w4mclassfilter: w4mclassfilter.xml comparison

comparison w4mclassfilter.xml @ 2:23c6d271def9 draft

planemo upload

author	eschen42
date	Wed, 10 May 2017 02:51:58 -0400
parents	bab3a658f74e
children	191a720488ce

comparison

equal deleted inserted replaced

-:371741d19743
+:23c6d271def9
 classnameColumn "$classnameColumn"
 samplenameColumn "$samplenameColumn"
 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="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, decimal: '.', missing: NA, mode: character and numerical, sep: tabular" />
+<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, 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 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>
 <option value="FALSE" selected="true">filter-out</option>
 </param>
 </inputs>
 <outputs>
 <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>
 <test>
 <param name="dataMatrix_in" value="input_dataMatrix.tsv"/>
 <param name="variableMetadata_in" value="input_variableMetadata.tsv"/>
 <param name="classnameColumn" value="gender"/>
 <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" />
 <not_has_text text="HU_051" />
 <not_has_text text="HU_060" />
 <param name="variableMetadata_in" value="input_variableMetadata.tsv"/>
 <param name="classnameColumn" value="gender"/>
 <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" />
 <not_has_text text="HU_051" />
 <not_has_text text="HU_060" />
 <param name="variableMetadata_in" value="input_variableMetadata.tsv"/>
 <param name="classnameColumn" value="gender"/>
 <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" />
 <not_has_text text="HMDB00822" />
 <has_text     text="HMDB01101" />
 </test>
 </tests>
-<help>
+	<help>
+		<![CDATA[
 .. class:: infomark
 **Author**	Arthur Eschenlauer (University of Minnesota, esch0041@umn.edu)
 -----------
 +---------------------------+------------+
 | File                      |   Format   |
 +===========================+============+
-| 1)  Data matrix           |   tabular  |
+|     Data matrix           |   tabular  |
 +---------------------------+------------+
-| 2)  Sample metadata       |   tabular  |
+|     Sample metadata       |   tabular  |
 +---------------------------+------------+
-| 3)  Variable metadata     |   tabular  |
+|     Variable metadata     |   tabular  |
 +---------------------------+------------+
 ----------
 Parameters
 ----------
 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)
 	| comma-separated names of sample classes to include or exclude
 	|
 Include named classes (default = filter-out)
-| *filter-in* - include only the named sample classes
+	| *filter-in* - include only the named sample classes
-| *filter-out* - exclude 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
 	|
 ------------
 Output files
 ------------
-sampleMetadata_out.tabular
+sampleMetadata
-	| **sampleMetadata** tabular separated file identical to the file given as argument, excepting lacking rows for samples that have been filtered out
+	| (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
-	| **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)
+	| (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_out.tabular
+dataMatrix
-	| **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)
+	| (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)
 	|
-information.txt
-	| Text file with all messages and warnings generated during the computation
+---------------
-	|
+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**
++------------------------------------+-----------------+
+| 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 |
++-------------------+-----------------------------------------------------------------------------------------------------------------+
 -----------------------------------------------------------------------------
 ----
 NEWS
 *dataMatrix* *is* modified by the tool, so it *does* appear as an output file
 INTERNAL MODIFICATIONS
 none
+]]>
 </help>
 <citations>
 </citations>
 </tool>
-<!-- vim: et sw=2 ts=2 :
+<!-- vim: noet sw=4 ts=4 :
 -->

Mercurial > repos > eschen42 > w4mclassfilter

comparison w4mclassfilter.xml @ 2:23c6d271def9 draft