comparison w4mclassfilter.xml @ 2:23c6d271def9 draft

planemo upload

1:371741d19743

  classnameColumn "$classnameColumn"
  samplenameColumn "$samplenameColumn"
  dataMatrix_out "$dataMatrix_out"
  sampleMetadata_out "$sampleMetadata_out"
  variableMetadata_out "$variableMetadata_out"
  information "$information"
  ]]></command>

  <inputs>
    <param name="dataMatrix_in" label="Data matrix file" type="data" format="tabular" help="variable x sample, decimal: '.', missing: NA, mode: numerical, sep: tabular" />
    <param name="sampleMetadata_in" label="Sample metadata file" type="data" format="tabular" help="sample x metadata, decimal: '.', missing: NA, mode: character and numerical, sep: tabular" />
    <param name="variableMetadata_in" label="Variable metadata file" type="data" format="tabular" help="variable x metadata, decimal: '.', missing: NA, mode: character and numerical, sep: tabular" />
    <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>

  </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>
    <data name="information" label="${tool.name}__information.txt" format="txt"/>
  </outputs>

  <tests>
    <test>
      <param name="dataMatrix_in" value="input_dataMatrix.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"/>
      <param name="information" value="test-information.txt"/>
      <output name="dataMatrix_out">
        <assert_contents>
          <not_has_text text="HU_028" />
          <not_has_text text="HU_051" />
          <not_has_text text="HU_060" />

      <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"/>
      <param name="information" value="test-information.txt"/>
      <output name="sampleMetadata_out">
        <assert_contents>
          <not_has_text text="HU_028" />
          <not_has_text text="HU_051" />
          <not_has_text text="HU_060" />

      <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"/>
      <param name="information" value="test-information.txt"/>
      <output name="variableMetadata_out">
        <assert_contents>
          <has_text     text="HMDB03193" />
          <not_has_text text="HMDB00822" />
          <has_text     text="HMDB01101" />

    </test>
  </tests>



  <help>

.. class:: infomark

**Author**	Arthur Eschenlauer (University of Minnesota, [e-mail])

-----------

+---------------------------+------------+
| File                      |   Format   |
+===========================+============+
| 1)  Data matrix           |   tabular  |
+---------------------------+------------+
| 2)  Sample metadata       |   tabular  |
+---------------------------+------------+
| 3)  Variable metadata     |   tabular  |
+---------------------------+------------+


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

Data matrix file
	| variable x sample **dataMatrix** tabular separated 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 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 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
	|

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


sampleMetadata_out.tabular
	| **sampleMetadata** tabular separated file identical to the file given as argument, excepting lacking rows for samples that have been filtered out
	|

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

dataMatrix_out.tabular
	| **dataMatrix** tabular separated file identical to the file given as argument, excepting lacking columns for samples that have been filtered out (because of the sample-classes specified in the input parameters) and rows for variables (xC-MS features) that have been filtered out (because of zero variance)
	|

information.txt
	| Text file with all messages and warnings generated during the computation
	|

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

----
NEWS

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

INTERNAL MODIFICATIONS

none

  </help>
  <citations>
  </citations>
</tool>
<!-- vim: et sw=2 ts=2 :
-->

2:23c6d271def9

  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>

  </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="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" />

      <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" />

      <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" />

    </test>
  </tests>



	<help>
		<![CDATA[

.. class:: infomark

**Author**	Arthur Eschenlauer (University of Minnesota, [e-mail])

-----------

+---------------------------+------------+
| 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
	|

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

*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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-->