diff Intchecks/xml_intensity_check.xml @ 0:c2c2e1be904a draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/Intchecks/xml_intensity_check.xml	Thu Oct 11 05:33:19 2018 -0400
@@ -0,0 +1,125 @@
+<tool id="intens_check" name="Intensity Check" version="1.0.1">
+	<description>Adding informations about intensities in the Variable metadata</description>
+	<requirements>
+	<requirement type="package" version="1.1_4">r-batch</requirement>
+	</requirements>
+	<command interpreter="Rscript">
+  
+		wrapper_intensity_check.R
+	
+		dataMatrix_in "$dataMatrix_in"
+		sampleMetadata_in "$sampleMetadata_in"
+		variableMetadata_in "$variableMetadata_in"
+	
+		class_col "$class_col"
+	
+		type "${type_cond.type}"
+		#if $type_cond.type == "One_class" :
+		class1 "${type_cond.class1}"
+		#end if
+	
+		variableMetadata_out "$variableMetadata_out"
+		graphs_out "$graphs_out"
+	</command>
+
+	<inputs>
+		<param name="dataMatrix_in" type="data" label="Data Matrix file" help="" format="tabular" />
+		<param name="sampleMetadata_in" type="data" label="Sample metadata file" help="" format="tabular" />
+		<param name="variableMetadata_in" type="data" label="Variable metadata file" help="" format="tabular" />
+		
+		<param name="class_col" type="data_column" data_ref="sampleMetadata_in" use_header_names="true" label="Class column" help="Class column in Sample metadata" />
+	
+		<conditional name="type_cond">
+			<param name="type" type="select" label="Type" display="radio" help="Which class do you want to test ?">
+				<option value="One_class">Tests between one class and the remaining samples </option>
+				<option value="Each_class">Tests for each class </option>
+			</param>
+			<when value="One_class">
+				<param name="class1" type="text" label="Selected class" help="This class is the numerator for the fold test" />
+			</when>
+			<when value="Each_class">
+			</when>
+		</conditional>
+		
+	</inputs>
+	
+	<outputs>
+		<data name="variableMetadata_out" label="IC_${variableMetadata_in.name}" format="tabular" />
+		<data name="graphs_out" label="IC_Graphs" format="pdf" />
+	</outputs>
+	
+	<help>
+
+.. class:: infomark
+
+**Authors** 
+  | Anthony Fernandes - PFEM ; INRA 
+
+---------------------------------------------------
+
+========================
+Intensity Check
+========================
+
+-----------
+Description
+-----------
+
+This tool performs two tests: the fold calculation, the number and the proportion of missing values. 
+
+**Fold:**
+The test calculates the ratio between two classes.
+In the column name, the first class specified is the one used like numerator for the ratio.
+
+**Missing values:**
+This tool calculates the number and the proportion of missing values considering the class. 
+Missing values in numerical columns of data must be coded NA.
+
+**Two types of tests:**
+	|	- Between **one class** and the remaining samples: if you have only two classes or if you want to test only one class.
+	|	- **Each class**: if the column class contains at least three classes and you want to test each of them.
+
+-----------
+Input files
+-----------
+
++----------------------------+------------+
+| Parameter                  |   Format   |
++============================+============+
+| 1 : Data Matrix file       |   tabular  |
++----------------------------+------------+
+| 2 : Sample metadata file   |   tabular  |
++----------------------------+------------+
+| 3 : Variable metadata file |   tabular  |
++----------------------------+------------+
+
+----------
+Parameters
+----------
+
+**Class column**
+	| Select the class column in Sample metadata.
+
+**Type**
+	|  Two options:
+	|     - "One class" allows to perform tests on one class against the remaining samples.
+	|     - "Each class" allows to add several columns with the ratio and the number of missing values for each class.
+
+**Selected class**
+	| If the type is "one class", specify it to calculate the ratio and the number of missing values. 
+
+------------
+Output file
+------------
+
+**Variable metadata file**
+	| Contains the previous columns in variable metadata and the new ones with fold tests, numbers and proportion of missing values.
+	
+**Graphs file**
+	| Contains barplots with the proportion of NA considering classes and boxplots with the folds values
+
+	</help>
+	
+	
+</tool>	
+	
\ No newline at end of file