r 8ad970e2c137 test_log.txt
--- /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 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
diff -r 000000000000 -r 8ad970e2c137 w4mclassfilter.xml
--- /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 @@
+
+ Filter W4M data by sample class
+
+
+ r-base
+ r-batch
+ w4mclassfilter
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
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+
+
+
+
+
+
+
+
+
+
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+
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+
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+
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+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ 10.1021/ac051437y
+ 10.1093/bioinformatics/btu813
+
+
+
diff -r 000000000000 -r 8ad970e2c137 w4mclassfilter_wrapper.R
--- /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())