| Previous changeset 1:371741d19743 (2017-05-09) Next changeset 3:191a720488ce (2017-05-11) |
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Commit message:
planemo upload |
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modified:
w4mclassfilter.xml w4mclassfilter_wrapper.R |
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added:
test_log.txt |
| b |
| diff -r 371741d19743 -r 23c6d271def9 test_log.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test_log.txt Wed May 10 02:51:58 2017 -0400 |
| [ |
| b'@@ -0,0 +1,334 @@\n+git --git-dir /home/backdoor/.planemo/gx_repo fetch >/dev/null 2>&1\n+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}\n+Cloning into \'galaxy-dev\'...\n+done.\n+Set COMMON_STARTUP_ARGS to --dev-wheels\n+Initializing config/migrated_tools_conf.xml from migrated_tools_conf.xml.sample\n+Initializing config/shed_tool_conf.xml from shed_tool_conf.xml.sample\n+Initializing config/shed_tool_data_table_conf.xml from shed_tool_data_table_conf.xml.sample\n+Initializing config/shed_data_manager_conf.xml from shed_data_manager_conf.xml.sample\n+Initializing tool-data/shared/ucsc/builds.txt from builds.txt.sample\n+Initializing tool-data/shared/ucsc/manual_builds.txt from manual_builds.txt.sample\n+Initializing tool-data/shared/ucsc/ucsc_build_sites.txt from ucsc_build_sites.txt.sample\n+Initializing tool-data/shared/igv/igv_build_sites.txt from igv_build_sites.txt.sample\n+Initializing tool-data/shared/rviewer/rviewer_build_sites.txt from rviewer_build_sites.txt.sample\n+Initializing static/welcome.html from welcome.html.sample\n+Activating virtualenv at /home/backdoor/.planemo/gx_venv\n+Requirement already satisfied: pip>=8.1 in /home/backdoor/.planemo/gx_venv/lib/python2.7/site-packages\n+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))\n+Requirement already satisfied: MarkupSafe==0.23 in /home/backdoor/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 3))\n+Requirement already satisfied: PyYAML==3.11 in /home/backdoor/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 4))\n+Requirement already satisfied: SQLAlchemy==1.0.15 in /home/backdoor/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 5))\n+Requirement already satisfied: mercurial==3.7.3 in /home/backdoor/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 6))\n+Requirement already satisfied: numpy==1.9.2 in /home/backdoor/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 7))\n+Requirement already satisfied: pycrypto==2.6.1 in /home/backdoor/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 8))\n+Requirement already satisfied: Paste==2.0.2 in /home/backdoor/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 15))\n+Requirement already satisfied: PasteDeploy==1.5.2 in /home/backdoor/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 16))\n+Requirement already satisfied: docutils==0.12 in /home/backdoor/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 17))\n+Requirement already satisfied: wchartype==0.1 in /home/backdoor/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 18))\n+Requirement already satisfied: repoze.lru==0.6 in /home/backdoor/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 19))\n+Requirement already satisfied: Routes==2.2 in /home/backdoor/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 20))\n+Requirement already satisfied: WebOb==1.4.1 in /home/backdoor/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 21))\n+Requirement already satisfied: WebHelpers==1.3 in /home/backdoor/.planemo/'..b',903 DEBUG [galaxy.tools.deps] Using dependency r-batch version 1.1_4 of type conda\n+2017-05-09 17:42:26,903 DEBUG [galaxy.tools.deps] Using dependency w4mclassfilter version 0.98.1 of type conda\n+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"]\n+2017-05-09 17:42:27,374 DEBUG [galaxy.tools.deps] Using dependency samtools version None of type conda\n+2017-05-09 17:42:27,375 DEBUG [galaxy.tools.deps] Using dependency samtools version None of type conda\n+ok\n+\n+----------------------------------------------------------------------\n+XML: /tmp/tmpBnX6kx/xunit.xml\n+----------------------------------------------------------------------\n+Ran 3 tests in 69.356s\n+\n+OK\n+2017-05-09 17:42:33,110 INFO [test_driver] Shutting down\n+2017-05-09 17:42:33,110 INFO [test_driver] Shutting down embedded galaxy web server\n+2017-05-09 17:42:33,112 INFO [test_driver] Embedded web server galaxy stopped\n+2017-05-09 17:42:33,112 INFO [test_driver] Stopping application galaxy\n+2017-05-09 17:42:33,112 INFO [galaxy.jobs.handler] sending stop signal to worker thread\n+2017-05-09 17:42:33,112 INFO [galaxy.jobs.handler] job handler queue stopped\n+2017-05-09 17:42:33,112 INFO [galaxy.jobs.runners] TaskRunner: Sending stop signal to 2 worker threads\n+2017-05-09 17:42:33,112 INFO [galaxy.jobs.runners] LocalRunner: Sending stop signal to 4 worker threads\n+2017-05-09 17:42:33,112 INFO [galaxy.jobs.handler] sending stop signal to worker thread\n+2017-05-09 17:42:33,112 INFO [galaxy.jobs.handler] job handler stop queue stopped\n+2017-05-09 17:42:33,113 INFO [test_driver] Application galaxy stopped.\n+2017-05-09 17:42:34,087 INFO [galaxy.jobs.handler] sending stop signal to worker thread\n+2017-05-09 17:42:34,088 INFO [galaxy.jobs.handler] job handler queue stopped\n+2017-05-09 17:42:34,088 INFO [galaxy.jobs.runners] TaskRunner: Sending stop signal to 2 worker threads\n+2017-05-09 17:42:34,089 INFO [galaxy.jobs.runners] LocalRunner: Sending stop signal to 4 worker threads\n+2017-05-09 17:42:34,089 INFO [galaxy.jobs.handler] sending stop signal to worker thread\n+2017-05-09 17:42:34,089 INFO [galaxy.jobs.handler] job handler stop queue stopped\n+Testing complete. HTML report is in "/home/backdoor/toolshed_test/w4mclassfilter/tool_test_output.html".\n+All 3 test(s) executed passed.\n+W4MClassFilter[0]: passed\n+W4MClassFilter[1]: passed\n+W4MClassFilter[2]: passed\n' |
| b |
| diff -r 371741d19743 -r 23c6d271def9 w4mclassfilter.xml --- a/w4mclassfilter.xml Tue May 09 18:37:51 2017 -0400 +++ b/w4mclassfilter.xml Wed May 10 02:51:58 2017 -0400 |
| [ |
| b'@@ -24,13 +24,12 @@\n dataMatrix_out "$dataMatrix_out"\n sampleMetadata_out "$sampleMetadata_out"\n variableMetadata_out "$variableMetadata_out"\n- information "$information"\n ]]></command>\n \n <inputs>\n- <param name="dataMatrix_in" label="Data matrix file" type="data" format="tabular" help="variable x sample, decimal: \'.\', missing: NA, mode: numerical, sep: tabular" />\n- <param name="sampleMetadata_in" label="Sample metadata file" type="data" format="tabular" help="sample x metadata, decimal: \'.\', missing: NA, mode: character and numerical, sep: tabular" />\n- <param name="variableMetadata_in" label="Variable metadata file" type="data" format="tabular" help="variable x metadata, decimal: \'.\', missing: NA, mode: character and numerical, sep: tabular" />\n+ <param name="dataMatrix_in" label="Data matrix file" type="data" format="tabular" help="variable x sample, decimal: \'.\', missing: NA, mode: numerical, separator: tab" />\n+ <param name="sampleMetadata_in" label="Sample metadata file" type="data" format="tabular" help="sample x metadata columns, separator: tab" />\n+ <param name="variableMetadata_in" label="Variable metadata file" type="data" format="tabular" help="variable x metadata columns, separator: tab" />\n <param name="sampleclassNames" label="Names of sample classes" type="text" value = "" help="comma-separated names of sample classes to filter in or out; defaults to no names" />\n <param name="inclusive" label="Include named classes" type="select" help="filter-in - include only the named sample classes; filter-out (the default) - exclude only the named sample classes">\n <option value="TRUE">filter-in</option>\n@@ -43,7 +42,6 @@\n <data name="dataMatrix_out" label="${tool.name}_${dataMatrix_in.name}" format="tabular" ></data>\n <data name="sampleMetadata_out" label="${tool.name}_${sampleMetadata_in.name}" format="tabular" ></data>\n <data name="variableMetadata_out" label="${tool.name}_${variableMetadata_in.name}" format="tabular" ></data>\n- <data name="information" label="${tool.name}__information.txt" format="txt"/>\n </outputs>\n \n <tests>\n@@ -55,7 +53,6 @@\n <param name="sampleclassNames" value="M"/>\n <param name="samplenameColumn" value="sampleMetadata"/>\n <param name="inclusive" value="filter-in"/>\n- <param name="information" value="test-information.txt"/>\n <output name="dataMatrix_out">\n <assert_contents>\n <not_has_text text="HU_028" />\n@@ -105,7 +102,6 @@\n <param name="sampleclassNames" value="M"/>\n <param name="samplenameColumn" value="sampleMetadata"/>\n <param name="inclusive" value="filter-in"/>\n- <param name="information" value="test-information.txt"/>\n <output name="sampleMetadata_out">\n <assert_contents>\n <not_has_text text="HU_028" />\n@@ -139,7 +135,6 @@\n <param name="sampleclassNames" value="M"/>\n <param name="samplenameColumn" value="sampleMetadata"/>\n <param name="inclusive" value="filter-in"/>\n- <param name="information" value="test-information.txt"/>\n <output name="variableMetadata_out">\n <assert_contents>\n <has_text text="HMDB03193" />\n@@ -165,7 +160,8 @@\n \n \n \n- <help>\n+\t<help>\n+\t\t<![CDATA[\n \n .. class:: infomark\n \n@@ -214,11 +210,11 @@\n +---------------------------+------------+\n | File | Format |\n +===========================+============+\n-| 1) Data matrix | tabular |\n+| Data matrix | tabular |\n +---------------------------+------------+\n-| 2) Sample metadata | tabular |\n+| Sample metadata | tabular |\n +---------------------------+------------+\n-| 3) Variable metadata | tabular |\n+| Variable metadata | tabular |\n +---------------------------+------------+\n \n \n@@ -227,15 +223,15 @@\n ----------\n \n Data matrix file\n-\t| variable x sample **dataMatrix** tabular separated file of the numeric data matrix, with . as '..b'of zero variance)\n \t|\n \n-dataMatrix_out.tabular\n-\t| **dataMatrix** tabular separated file identical to the file given as argument, excepting lacking columns for samples that have been filtered out (because of the sample-classes specified in the input parameters) and rows for variables (xC-MS features) that have been filtered out (because of zero variance)\n-\t|\n+\n+---------------\n+Working example\n+---------------\n+\n+.. class:: infomark\n+\n+**Input files**\n+\n++-------------------+--------------------------------------------------------------------------------------------------------------+\n+| Input File | Download from URL |\n++===================+==============================================================================================================+\n+| Data matrix | https://raw.githubusercontent.com/HegemanLab/w4mclassfilter/master/tests/testthat/input_dataMatrix.tsv |\n++-------------------+--------------------------------------------------------------------------------------------------------------+\n+| Sample metadata | https://raw.githubusercontent.com/HegemanLab/w4mclassfilter/master/tests/testthat/input_sampleMetadata.tsv |\n++-------------------+--------------------------------------------------------------------------------------------------------------+\n+| Variable metadata | https://raw.githubusercontent.com/HegemanLab/w4mclassfilter/master/tests/testthat/input_variableMetadata.tsv |\n++-------------------+--------------------------------------------------------------------------------------------------------------+\n+\n+.. class:: infomark\n+\n+**Other input parameters**\n \n-information.txt\n-\t| Text file with all messages and warnings generated during the computation\n-\t|\n++------------------------------------+-----------------+\n+| Input Parameter | Value |\n++====================================+=================+\n+| Names of sample classes | M |\n++------------------------------------+-----------------+\n+| Include named classes | filter-in |\n++------------------------------------+-----------------+\n+| Column that names the sample-class | gender |\n++------------------------------------+-----------------+\n+| Column that names the sample | sampleMetadata |\n++------------------------------------+-----------------+\n+\n+.. class:: infomark\n+\n+**Expected outputs**\n+\n++-------------------+-----------------------------------------------------------------------------------------------------------------+\n+| Expected Output | Download from URL |\n++===================+=================================================================================================================+\n+| Data matrix | https://raw.githubusercontent.com/HegemanLab/w4mclassfilter/master/tests/testthat/expected_dataMatrix.tsv |\n++-------------------+-----------------------------------------------------------------------------------------------------------------+\n+| Sample metadata | https://raw.githubusercontent.com/HegemanLab/w4mclassfilter/master/tests/testthat/expected_sampleMetadata.tsv |\n++-------------------+-----------------------------------------------------------------------------------------------------------------+\n+| Variable metadata | https://raw.githubusercontent.com/HegemanLab/w4mclassfilter/master/tests/testthat/expected_variableMetadata.tsv |\n++-------------------+-----------------------------------------------------------------------------------------------------------------+\n+\n \n -----------------------------------------------------------------------------\n \n@@ -295,10 +338,10 @@\n INTERNAL MODIFICATIONS\n \n none\n-\n+ ]]>\n </help>\n <citations>\n </citations>\n </tool>\n-<!-- vim: et sw=2 ts=2 :\n+<!-- vim: noet sw=4 ts=4 :\n -->\n' |
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| diff -r 371741d19743 -r 23c6d271def9 w4mclassfilter_wrapper.R --- 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: ", |