| Previous changeset 8:22a08e1dc675 (2018-01-12) Next changeset 10:73656b244cfe (2018-01-15) |
|
Commit message:
planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 1282ce98bfc1f7e724c0b22bac43a560753fcab8 |
|
modified:
w4mclassfilter.xml |
| b |
| diff -r 22a08e1dc675 -r de314813b7fe w4mclassfilter.xml --- a/w4mclassfilter.xml Fri Jan 12 04:09:38 2018 -0500 +++ b/w4mclassfilter.xml Mon Jan 15 10:45:25 2018 -0500 |
| b |
| b'@@ -565,27 +565,37 @@\n \n - Note, however, that when the "maximum" is greater than the "minimum" for the FEATMAX range specification, then the specification is ignored.\n \n----------------\n-Working example\n----------------\n+-----------------------------------------------------------------------------\n+\n+----------------\n+WORKING EXAMPLES\n+----------------\n \n .. class:: infomark\n \n-**Input files**\n+-----------\n+Input Files\n+-----------\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+| Input File URL |\n++==============================================================================================================+\n+| https://raw.githubusercontent.com/HegemanLab/w4mclassfilter/master/tests/testthat/input_dataMatrix.tsv |\n++--------------------------------------------------------------------------------------------------------------+\n+| https://raw.githubusercontent.com/HegemanLab/w4mclassfilter/master/tests/testthat/input_sampleMetadata.tsv |\n++--------------------------------------------------------------------------------------------------------------+\n+| https://raw.githubusercontent.com/HegemanLab/w4mclassfilter/master/tests/testthat/input_variableMetadata.tsv |\n++--------------------------------------------------------------------------------------------------------------+\n \n .. class:: infomark\n \n-**Other input parameters**\n+-------------------------------\n+Running Without Range-Filtering\n+-------------------------------\n+\n+This example retains only samples whose \'gender\' attribute is \'M\'.\n+\n+**Input parameters**\n \n +------------------------------------+-----------------+\n | Input Parameter | Value |\n@@ -599,8 +609,6 @@\n | Column that names the sample | sampleMetadata |\n +------------------------------------+-----------------+\n \n-.. class:: infomark\n-\n **Expected outputs**\n \n +-------------------+-----------------------------------------------------------------------------------------------------------------+\n@@ -613,6 +621,42 @@\n | Variable metadata | https://raw.githubusercontent.com/HegemanLab/w4mclassfilter/master/tests/testthat/expected_variableMetadata.tsv |\n +-------------------+-----------------------------------------------------------------------------------------------------------------+\n \n+.. class:: infomark\n+\n+----------------------------\n+Running With Range-Filtering\n+----------------------------\n+\n+This example retains only samples whose \'gender\' attribute is \'M\'.\n+\n+**Input parameters**\n+\n++------------------------------------+-------------------------------+\n+| Input Parameter | Value '..b'--------------------------+\n+| Column that names the sample-class | class |\n++------------------------------------+-------------------------------+\n+| Column that names the sample | sampleMetadata |\n++------------------------------------+-------------------------------+\n+| Variable range-filters | FEATMAX:2e6:,mz:200:,rt::800 |\n++------------------------------------+-------------------------------+\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/rangefilter_dataMatrix.tsv |\n++-------------------+--------------------------------------------------------------------------------------------------------------------+\n+| Sample metadata | https://raw.githubusercontent.com/HegemanLab/w4mclassfilter/master/tests/testthat/rangefilter_sampleMetadata.tsv |\n++-------------------+--------------------------------------------------------------------------------------------------------------------+\n+| Variable metadata | https://raw.githubusercontent.com/HegemanLab/w4mclassfilter/master/tests/testthat/rangefilter_variableMetadata.tsv |\n++-------------------+--------------------------------------------------------------------------------------------------------------------+\n+\n \n -----------------------------------------------------------------------------\n \n@@ -620,55 +664,54 @@\n NEWS\n ----\n \n-CHANGES IN VERSION 0.98.6\n+Changes in version 0.98.6\n =========================\n \n-NEW FEATURES\n+New features\n \n * Added support for filtering out features whose attributes fall outside specified ranges.\n For more detail, see "Variable-range filters" above.\n \n-INTERNAL MODIFICATIONS\n+Internal modifications\n \n * Now uses w4mclassfilter R package v0.98.6.\n * Now sorts sample names and feature names in output files because some statistical tools expect the same order in `dataMatrix` row and column names as in the corresponding metadata files.\n \n-CHANGES IN VERSION 0.98.3\n+Changes in version 0.98.3\n =========================\n \n-INTERNAL MODIFICATIONS\n+Internal modifications\n \n * Improved input handling.\n * Now uses w4mclassfilter R package v0.98.3, although that version has no functional implications for this tool.\n * Improved reference-list.\n \n-CHANGES IN VERSION 0.98.2\n+Changes in version 0.98.2\n =========================\n \n-NEW FEATURES\n+New features\n \n * Added support for R-flavored regular expression pattern-matching when selecting names of sample-classes.\n * Empty classes argument or zero-length class_column result in no samples filtered out.\n \n-INTERNAL MODIFICATIONS\n+Internal modifications\n \n * Support and tests for new features.\n \n-\n-CHANGES IN VERSION 0.98.1\n+Changes in version 0.98.1\n =========================\n \n-NEW FEATURES\n-\n First release - Wrap the w4mclassfilter R package that implements filtering of W4M data matrix, variable metadata, and sample metadata by class of sample.\n \n-*dataMatrix* *is* modified by the tool, so it *does* appear as an output file\n-*sampleMetadata* *is* modified by the tool, so it *does* appear as an output file\n-*variableMetadata* *is* modified by the tool, so it *does* appear as an output file\n+New features\n \n-INTERNAL MODIFICATIONS\n+* *dataMatrix* *is* modified by the tool, so it *does* appear as an output file\n+* *sampleMetadata* *is* modified by the tool, so it *does* appear as an output file\n+* *variableMetadata* *is* modified by the tool, so it *does* appear as an output file\n \n-none\n+Internal modifications\n+\n+* N/A\n \n ]]></help>\n <citations>\n' |