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

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0:902ab790fb7b

<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>