# HG changeset patch
# User eschen42
# Date 1494398984 14400
# Node ID 0c312f3a4a172c30c2baa9949fd3cbb523869d18
# Parent  9549cc9e8ec64c1f20cb9829e2ff98d2132b4306
planemo upload

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
@@ -24,13 +24,12 @@
   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="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="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="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 columns, separator: tab" />
+    <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>
@@ -43,7 +42,6 @@
     <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>
@@ -55,7 +53,6 @@
       <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" />
@@ -105,7 +102,6 @@
       <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" />
@@ -139,7 +135,6 @@
       <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" />
@@ -165,7 +160,8 @@
 
 
 
-  <help>
+	<help>
+		<![CDATA[
 
 .. class:: infomark
 
@@ -214,11 +210,11 @@
 +---------------------------+------------+
 | File                      |   Format   |
 +===========================+============+
-| 1)  Data matrix           |   tabular  |
+|     Data matrix           |   tabular  |
 +---------------------------+------------+
-| 2)  Sample metadata       |   tabular  |
+|     Sample metadata       |   tabular  |
 +---------------------------+------------+
-| 3)  Variable metadata     |   tabular  |
+|     Variable metadata     |   tabular  |
 +---------------------------+------------+
 
 
@@ -227,15 +223,15 @@
 ----------
 
 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)
@@ -243,10 +239,11 @@
 	|
 
 Include named classes (default = filter-out)
-  | *filter-in* - include only the named sample classes
-  | *filter-out* - exclude only the named sample classes
+	| *filter-in* - include 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
 	|
@@ -261,21 +258,67 @@
 ------------
 
 
-sampleMetadata_out.tabular
-	| **sampleMetadata** tabular separated file identical to the file given as argument, excepting lacking rows for samples that have been filtered out
+sampleMetadata
+	| (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** 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)
+variableMetadata
+	| (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
+	| (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)
 	|
 
-dataMatrix_out.tabular
-	| **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)
-	|
+
+---------------
+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**
 
-information.txt
-	| Text file with all messages and warnings generated during the computation
-	|
++------------------------------------+-----------------+
+| 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 |
++-------------------+-----------------------------------------------------------------------------------------------------------------+
+
 
 -----------------------------------------------------------------------------
 
@@ -295,10 +338,10 @@
 INTERNAL MODIFICATIONS
 
 none
-
+    ]]>
   </help>
   <citations>
   </citations>
 </tool>
-<!-- vim: et sw=2 ts=2 :
+<!-- vim: noet sw=4 ts=4 :
 -->
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: ",