<tool id="galaxy_intermine_exchange" name="Create InterMine Interchange" version="0.0.1">
    <description>Dataset</description>
    <requirements>
        <requirement type="package" version="8.25">coreutils</requirement>
    </requirements>
    <command detect_errors="exit_code"><![CDATA[
        awk -F \$'\t' ' {
        #if str($feature_text):
        f = "${feature_text}";
        #else:
        f = \$${feature_column};
        #end if

        #if str($feature_id_text):
        i = "${feature_id_text}";
        #else:
        i = \$${feature_id_column};
        #end if

        #if str($organism_text):
        o = "${organism_text}";
        #elif $organism_column:
        o = \$${organism_column};
        #else:
        o= "";
        #end if

        print f, i, o; } ' OFS=\$'\t' '${input_tabular}' > '${intermine_output}'
    ]]>
    </command>
    <inputs>
        <param name="input_tabular" type="data" format="txt" multiple="False" optional="False" label="Tabular file"/>
        <param name="feature_column" type="data_column" data_ref="input_tabular" optional="False" label="Feature Type column" value="1"/>
        <param name="feature_text" type="text" value="" optional="True" label="Feature Type" help="Optional, will override column selection with static text value"/>
        <param name="feature_id_column" type="data_column" data_ref="input_tabular" optional="False" label="Feature Identifier column" value="2"/>
        <param name="feature_id_text" type="text" value="" optional="True" label="Feature Identifier" help="Optional, will override column selection with static text value"/>
        <param name="organism_column" type="data_column" data_ref="input_tabular" optional="True" label="Organism Name column" value="3"/>
        <param name="organism_text" type="text" value="" optional="True" label="Organism Name" help="Optional, will override column selection with static text value"/>
    </inputs>
    <outputs>
        <data format="intermine_tabular" name="intermine_output"/>
    </outputs>
    <tests>
        <test>
            <param name="input_tabular" value="intermine-format-example.tsv" ftype="tabular"/>
            <param name="feature_column" value="1"/>
            <param name="feature_id_text" value=""/>
            <param name="feature_id_column" value="2"/>
            <param name="feature_text" value=""/>
            <param name="forganism_column" value="2"/>
            <param name="organism_text" value=""/>
            <output name="intermine_output" file="intermine-format-example.tsv" ftype="intermine_tabular"/>
        </test>
    </tests>
    <help>
        <![CDATA[
InterMine-Galaxy exchange format
================================
This file format exists as an intermediate step to import from Galaxy to InterMines and is not in itself a data format intended to be used for data storage or any purpose apart from Galaxy->InterMine interoperability.

This file has two mandatory columns and one optional column

Column 1 (mandatory)
--------------------
**Type of identifier**, e.g. `Gene` or `Protein`. Must be a class in the `InterMine data model`_. Gene or Protein is always a safe option.

Column 2 (mandatory)
--------------------
**Identifier** this could be, as an example, a gene symbol like `GATA1` or another other identifier, e.g. `FBGN0000099` or perhaps a protein accession, or some other identifier.

Column 3 (optional)
-------------------
**Organism name** - e.g. `H. sapiens` or `Drosophila melanogaster`. This is optional and does not have to be precise, but is good to provide if it is known.

----

For additional information, please see:

- https://github.com/intermine/galaxy-integration/blob/master/intermine-file-format/intermine-format-definition.md
- https://raw.githubusercontent.com/intermine/galaxy-integration/master/intermine-file-format/intermine-format-example.tsv

.. _InterMine data model: http://intermine.readthedocs.io/en/latest/data-model/model/#a-short-example
        ]]>
    </help>
    <citations>
        <citation type="doi">10.1093/nar/gku301</citation>
    </citations>
</tool>