| Previous changeset 2:23c6d271def9 (2017-05-10) Next changeset 4:499c7ecfa834 (2017-06-19) |
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Commit message:
planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit dacc1bae8e60340a431907fe8a8b490357e1bfc0 |
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modified:
README w4mclassfilter.xml |
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removed:
README.md test_log.txt |
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| diff -r 23c6d271def9 -r 191a720488ce README --- a/README Wed May 10 02:51:58 2017 -0400 +++ b/README Thu May 11 00:05:51 2017 -0400 |
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| @@ -1,6 +1,6 @@ -# w4mclassfilter_galaxy_wrapper +Galaxy Wrapper for the w4mclassfilter R Package -planemo <http://planemo.readthedocs.io/en/latest/> +This is a 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/> |
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| diff -r 23c6d271def9 -r 191a720488ce README.md --- a/README.md Wed May 10 02:51:58 2017 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,7 +0,0 @@ -# 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/) |
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| diff -r 23c6d271def9 -r 191a720488ce test_log.txt --- a/test_log.txt Wed May 10 02:51:58 2017 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| b'@@ -1,334 +0,0 @@\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' |
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| diff -r 23c6d271def9 -r 191a720488ce w4mclassfilter.xml --- a/w4mclassfilter.xml Wed May 10 02:51:58 2017 -0400 +++ b/w4mclassfilter.xml Thu May 11 00:05:51 2017 -0400 |
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| @@ -1,4 +1,4 @@ -<tool id="W4MClassFilter" name="W4MClassFilter" version="0.98.1"> +<tool id="w4mclassfilter" name="Sample_Subset" version="0.98.1"> <description>Filter W4M data by sample class</description> <requirements> @@ -193,15 +193,37 @@ Description ----------- -Filter set of retention-corrected W4M files (dataMatrix, sampleMetadata, variableMetadata) by sample class +Filter a set of retention-corrected W4M files (dataMatrix, sampleMetadata, variableMetadata) by sample-class + +----------------- +Workflow Position +----------------- + + - Upstream tool category: Preprocessing + - Downstream tool categories: Normalisation, Statistical Analysis, Quality Control + +---------- +Motivation +---------- --------- -Comments --------- +GC-MS1 and LC-MS1 experiments seek to resolve chemicals as features that have distinct chromatographic behavior and (after ionization) mass-to-charge ratio. +Data for a sample are collected as MS intensities, each of which is associated with a position on a 2D plane with dimensions of m/z ratio and chromatographic retention time. +Ideally, features would be sufficiently reproducible from sample-run to sample-run to identify features that are commmon among samples and those that differ. +However, the chromatographic retention time for a chemical can vary from one run to another. +In the Workflow4Metabolomics (W4M, [Giacomoni *et al.*, 2014]) "flavor" of Galaxy, the XCMS [Smith *et al.*, 2006] preprocessing tools provide for "retention time correction" to align features among samples, but features may be better aligned if pooled samples and blanks are included. -The *inclusive* parameter indicates: - - when 'filter-in', that only the sample-classes named should be included - - when 'filter-out', that all sample-classes should be included excepting the sample-classes named +Multivariate statistical techniques may be used to discover clusters of similar samples, and sometimes it is desirable to apply clustering iteratively to smaller and smaller subsets of samples until observable separation of clusters is no longer significant. +Once feature-alignment has been achieved among samples in GC-MS and LC-MS datasets, however, the presence of pools and blanks may confound identification and separation of clusters. +Multivariate statistical algorithms also may be impacted by missing values or dimensions that have zero variance. + +The w4mclassfilter tool provides a way to choose subsets of samples for further analysis. +The tool takes as input the data matrix, sample metadata, and variable metadata Galaxy datasets produced by W4M and produces the same trio of datasets with data only for the selected samples. +The tool uses a "sample-class" column in the sample metadata as the basis for including or eliminating samples for further analysis. +Class-values to be considered are provided by the user as a comma-separated list. +The user also provides an indication whether the list specifies classes to be included in further analysis ("filter-in") or rather to be excluded from it ("filter-out"). +Next, missing and negative intensites for features of the remaining samples are imputed to zero. +Finally, samples or features with zero variance are eliminated. + ----------- Input files @@ -331,17 +353,22 @@ NEW FEATURES -First release - R package that implements filtering of W4M data matrix, variable metadata, and sample metadata by class of sample. +First release - Wrap the w4mclassfilter R package that implements filtering of W4M data matrix, variable metadata, and sample metadata by class of sample. *dataMatrix* *is* modified by the tool, so it *does* appear as an output file +*sampleMetadata* *is* modified by the tool, so it *does* appear as an output file +*variableMetadata* *is* modified by the tool, so it *does* appear as an output file INTERNAL MODIFICATIONS none + ]]> </help> <citations> + <citation type="doi">10.1021/ac051437y</citation> + <citation type="doi">10.1093/bioinformatics/btu813</citation> </citations> -</tool> -<!-- vim: noet sw=4 ts=4 : ---> + <!-- + vim:noet:sw=4:ts=4 +--> </tool> |