diff TableMerge/tablemerge.xml @ 0:902ab790fb7b draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/TableMerge/tablemerge.xml	Thu Feb 23 04:37:49 2017 -0500
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+<tool id="tablemerge" name="Table Merge" version="1.0.1">
+  <description>Merging dataMatrix with a metadata table</description>
+  <requirements>
+	    <requirement type="package" version="1.1_4">r-batch</requirement>
+  </requirements>
+  <command interpreter="Rscript">
+	tablemerge_wrap.R
+      dataMatrix_in "$dataMatrix_in"
+      Metadata_in "$Metadata_in"
+              
+      metatype "$metatype"
+      
+      combined_out "$combined_out"
+
+  </command>
+  
+  <inputs>
+    <param name="dataMatrix_in" type="data" label="Data matrix file" help="" format="tabular" />
+    <param name="Metadata_in" type="data" label="Metadata file" help="Sample metadata or variable metadata" format="tabular" />
+	
+    <param name="metatype" label="Type of metadata" type="select" display="radio" help="">
+      <option value="sample">Sample metadata</option>
+      <option value="variable">Variable metadata</option>
+    </param>
+
+  </inputs>
+  
+  <outputs>
+    <data name="combined_out" label="Combined_${Metadata_in.name}" format="tabular" ></data>
+  </outputs>
+  
+  <tests>
+	<test>
+      <param name="dataMatrix_in" value="input_TM12_dataMatrix.txt"/>
+      <param name="Metadata_in" value="input_TM1_variableMetadata.txt"/>
+      <param name="metatype" value="variable"/>
+      <output name="combined_out" file="output_TM1_expected.tabular"/>
+	</test>
+	<test>
+      <param name="dataMatrix_in" value="input_TM12_dataMatrix.txt"/>
+      <param name="Metadata_in" value="input_TM2_sampleMetadata.txt"/>
+      <param name="metatype" value="sample"/>
+      <output name="combined_out" file="output_TM2_expected.tabular"/>
+	</test>
+  </tests>
+  
+  
+  <help>
+
+.. class:: infomark
+
+**Authors** 
+  | Melanie Petera - PFEM ; INRA ; MetaboHUB 
+
+---------------------------------------------------
+
+========================
+Table Merge
+========================
+
+-----------
+Description
+-----------
+
+Merges the data matrix with a selected metadata file (sample metadata or variable metadata)
+to obtain a single file. 
+
+
+
+-----------
+Input files
+-----------
+
++----------------------------+---------+
+| Parameter : num + label    |  Format |
++============================+=========+
+| 1 : Data matrix file       | tabular |
++----------------------------+---------+
+| 2 : Metadata file          | tabular |
++----------------------------+---------+
+
+
+Data matrix file contains the intensity values of the variables.
+	| 
+
+Metadata file is meant to be chosen from sample metadata and variable metadata files. 
+	| 
+
+----------
+Parameter
+----------
+
+Type of metadata
+	| Specify which type of metadata table is given as Metadata file
+	| 
+
+
+------------
+Output file
+------------
+
+
+Combined_Metadata
+	| tabular output
+	| Corresponds to the input metadata file completed as new columns by the intensities in the input data matrix file
+	|
+
+
+---------------------------------------------------
+
+---------------
+Working example
+---------------
+
+
+.. class:: warningmark
+
+For more information about input files, refer to the corresponding "W4M HowTo" page:
+ | `W4M table format for Galaxy &lt;http://workflow4metabolomics.org/sites/workflow4metabolomics.org/files/files/w4m_TableFormatForGalaxy_150908.pdf&gt;`_
+ |
+
+
+
+
+	</help>
+</tool>
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