Mercurial > repos > eschen42 > w4mclassfilter

changeset 2:23c6d271def9 draft

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planemo upload
author eschen42
date Wed, 10 May 2017 02:51:58 -0400
parents 371741d19743
children 191a720488ce
files test_log.txt w4mclassfilter.xml w4mclassfilter_wrapper.R
diffstat 3 files changed, 406 insertions(+), 33 deletions(-) [+]
line wrap: on
line diff
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test_log.txt	Wed May 10 02:51:58 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
--- a/w4mclassfilter.xml	Tue May 09 18:37:51 2017 -0400
+++ b/w4mclassfilter.xml	Wed May 10 02:51:58 2017 -0400
@@ -24,13 +24,12 @@
   dataMatrix_out "$dataMatrix_out"
   sampleMetadata_out "$sampleMetadata_out"
   variableMetadata_out "$variableMetadata_out"
-  information "$information"
   ]]></command>
 
   <inputs>
-    <param name="dataMatrix_in" label="Data matrix file" type="data" format="tabular" help="variable x sample, decimal: '.', missing: NA, mode: numerical, sep: tabular" />
-    <param name="sampleMetadata_in" label="Sample metadata file" type="data" format="tabular" help="sample x metadata, decimal: '.', missing: NA, mode: character and numerical, sep: tabular" />
-    <param name="variableMetadata_in" label="Variable metadata file" type="data" format="tabular" help="variable x metadata, decimal: '.', missing: NA, mode: character and numerical, sep: tabular" />
+    <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>
@@ -43,7 +42,6 @@
     <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>
-    <data name="information" label="${tool.name}__information.txt" format="txt"/>
   </outputs>
 
   <tests>
@@ -55,7 +53,6 @@
       <param name="sampleclassNames" value="M"/>
       <param name="samplenameColumn" value="sampleMetadata"/>
       <param name="inclusive" value="filter-in"/>
-      <param name="information" value="test-information.txt"/>
       <output name="dataMatrix_out">
         <assert_contents>
           <not_has_text text="HU_028" />
@@ -105,7 +102,6 @@
       <param name="sampleclassNames" value="M"/>
       <param name="samplenameColumn" value="sampleMetadata"/>
       <param name="inclusive" value="filter-in"/>
-      <param name="information" value="test-information.txt"/>
       <output name="sampleMetadata_out">
         <assert_contents>
           <not_has_text text="HU_028" />
@@ -139,7 +135,6 @@
       <param name="sampleclassNames" value="M"/>
       <param name="samplenameColumn" value="sampleMetadata"/>
       <param name="inclusive" value="filter-in"/>
-      <param name="information" value="test-information.txt"/>
       <output name="variableMetadata_out">
         <assert_contents>
           <has_text     text="HMDB03193" />
@@ -165,7 +160,8 @@
 
 
 
-  <help>
+	<help>
+		<![CDATA[
 
 .. class:: infomark
 
@@ -214,11 +210,11 @@
 +---------------------------+------------+
 | File                      |   Format   |
 +===========================+============+
-| 1)  Data matrix           |   tabular  |
+|     Data matrix           |   tabular  |
 +---------------------------+------------+
-| 2)  Sample metadata       |   tabular  |
+|     Sample metadata       |   tabular  |
 +---------------------------+------------+
-| 3)  Variable metadata     |   tabular  |
+|     Variable metadata     |   tabular  |
 +---------------------------+------------+
 
 
@@ -227,15 +223,15 @@
 ----------
 
 Data matrix file
-	| variable x sample **dataMatrix** tabular separated file of the numeric data matrix, with . as decimal, and NA for missing values; the table must not contain metadata apart from row and column names; the row and column names must be identical to the rownames of the sample and variable metadata, respectively (see below)
+	| 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 file of the numeric and/or character sample metadata, with . as decimal and NA for missing values
+	| 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 file of the numeric and/or character variable metadata, with . as decimal and NA for missing values
+	| 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)
@@ -243,10 +239,11 @@
 	|
 
 Include named classes (default = filter-out)
-  | *filter-in* - include only the named sample classes
-  | *filter-out* - exclude only the named sample classes
+	| *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
 	|
@@ -261,21 +258,67 @@
 ------------
 
 
-sampleMetadata_out.tabular
-	| **sampleMetadata** tabular separated file identical to the file given as argument, excepting lacking rows for samples that have been filtered out
+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_out.tabular
-	| **variableMetadata** tabular separated file identical to the file given as argument, excepting lacking rows for variables (xC-MS features) that have been filtered out (because of zero variance)
+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)
 	|
 
-dataMatrix_out.tabular
-	| **dataMatrix** tabular separated file identical to the file given as argument, excepting lacking columns for samples that have been filtered out (because of the sample-classes specified in the input parameters) and rows for variables (xC-MS features) that have been filtered out (because of zero variance)
-	|
+
+---------------
+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**
 
-information.txt
-	| Text file with all messages and warnings generated during the computation
-	|
++------------------------------------+-----------------+
+| 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 |
++-------------------+-----------------------------------------------------------------------------------------------------------------+
+
 
 -----------------------------------------------------------------------------
 
@@ -295,10 +338,10 @@
 INTERNAL MODIFICATIONS
 
 none
-
+    ]]>
   </help>
   <citations>
   </citations>
 </tool>
-<!-- vim: et sw=2 ts=2 :
+<!-- vim: noet sw=4 ts=4 :
 -->
--- a/w4mclassfilter_wrapper.R	Tue May 09 18:37:51 2017 -0400
+++ b/w4mclassfilter_wrapper.R	Wed May 10 02:51:58 2017 -0400
@@ -61,10 +61,6 @@
 ## log file
 ##---------
 
-information <- as.character(argVc["information"])
-
-#sink(information)
-
 my_print <- function(x, ...) { cat(c(x, ...))}
 
 my_print("\nStart of the '", modNamC, "' Galaxy module call: ",