<tool id="idchoice" name="ID choice" version="19.12">
  <description>Choosing a particular column in your metadata to be considered as Identifiers</description>
  <requirements>
	    <requirement type="package" version="1.1_4">r-batch</requirement>
  </requirements>
  <command interpreter="Rscript">
	IDchoice_wrap.R
      dataMatrix_in "$dataMatrix_in"
      Metadata_in "$Metadata_in"
              
      metatype "$metatype"
	  col_name "$col_name"
	  makeunique "$makeunique"
      
      DM_out "$DM_out"
	  meta_out "$meta_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 containing your new IDs" help="Sample metadata or variable metadata" format="tabular" />

    <param name="metatype" label="Which ID do you want to change?" type="select" display="radio" help="">
      <option value="sample">Samples</option>
      <option value="variable" selected="True">Variables</option>
    </param>

	<param name="col_name" label="Name of the column to consider as new ID" type="text" value="" help="Exact name; must be in your metadata file" />

    <param name="makeunique" label="Force unicity if not unique?" type="select" display="radio" help="">
      <option value="yes">Yes</option>
      <option value="no" selected="True">No</option>
    </param>

  </inputs>
  
  <outputs>
    <data name="DM_out" label="ID_${dataMatrix_in.name}" format="tabular" ></data>
	<data name="meta_out" label="ID_${Metadata_in.name}" format="tabular" ></data>
  </outputs>
  
  
   <tests>
	<test>
      <param name="dataMatrix_in" value="input_IDc_dataMatrix.txt"/>
      <param name="Metadata_in" value="input_IDc_variableMetadata.txt"/>
      <param name="metatype" value="variable"/>
	  <param name="col_name" value="B"/>
	  <param name="makeunique" value="yes"/>
      <output name="DM_out" file="output1_IDc_dataMatrix.tabular"/>
	  <output name="meta_out" file="output1_IDc_variableMetadata.tabular"/>
	</test>
	<test>
      <param name="dataMatrix_in" value="input_IDc_dataMatrix.txt"/>
      <param name="Metadata_in" value="input_IDc_sampleMetadata.txt"/>
      <param name="metatype" value="sample"/>
	  <param name="col_name" value="AAA"/>
	  <param name="makeunique" value="yes"/>
      <output name="DM_out" file="output2_IDc_dataMatrix.tabular"/>
	  <output name="meta_out" file="output2_IDc_sampleMetadata.tabular"/>
	</test>
  </tests>
  
  
  <help>

.. class:: infomark

**Authors** 
  | Melanie Petera - PFEM ; INRA ; MetaboHUB 

---------------------------------------------------

========================
ID Choice
========================

-----------
Description
-----------

Change the current identifiers into new ones defined in your metadata file. 
Can be used for sample ID as well as variable ID. 



-----------
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. 
	| It should include a column containing your wanted IDs. 
	| 

-----------
Parameters
-----------

Which ID do you want to change?
	| This must be consistant with the metadata file you chose as input
	| 

Name of the column to consider as new ID
	| Must be one of your metadata file's column
	|

Force unicity if not unique?
	| If no (default value), if your ID column does not contain unique values, it will stop the process and send you back an explicit error.
	| If yes, non-unique values will be converted by adding "_x" at the end of concerned IDs. 
	|


-------------
Output files
-------------

ID_metadata
	| tabular output
	| Corresponds to the input metadata file with new IDs as first column
	|

ID_datamatrix
	| tabular output
	| Corresponds to the input data matrix file with new IDs
	|


---------------------------------------------------

----------------------
Additional information
----------------------


.. 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>