| Previous changeset 0:9549cc9e8ec6 (2017-05-09) Next changeset 2:9a3462eff3bf (2017-05-10) |
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Commit message:
planemo upload |
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modified:
w4mclassfilter.xml w4mclassfilter_wrapper.R |
| b |
| diff -r 9549cc9e8ec6 -r 0c312f3a4a17 w4mclassfilter.xml --- a/w4mclassfilter.xml Tue May 09 19:31:21 2017 -0400 +++ b/w4mclassfilter.xml Wed May 10 02:49:44 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 9549cc9e8ec6 -r 0c312f3a4a17 w4mclassfilter_wrapper.R --- a/w4mclassfilter_wrapper.R Tue May 09 19:31:21 2017 -0400 +++ b/w4mclassfilter_wrapper.R Wed May 10 02:49:44 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: ", |