view tabular_label_convert/tabular_label_convert.xml @ 0:1f93906c2945 draft default tip

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<tool id="tabular_label_convert" name="Tabular Label Convert" version="1.0.0">
  <description>Tabular Label Convert</description>
  <command interpreter="python">tabular_label_convert.py -m ${dim} -c ${merge_mode} $intab $aliasMap -o $outfile</command>
  <inputs>
	  <param name="intab" type="data" format="tabular" label="Tabular Input"/>
	  <param name="aliasMap" type="data" format="tabular" label="AliasMap"/>
	  <param name="dim" type="select" label="Merge Across">
	  	<option value="row">Rows</option>
	  	<option value="col">Columns</option>
	  </param>
	  <param name="merge_mode" type="select" label="Merge Mode">
	  	<option value="mean">Mean</option>
	  	<option value="median">Median</option>
	  	<option value="min">Min</option>
	  	<option value="max">Max</option>
	  </param>
  </inputs>
  <outputs>
      <data name="outfile" format="tabular"/>
  </outputs>
  <help>
This tool takes a tabular format file of numerical values and converts the labels of the 
rows or columns using an alias map. If two or more labels map to the same alias, then the mean/median/min/max
value is selected to represent the new alias.

Input tabular format
    A tab seperated matrix for floats, with the row and column serving as labels.


+-----------+----------------------+-----------------------+-----------------------+-----------------------+
|probe      |  sample_1            |  sample_2             |   sample_3            |  sample_4             |
+-----------+----------------------+-----------------------+-----------------------+-----------------------+
|207189_s_at|     -0.210051        | -0.492633             | -0.133921             |  -0.462803            |
+-----------+----------------------+-----------------------+-----------------------+-----------------------+
|207190_at  |    -0.427553         |  -0.021174            |-0.398800              | -0.518978             |
+-----------+----------------------+-----------------------+-----------------------+-----------------------+
|216013_at  |     -0.764110        | -0.911805             | -1.450937             |  -1.201317            |
+-----------+----------------------+-----------------------+-----------------------+-----------------------+

Alias map format
    A two column tab seperated files, the first column is the source label with the second column the destination alias.

+-------------+-----+
|216013_at    |ZXDB |
+-------------+-----+
|207189_s_at  |ZZEF1|
+-------------+-----+
|207190_at    |ZZEF1|
+-------------+-----+

Results
    With the doing row relabel with 'mean' combination the matrix becomes:


+-----------+----------------------+-----------------------+-----------------------+-----------------------+
|probe      |  sample_1            |  sample_2             |   sample_3            |  sample_4             |
+-----------+----------------------+-----------------------+-----------------------+-----------------------+
|ZZEF1      |     -0.3188020       | -0.2569035            | -0.2663605            | -0.4908905            |
+-----------+----------------------+-----------------------+-----------------------+-----------------------+
|ZXDB       |     -0.764110        | -0.911805             | -1.450937             |  -1.201317            |
+-----------+----------------------+-----------------------+-----------------------+-----------------------+


  </help>
</tool>