diff galaxy-tools/biobank_tool_conf.xml @ 0:ba6cf6ede027 draft default tip

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/galaxy-tools/biobank_tool_conf.xml	Wed Sep 28 06:03:30 2016 -0400
@@ -0,0 +1,81 @@
+<?xml version="1.0"?>
+<toolbox tool_path="../galaxy-tools">
+  <label text="OMERO.biobank Tools" id="biobank_label"/>
+  <section name="BIOBANK import" id="bbSection.import">
+    <tool file="biobank/importer/biosample.xml"/>
+    <tool file="biobank/importer/birth_data.xml"/>
+    <tool file="biobank/importer/data_collection.xml"/>
+    <tool file="biobank/importer/data_sample.xml"/>
+    <tool file="biobank/importer/device.xml"/>
+    <tool file="biobank/importer/diagnosis.xml"/>
+    <tool file="biobank/importer/enrollment.xml"/>
+    <tool file="biobank/importer/group.xml"/>
+    <tool file="biobank/importer/individual.xml"/>
+    <tool file="biobank/importer/laneslot.xml"/>
+    <tool file="biobank/importer/marker_alignment.xml"/>
+    <tool file="biobank/importer/marker_definition.xml"/>
+    <tool file="biobank/importer/markers_set.xml"/>
+    <tool file="biobank/importer/samples_container.xml"/>
+    <tool file="biobank/importer/sequencing_data_sample.xml"/>
+    <tool file="biobank/importer/study.xml"/>
+    <tool file="biobank/importer/vessels_collection.xml"/>
+    <tool file="biobank/importer/data_object.xml"/>
+    <tool file="biobank/importer/illumina_bead_chip_measures.xml"/>
+  </section>
+
+  <section name="BIOBANK library" id="bbSection.library">
+    <tool file="biobank/library/import_to_library.xml"/>
+  </section>
+
+  <section name="BIOBANK tools" id="bbSection.tools">
+    <tool file="biobank/tools/all_enrollments.xml"/>
+    <tool file="biobank/tools/build_miniped.xml"/>
+    <tool file="biobank/tools/check_merge_individuals.xml"/>
+    <tool file="biobank/tools/check_update_parents_data.xml"/>
+    <tool file="biobank/tools/convert_sam.xml"/>
+    <tool file="biobank/tools/drop_parental_info.xml"/>
+    <tool file="biobank/tools/enrollments_by_platewells.xml"/>	
+    <tool file="biobank/tools/get_kinship_input.xml"/>
+    <tool file="biobank/tools/get_parents_from_sibling.xml"/>
+    <tool file="biobank/tools/get_studies_details.xml"/>
+    <tool file="biobank/tools/get_titerplates_details.xml"/>
+    <tool file="biobank/tools/global_stats.xml"/>
+    <tool file="biobank/tools/gstudio_datasheet.xml"/>
+    <tool file="biobank/tools/lookup_index.xml"/>
+    <tool file="biobank/tools/map_to_collection.xml"/>
+    <tool file="biobank/tools/map_vid.xml"/>
+    <tool file="biobank/tools/markers_to_fastq.xml"/>
+    <tool file="biobank/tools/plate_dsamples_details.xml"/>
+    <tool file="biobank/tools/query.xml"/>
+    <tool file="biobank/tools/select_sub_group.xml"/>
+    <tool file="biobank/tools/snp_manager.xml"/>
+    <tool file="biobank/tools/vessels_by_individual.xml"/>
+    <tool file="biobank/tools/flowcell_samplesheet.xml"/>
+  </section>
+
+  <section name="BIOBANK updater" id="bbSection.updater">
+    <tool file="biobank/updater/change_source_item.xml"/>
+    <tool file="biobank/updater/discard_from_collection.xml"/>
+    <tool file="biobank/updater/merge_individuals.xml"/>
+    <tool file="biobank/updater/update_parents_data.xml"/>
+  </section>
+
+  <section name="BIOBANK utils" id="bbSection.utils">
+    <tool file="biobank/utils/format_vessels_by_individual_output.xml"/>
+    <tool file="biobank/utils/gdoize_ms.xml"/>
+    <tool file="biobank/utils/before_prepare_seq_dsample_inputs.xml"/>
+    <tool file="biobank/utils/prepare_seq_dsample_inputs.xml"/>
+    <tool file="biobank/utils/prepare_seq_out_inputs.xml"/>
+    <tool file="biobank/utils/delete_flowcell_results.xml"/>
+    <tool file="biobank/utils/prepare_illumina_import_inputs.xml"/>
+    <tool file="biobank/utils/check_tsv_header.xml"/>
+    <tool file="biobank/utils/from_well_to_illumina_measures.xml"/>
+    <tool file="biobank/utils/wells_barcode_to_label.xml"/>
+    <tool file="biobank/utils/split_by_study.xml"/>
+    <tool file="biobank/utils/prepare_individuals_import.xml"/>
+    <tool file="biobank/utils/prepare_enrollments_import.xml"/>
+    <tool file="biobank/utils/prepare_genome_variations_dsample_import.xml"/>
+    <tool file="biobank/utils/prepare_aligned_seq_dsample_import.xml"/>
+  </section>
+
+</toolbox>