comparison concat.xml @ 0:c577f13705f2 draft default tip

planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec

0:c577f13705f2

<tool id="W4Mconcatenate" name="W4M concatenate" version="1.0.0+galaxy0">
  <description>to merge two metadata tables</description>
  <requirements>
   <requirement type="package" version="4.3.3">r-base</requirement>
   <requirement type="package" version="1.1.4">r-dplyr</requirement>
   <requirement type="package" version="1.0.0">r-w4mrutils</requirement>
  </requirements>
  <command detect_errors="exit_code">
  <![CDATA[
    
    Rscript '$__tool_directory__/concatenation_wrapper.R'
    
    dataMatrix_1 '$dataMatrix_1'
    
    dataMatrix_2 '$dataMatrix_2'
    
    metadata_1 '$metadata_1'
    
    metadata_2 '$metadata_2'
    
    type '$type'
    
    tab1 '$tab1'
    
    tab2 '$tab2'
    
    concatenation '$concatenation'
    
    choice_keep '$choice.choice_keep'
    #if str($choice.choice_keep) == 'yes':
        keep 0
    #end if
    #if str($choice.choice_keep) == 'no':
        keep "$choice.keep"
    #end if
    
    dataMatrix_1_out '$dataMatrix_1_out'
    dataMatrix_2_out '$dataMatrix_2_out'
    metadata_out '$metadata_out'
    
  ]]></command>
  
  
  <inputs>
  
   <param name="dataMatrix_1" type="data" label="Data matrix file 1" format="tabular"/>
   <param name="dataMatrix_2" type="data" label="Data matrix file 2" format="tabular"/>
   <param name="metadata_1" type="data" label="Metadata file 1" format="tabular"/>
   <param name="metadata_2" type="data" label="Metadata file 2" format="tabular"/>
  
   <param name="type" type="select" display="radio" label="Type of metadata">
    <option value="sample">Sample metadata</option>
    <option value="variable">Variable metadata</option>
   </param>
  
   <param name="concatenation" type="select" display="radio" label="Type of concatenation">
    <option value="unique">Unique</option>
    <option value="intersection">Intersection</option>
    <option value="union">Union</option>
   </param>
  
   <conditional name="choice">
    <param name="choice_keep" type="select" display="radio" label="Keep all or just one">
     <option value="yes">Keep all</option>
     <option value="no">Keep one</option>
    </param>
    <when value="no">
     <param name="keep" type="select" display="radio" label="Which Metadata to keep">
      <option value="1">Metadata 1</option>
      <option value="2">Metadata 2</option>
     </param>
    </when>
    <when value="yes">
    </when>
   </conditional>
  
  <param name="tab1" type="text" label="Suffix for Metadata 1" value="Tab1"/>
  <param name="tab2" type="text" label="Suffix for Metadata 2" value="Tab2"/>
  
  </inputs>
  
  
  
  <outputs>
  
   <data name="dataMatrix_1_out" label="Concat_${dataMatrix_1.name}" format="tabular"></data>
   <data name="dataMatrix_2_out" label="Concat_${dataMatrix_2.name}" format="tabular"></data>
   <data name="metadata_out" label="Concat_${metadata_1.name}" format="tabular"></data>
  
  </outputs>
  
  <tests>
   <test>
    <param name="dataMatrix_1" value="Input_Unique_Test_1-2-3-4-5_DM1.txt"/>
    <param name="dataMatrix_2" value="Input_Unique_Test_1-2-3_DM2.txt"/>
    <param name="metadata_1" value="Input_Unique_Test_1_SM1.txt"/>
    <param name="metadata_2" value="Input_Unique_Test_1_SM2.txt"/>
    <param name="concatenation" value="unique"/>
    <param name="choice_keep" value="yes"/>
    <param name="tab1" value="tab1"/>
    <param name="tab2" value="tab2"/>
  
    <output name="dataMatrix_1_out" file="Output_Attendu_Unique_Test_1-2-3_DM1.txt"/>
    <output name="dataMatrix_2_out" file="Output_Attendu_Unique_Test_1-2-3_DM2.txt"/>
    <output name="metadata_out" file="Output_Attendu_Unique_Test_1_Metadata.txt"/>
  
  
   </test>
  
   <test expect_failure="true">
    <param name="dataMatrix_1" value="Input_Unique_Test_1-2-3-4-5_DM1.txt"/>
    <param name="dataMatrix_2" value="Input_Unique_Test_4_DM2.txt"/>
    <param name="metadata_1" value="Input_Unique_Test_4_SM1.txt"/>
    <param name="metadata_2" value="Input_Unique_Test_4_SM2.txt"/>
    <param name="concatenation" value="unique"/>
    <param name="choice_keep" value="yes"/>
    <param name="tab1" value="tab1"/>
    <param name="tab2" value="tab2"/>
  
   </test>
  
  </tests>
  
  <help><![CDATA[
    
.. class:: infomark
    
**Credits**
 | **Original tool code:** Hanane Nourine
 | **Original tool wrapping:** Hanane Nourine 
 | **Tool maintainer:** Melanie Petera (PFEM - INRAE - MetaboHUB)
 | **Wrapper maintainer:** Melanie Petera (PFEM - INRAE - MetaboHUB)
    
.. class:: infomark
    
**Contact:** Melanie Petera (PFEM - INRAE - MetaboHUB)
      
---------------------------------------------------
      
******************
Concatenation
******************
      
===========
DESCRIPTION
===========        
      
Concatenate two Metadata tables
    
    
---------------------------------------------------
      
==========================
ALIGNMENT WITH OTHER TOOLS
==========================
     
This tool is designed to work with the W4M 3-tables format. Inputs are supposed to follow this standard. 
Outputs follows the standard and thus can be used in further W4M-supported workflows.

-----------
Input files
-----------
      
+----------------------------------+------------+
| Parameter : num + label          |   Format   |
+==================================+============+
| 1 : First Data matrix file       |   tabular  |
+----------------------------------+------------+
| 2 : First metadata file          |   tabular  |
+----------------------------------+------------+
| 3 : Second Data matrix file      |   tabular  |
+----------------------------------+------------+
| 4 : Second metadata file         |   tabular  |
+----------------------------------+------------+
      
------------
Output files
------------
      
+----------------------------------+------------+
| Parameter : num + label          |   Format   |
+==================================+============+
| 1 : Metadata concatenate file    |   tabular  |
+----------------------------------+------------+
| 2 : First Data matrix file       |   tabular  |
+----------------------------------+------------+
| 3 : Second Data matrix file      |   tabular  |
+----------------------------------+------------+
      
---------------------------------------------------
      
      
===============
TOOL PARAMETERS
===============
      

Data matrix 
 | contains the intensity values of the analytical variables. 
 | First line is the sample identifiers and first column the variable identifiers.
 |
      
      
Metadata file
 | contains metadata about samples OR variables (only one type possible at a time). 
 | Each metadata file must match its corresponding data matrix file regarding identifiers.
 |
      
Type of metadata
 | Specify which type of metadata table is given as metadata file
 | 
      
      
Type of concatenation 
 | Selects the type of concatenation
 | Unique: identifiers are the same in both datasets (i.e. metadata file 1 and metadata file 2 are expected to match perfectly regarding identifiers)
 | Intersection: keep only identifiers in common 
 | Union: keep all identifiers in both datasets
 |
      
Choice_keep 
 | Determine what to do in case a column name is found in the two metadata files
 | - Keep all: both columns and change their names by adding a prefix
 | - Keep one: the column belonging to metadata 1 or metadata 2
 |
      
Prefixes for redundant columns
 | By default, the prefixes are Tab1 and Tab2
 |
      
==================
OUTPUT DESCRIPTION
==================
      
**Unique**: the tables must have the same identifiers, otherwise a warning will be generated. 
The output returned is a unique merged metadata file without modifying the DataMatrices.
    
**Intersection**: there must be identifiers in common between the two metadata tables, otherwise an error will be displayed. 
Moreover, if the number of identifiers in common is less than 5, a warning will be generated. 
The DataMatrix outputs will only keep common identifiers.
    
**Union**: the identifiers don't necessarily have to be the same between the metadata tables. If no identifiers are common, a warning will be generated. 
The modified DataMatrix will then include all the individuals, adding NA values for those that are missing.
If common pairs of sample and variable exist between the dataset 1 and dataset 2 with no difference in the intensity values, 
the intersections will be added instead of NA.



]]></help>
	<citations>
    <citation type="doi">10.1093/bioinformatics/btu813</citation>
  </citations>
  
  <creator>
    <organization name="PFEM" url="https://eng-pfem.isc.inrae.fr/"></organization>
    <organization name="Workflow4metabolomics" url="https://workflow4metabolomics.org/"></organization>
    
    <person givenName="Hanane" familyName="Nourine" jobTitle="Intern"></person>
    <person givenName="Mélanie" familyName="Petera"></person>
  </creator>
</tool>