<tool id="gd_new_oscar" name="Get Pathways" version="1.0.0">
  <description>: Look up KEGG pathways for given Ensembl transcripts</description>

  <command interpreter="python">
    rtrnKEGGpthwfENSEMBLTc.py
      "--loc_file=${GALAXY_DATA_INDEX_DIR}/gd.oscar.loc"
      "--species=${input.metadata.dbkey}"
      "--input=${input}"
      "--posENSEMBLclmn=${ensembl_col}"
      "--output=${output}"
  </command>

  <inputs>
    <param name="input" type="data" format="tabular" label="Dataset" >
       <validator type="unspecified_build" message="This dataset does not have a database/build and cannot be used with this tool" />
    </param>
    <param name="ensembl_col" type="data_column" data_ref="input" label="Column with ENSEMBL transcript ID" />
  </inputs>

  <outputs>
    <data name="output" format="tabular" />
  </outputs>

  <!--
  <tests>
    <test>
      <param name="input" value="test_in/ensembl.tabular" ftype="tabular">
        <metadata name="dbkey" value="canFam2" />
      </param>
      <param name="ensembl_col" value="1" />

      <output name="output" file="test_out/map_ensembl_transcripts/map_ensembl_transcripts.tabular" />
    </test>
  </tests>
  -->

  <help>

**Dataset formats**

The input and output datasets are in tabular_ format.
The input dataset must have a column with an ENSEMBL transcript ID and have
the database/build set.  Even though positions are not needed the correct
database/build must be given to look up the pathways.
The output dataset will have added columns for the pathway.
(`Dataset missing?`_)

.. _tabular: ./static/formatHelp.html#tab
.. _Dataset missing?: ./static/formatHelp.html

-----

**What it does**

Adds the fields "KEGG gene ID" and "KEGG pathways" to an input table of ENSEMBL 
transcript IDs.  A "U" in the KEGG gene ID field indicates that the 
tool cannot link the ENSEMBL transcript ID to a KEGG gene ID.
An "N" in the pathway field means the KEGG pathway is unknown.

-----

**Example**

- input::

   ENSCAFT00000000001
   ENSCAFT00000000144
   ENSCAFT00000000160
   ENSCAFT00000000215
   etc.

- output::

   ENSCAFT00000000001      476153  cfa00230=Purine metabolism.cfa00500=Starch and sucrose metabolism.cfa00740=Riboflavin metabolism.cfa00760=Nicotinate and nicotinamide metabolism.cfa00770=Pantothenate and CoA biosynthesis.cfa01100=Metabolic pathways
   ENSCAFT00000000144      483960  N
   ENSCAFT00000000160      610160  N
   ENSCAFT00000000215      U       N
   etc.
 
  </help>
</tool>