<tool id="W4MClassFilter" name="W4MClassFilter" version="0.98.1">
  <description>Filter W4M data by sample class</description>

  <requirements>
    <requirement type="package" version="3.3.1">r-base</requirement>
    <requirement type="package" version="1.1_4">r-batch</requirement>
    <requirement type="package" version="0.98.1">w4mclassfilter</requirement>
  </requirements>

  <stdio>
    <exit_code range="1:" level="fatal" />
  </stdio>


  <command detect_errors="aggressive"><![CDATA[
  Rscript $__tool_directory__/w4mclassfilter_wrapper.R
  dataMatrix_in "$dataMatrix_in"
  sampleMetadata_in "$sampleMetadata_in"
  variableMetadata_in "$variableMetadata_in"
  sampleclassNames "$sampleclassNames"
  inclusive "$inclusive"
  classnameColumn "$classnameColumn"
  samplenameColumn "$samplenameColumn"
  dataMatrix_out "$dataMatrix_out"
  sampleMetadata_out "$sampleMetadata_out"
  variableMetadata_out "$variableMetadata_out"
  ]]></command>

  <inputs>
    <param name="dataMatrix_in" label="Data matrix file" type="data" format="tabular" help="variable x sample, decimal: '.', missing: NA, mode: numerical, separator: tab" />
    <param name="sampleMetadata_in" label="Sample metadata file" type="data" format="tabular" help="sample x metadata columns, separator: tab" />
    <param name="variableMetadata_in" label="Variable metadata file" type="data" format="tabular" help="variable x metadata columns, separator: tab" />
    <param name="sampleclassNames" label="Names of sample classes" type="text" value = "" help="comma-separated names of sample classes to filter in or out; defaults to no names" />
    <param name="inclusive" label="Include named classes" type="select" help="filter-in - include only the named sample classes; filter-out (the default) - exclude only the named sample classes">
      <option value="TRUE">filter-in</option>
      <option value="FALSE" selected="true">filter-out</option>
    </param>
    <param name="classnameColumn" label="Column that names the sample-class" type="text" value = "class" help="name of the column in sample metadata that has the values to be tested against the 'classes' input parameter - defaults to 'class'" />
    <param name="samplenameColumn" label="Column that names the sample" type="text" value = "sampleMetadata" help="name of the column in sample metadata that has the name of the sample - defaults to 'sampleMetadata'" />
  </inputs>
  <outputs>
    <data name="dataMatrix_out" label="${tool.name}_${dataMatrix_in.name}" format="tabular" ></data>
    <data name="sampleMetadata_out" label="${tool.name}_${sampleMetadata_in.name}" format="tabular" ></data>
    <data name="variableMetadata_out" label="${tool.name}_${variableMetadata_in.name}" format="tabular" ></data>
  </outputs>

  <tests>
    <test>
      <param name="dataMatrix_in" value="input_dataMatrix.tsv"/>
      <param name="sampleMetadata_in" value="input_sampleMetadata.tsv"/>
      <param name="variableMetadata_in" value="input_variableMetadata.tsv"/>
      <param name="classnameColumn" value="gender"/>
      <param name="sampleclassNames" value="M"/>
      <param name="samplenameColumn" value="sampleMetadata"/>
      <param name="inclusive" value="filter-in"/>
      <output name="dataMatrix_out">
        <assert_contents>
          <not_has_text text="HU_028" />
          <not_has_text text="HU_051" />
          <not_has_text text="HU_060" />
          <not_has_text text="HU_110" />
          <not_has_text text="HU_149" />
          <not_has_text text="HU_152" />
          <not_has_text text="HU_175" />
          <not_has_text text="HU_178" />
          <not_has_text text="HU_185" />
          <not_has_text text="HU_204" />
          <not_has_text text="HU_208" />
          <has_text     text="HU_017" />
          <has_text     text="HU_034" />
          <has_text     text="HU_078" />
          <has_text     text="HU_091" />
          <has_text     text="HU_093" />
          <has_text     text="HU_099" />
          <has_text     text="HU_130" />
          <has_text     text="HU_134" />
          <has_text     text="HU_138" />
          <has_text     text="HMDB03193" />
          <not_has_text text="HMDB00822" />
          <has_text     text="HMDB01101" />
          <has_text     text="HMDB01101.1" />
          <has_text     text="HMDB10348" />
          <has_text     text="HMDB59717" />
          <has_text     text="HMDB13189" />
          <has_text     text="HMDB00299" />
          <has_text     text="HMDB00191" />
          <has_text     text="HMDB00518" />
          <has_text     text="HMDB00715" />
          <has_text     text="HMDB01032" />
          <has_text     text="HMDB00208" />
          <has_text     text="HMDB04824" />
          <has_text     text="HMDB00512" />
          <has_text     text="HMDB00251" />
        </assert_contents>
      </output>
    </test>
    <test>
      <param name="dataMatrix_in" value="input_dataMatrix.tsv"/>
      <param name="sampleMetadata_in" value="input_sampleMetadata.tsv"/>
      <param name="variableMetadata_in" value="input_variableMetadata.tsv"/>
      <param name="classnameColumn" value="gender"/>
      <param name="sampleclassNames" value="M"/>
      <param name="samplenameColumn" value="sampleMetadata"/>
      <param name="inclusive" value="filter-in"/>
      <output name="sampleMetadata_out">
        <assert_contents>
          <not_has_text text="HU_028" />
          <not_has_text text="HU_051" />
          <not_has_text text="HU_060" />
          <not_has_text text="HU_110" />
          <not_has_text text="HU_149" />
          <not_has_text text="HU_152" />
          <not_has_text text="HU_175" />
          <not_has_text text="HU_178" />
          <not_has_text text="HU_185" />
          <not_has_text text="HU_204" />
          <not_has_text text="HU_208" />
          <has_text     text="HU_017" />
          <has_text     text="HU_034" />
          <has_text     text="HU_078" />
          <has_text     text="HU_091" />
          <has_text     text="HU_093" />
          <has_text     text="HU_099" />
          <has_text     text="HU_130" />
          <has_text     text="HU_134" />
          <has_text     text="HU_138" />
        </assert_contents>
      </output>
    </test>
    <test>
      <param name="dataMatrix_in" value="input_dataMatrix.tsv"/>
      <param name="sampleMetadata_in" value="input_sampleMetadata.tsv"/>
      <param name="variableMetadata_in" value="input_variableMetadata.tsv"/>
      <param name="classnameColumn" value="gender"/>
      <param name="sampleclassNames" value="M"/>
      <param name="samplenameColumn" value="sampleMetadata"/>
      <param name="inclusive" value="filter-in"/>
      <output name="variableMetadata_out">
        <assert_contents>
          <has_text     text="HMDB03193" />
          <not_has_text text="HMDB00822" />
          <has_text     text="HMDB01101" />
          <has_text     text="HMDB01101.1" />
          <has_text     text="HMDB10348" />
          <has_text     text="HMDB59717" />
          <has_text     text="HMDB13189" />
          <has_text     text="HMDB00299" />
          <has_text     text="HMDB00191" />
          <has_text     text="HMDB00518" />
          <has_text     text="HMDB00715" />
          <has_text     text="HMDB01032" />
          <has_text     text="HMDB00208" />
          <has_text     text="HMDB04824" />
          <has_text     text="HMDB00512" />
          <has_text     text="HMDB00251" />
        </assert_contents>
      </output>
    </test>
  </tests>



	<help>
		<![CDATA[

.. class:: infomark

**Author**	Arthur Eschenlauer (University of Minnesota, esch0041@umn.edu)

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

.. class:: infomark

**R package**

The *w4mclassfilter* package is available from the Hegeman lab github repository (https://github.com/HegemanLab/w4mclassfilter/releases).

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

.. class:: infomark

**Tool updates**

See the **NEWS** section at the bottom of this page

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

==============================================
Filter Workflow4Metabolomics data matrix files
==============================================

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

Filter set of retention-corrected W4M files (dataMatrix, sampleMetadata, variableMetadata) by sample class

--------
Comments
--------

The *inclusive* parameter indicates:
  - when 'filter-in', that only the sample-classes named should be included
  - when 'filter-out', that all sample-classes should be included excepting the sample-classes named

-----------
Input files
-----------

+---------------------------+------------+
| File                      |   Format   |
+===========================+============+
|     Data matrix           |   tabular  |
+---------------------------+------------+
|     Sample metadata       |   tabular  |
+---------------------------+------------+
|     Variable metadata     |   tabular  |
+---------------------------+------------+


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

Data matrix file
	| variable x sample **dataMatrix** (tabular separated values) file of the numeric data matrix, with . as decimal, and NA for missing values; the table must not contain metadata apart from row and column names; the row and column names must be identical to the rownames of the sample and variable metadata, respectively (see below)
	|

Sample metadata file
	| sample x metadata **sampleMetadata** (tabular separated values) file of the numeric and/or character sample metadata, with . as decimal and NA for missing values
	|

Variable metadata file
	| variable x metadata **variableMetadata** (tabular separated values) file of the numeric and/or character variable metadata, with . as decimal and NA for missing values
	|

Names of sample classes (default = no names)
	| comma-separated names of sample classes to include or exclude
	|

Include named classes (default = filter-out)
	| *filter-in* - include only the named sample classes
	| *filter-out* - exclude only the named sample classes
	|


Column that names the sample-class (default = 'class')
	| name of the column in sample metadata that has the values to be tested against the 'classes' input parameter
	|

Column that names the sample (default = 'sampleMetadata')
	| name of the column in sample metadata that has the name of the sample
	|


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


sampleMetadata
	| (tabular separated values) file identical to the **sampleMetadata** file given as an input argument, excepting lacking rows for samples (xC-MS features) that have been filtered out (by the sample-class filter or because of zero variance)
	|

variableMetadata
	| (tabular separated values) file identical to the **variableMetadata** file given as an input argument, excepting lacking rows for variables (xC-MS features) that have been filtered out (because of zero variance)
	|

dataMatrix
	| (tabular separated values) file identical to the **dataMatrix** file given as an input argument, excepting lacking rows for variables (xC-MS features) that have been filtered out (because of zero variance) and columns that have been filtered out (by the sample-class filter or because of zero variance)
	|


---------------
Working example
---------------

.. class:: infomark

**Input files**

+-------------------+--------------------------------------------------------------------------------------------------------------+
| Input File        | Download from URL                                                                                            |
+===================+==============================================================================================================+
| Data matrix       | https://raw.githubusercontent.com/HegemanLab/w4mclassfilter/master/tests/testthat/input_dataMatrix.tsv       |
+-------------------+--------------------------------------------------------------------------------------------------------------+
| Sample metadata   | https://raw.githubusercontent.com/HegemanLab/w4mclassfilter/master/tests/testthat/input_sampleMetadata.tsv   |
+-------------------+--------------------------------------------------------------------------------------------------------------+
| Variable metadata | https://raw.githubusercontent.com/HegemanLab/w4mclassfilter/master/tests/testthat/input_variableMetadata.tsv |
+-------------------+--------------------------------------------------------------------------------------------------------------+

.. class:: infomark

**Other input parameters**

+------------------------------------+-----------------+
| Input Parameter                    | Value           |
+====================================+=================+
| Names of sample classes            | M               |
+------------------------------------+-----------------+
| Include named classes              | filter-in       |
+------------------------------------+-----------------+
| Column that names the sample-class | gender          |
+------------------------------------+-----------------+
| Column that names the sample       | sampleMetadata  |
+------------------------------------+-----------------+

.. class:: infomark

**Expected outputs**

+-------------------+-----------------------------------------------------------------------------------------------------------------+
| Expected Output   | Download from URL                                                                                               |
+===================+=================================================================================================================+
| Data matrix       | https://raw.githubusercontent.com/HegemanLab/w4mclassfilter/master/tests/testthat/expected_dataMatrix.tsv       |
+-------------------+-----------------------------------------------------------------------------------------------------------------+
| Sample metadata   | https://raw.githubusercontent.com/HegemanLab/w4mclassfilter/master/tests/testthat/expected_sampleMetadata.tsv   |
+-------------------+-----------------------------------------------------------------------------------------------------------------+
| Variable metadata | https://raw.githubusercontent.com/HegemanLab/w4mclassfilter/master/tests/testthat/expected_variableMetadata.tsv |
+-------------------+-----------------------------------------------------------------------------------------------------------------+


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

----
NEWS
----

CHANGES IN VERSION 0.98.1
=========================

NEW FEATURES

First release - R package that implements filtering of W4M data matrix, variable metadata, and sample metadata by class of sample.

*dataMatrix* *is* modified by the tool, so it *does* appear as an output file

INTERNAL MODIFICATIONS

none
    ]]>
  </help>
  <citations>
  </citations>
</tool>
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