diff IDchoice/IDchoice.xml @ 0:b7a6a88f518a draft

Uploaded

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+++ b/IDchoice/IDchoice.xml	Thu Oct 11 05:47:29 2018 -0400
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+<tool id="idchoice" name="ID choice" version="18.01">
+  <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. 
+	| 
+
+----------
+Parameter
+----------
+
+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 file
+------------
+
+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>
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