<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="Table" />
    <param name="ensembl_col" type="data_column" data_ref="input" label="Column with ENSEMBL transcript code" />
  </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>

**What it does**

Adds the fields KEGG gene codes and KEGG pathways to an input table of ENSEMBL transcript codes.

  </help>
</tool>