<?xml version="1.0"?>
<!--  *********************  -->
<!--  Config for Galaxy-OBO  -->
<!--  *********************  -->
<toolbox>

  <!-- We remove most tools for now  -->
  <section name="Get Data" id="getext">
    <tool file="data_source/upload.xml"/>
      <!--
    <tool file="data_source/ucsc_tablebrowser.xml" />
    <tool file="data_source/ucsc_tablebrowser_test.xml" /> 
    <tool file="data_source/ucsc_tablebrowser_archaea.xml" />
    <tool file="data_source/bx_browser.xml" />
    <tool file="data_source/microbial_import.xml" />
    <tool file="data_source/biomart.xml" />
    <tool file="data_source/biomart_test.xml" />
    <tool file="data_source/cbi_rice_mart.xml" />
    <tool file="data_source/gramene_mart.xml" />
    <tool file="data_source/fly_modencode.xml" />
    <tool file="data_source/flymine.xml" />
    <tool file="data_source/flymine_test.xml" />
    <tool file="data_source/modmine.xml" />
    <tool file="data_source/ratmine.xml" />
    <tool file="data_source/worm_modencode.xml" />
    <tool file="data_source/wormbase.xml" />
    <tool file="data_source/wormbase_test.xml" />
    <tool file="data_source/eupathdb.xml" />
    <tool file="data_source/encode_db.xml" />
    <tool file="data_source/epigraph_import.xml" />
    <tool file="data_source/epigraph_import_test.xml" />
    <tool file="data_source/hbvar.xml" /> 
    <tool file="validation/fix_errors.xml" />
      -->
  </section>

 <!-- **************************************** -->
 <!-- GOtools                                  -->
 <!-- **************************************** -->
 <!-- Goose and gannet -->
 <section name="GOtools" id="gotools">
    <tool file="data_source/go_goose.xml" /> 
    <tool file="data_source/go_gannet.xml" /> 
    <tool file="data_source/general.xml" /> 
 </section>

 <!-- **************************************** -->
 <!-- NIF                                      -->
 <!-- **************************************** -->
 <!-- These tools make use of the Neuroscience Information Framework services -->
 <section name="NIFtools" id="niftools">
    <tool file="data_source/nif.xml" /> 
    <tool file="annotation/nif_annotate.xml" /> 
 </section>

 <!-- **************************************** -->
 <!-- OBO/OWLTools                             -->
 <!-- **************************************** -->
 <!-- Mostly depend on OWLTools -->
 <section name="OBO/OWL Tools" id="owltools">

    <!-- uses obo-scripts; may want to make this more robust in future -->
    <tool file="owltools/fetch_ontology.xml" />

    <!-- obo/owl translation -->
    <tool file="owltools/obo_to_owl.xml" />
    <tool file="owltools/owl_to_obo.xml" />

    <!-- reasoning -->
    <tool file="owltools/save_owl_graph_closure.xml" />
    <tool file="owltools/owl_reasoner_report.xml" />
    <tool file="owltools/class_ancestor_edges.xml" />
    <tool file="owltools/class_descendant_edges.xml" />

    <!-- <tool file="owltools/lcs_expression.xml" /> -->

    <tool file="owltools/filter_relations.xml" />

    <!-- vis -->
    <tool file="owltools/visualize_class_via_quickgo.xml" />
 </section>

 <!-- These tools are specific to OBO-Format -->
 <!-- Most depend on obo-scripts -->
 <section name="OBO Diff Tools" id="obodiff">

    <!-- These are now part of OWLTools -->
    <tool file="obodiff/def_differ.xml" />
    <tool file="obodiff/compare_obo_files.xml" />

    <!-- <tool file="obo/obo_filter_relationships.xml"/> -->

    <!-- DEPRECATED: use OWLTools -->
    <!-- <tool file="obo/extract_slim.xml" /> -->

    <!-- DEPRECATED: use OWLTools -->
    <!-- <tool file="obo/obo2linkfile.xml" /> -->

    <!-- <tool file="obo/get_descendent_terms2.xml"/> -->

 </section>

 <section name="Ontology Annotation" id="annotation">

    <!-- fetching from external sources: TODO - replace this. Golr? -->
    <tool file="annotation/extract_gaf.xml" />
    <!-- <tool file="annotation/biopax_to_go_gaf.xml" /> -->

    <!-- mapping -->
    <tool file="annotation/map2slim.xml" />

    <!-- map2slim, but with an id set. instead turn IDs into slim -->
    <tool file="annotation/map2slim_by_ids.xml" />

    <tool file="annotation/map_annotations2table.xml" />
    <!-- <tool file="annotation/filter_annotations.xml" /> -->

    <!-- requires moose -->
    <!-- <tool file="annotation/summarize_gaf.xml" /> -->

    <tool file="annotation/gaf2slim.xml" />
    <tool file="annotation/gaf_query_items.xml" />


    <tool file="annotation/uniprot_id_mapping.xml" />


    <tool file="annotation/fetch_phenotype_annotations.xml" />


    <tool file="annotation/add_labels.xml" />


    <!-- prediction -->
    <!-- <tool file="annotation/gaf_xp_predict.xml" /> -->

    <!-- conversion -->
    <tool file="annotation/gaf2owl.xml" />


    <tool file="annotation/bbop_test.xml" />

 </section>

 <section name="Annotation (advanced)" id="annotation_advanced">
    <tool file="annotation/unfold_gaf.xml" />
    <tool file="annotation/fold_gaf.xml" />
 </section>


 <section name="Term Enrichment" id="enrichment">

    <!-- enrichment analysis tools -->
    <!-- <tool file="annotation/enrichment.xml" /> -->
    <tool file="termenrichment/go_termfinder.xml" />
    <tool file="termenrichment/ontologizer.xml" />
    <tool file="termenrichment/get_population.xml" />
    <tool file="termenrichment/terf2ttl.xml" />

 </section>

<!--
 <section name="Thea OWL Lib" id="owl">
    <tool file="owl/popl.xml" />
 </section>
-->

  <section name="Text Manipulation" id="textutil">
    <tool file="filters/fixedValueColumn.xml" />
    <tool file="stats/column_maker.xml" />
    <tool file="filters/catWrapper.xml" />
    <tool file="filters/cutWrapper.xml" />
    <tool file="filters/mergeCols.xml" />
    <tool file="filters/convert_characters.xml" />
    <tool file="filters/CreateInterval.xml" />
    <tool file="filters/cutWrapper.xml" />
    <tool file="filters/changeCase.xml" />
    <tool file="filters/pasteWrapper.xml" />
    <tool file="filters/remove_beginning.xml" />
    <tool file="filters/randomlines.xml" />
    <tool file="filters/headWrapper.xml" />
    <tool file="filters/tailWrapper.xml" />
    <tool file="filters/trimmer.xml" />
    <tool file="stats/dna_filtering.xml" />
    <tool file="new_operations/tables_arithmetic_operations.xml" />
  </section>
</toolbox>