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1 <?xml version="1.0"?>
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2 <toolbox tool_path="../galaxy-tools">
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3 <label text="OMERO.biobank Tools" id="biobank_label"/>
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4 <section name="BIOBANK import" id="bbSection.import">
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5 <tool file="biobank/importer/biosample.xml"/>
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6 <tool file="biobank/importer/birth_data.xml"/>
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7 <tool file="biobank/importer/data_collection.xml"/>
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8 <tool file="biobank/importer/data_sample.xml"/>
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9 <tool file="biobank/importer/device.xml"/>
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10 <tool file="biobank/importer/diagnosis.xml"/>
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11 <tool file="biobank/importer/enrollment.xml"/>
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12 <tool file="biobank/importer/group.xml"/>
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13 <tool file="biobank/importer/individual.xml"/>
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14 <tool file="biobank/importer/laneslot.xml"/>
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15 <tool file="biobank/importer/marker_alignment.xml"/>
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16 <tool file="biobank/importer/marker_definition.xml"/>
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17 <tool file="biobank/importer/markers_set.xml"/>
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18 <tool file="biobank/importer/samples_container.xml"/>
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19 <tool file="biobank/importer/sequencing_data_sample.xml"/>
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20 <tool file="biobank/importer/study.xml"/>
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21 <tool file="biobank/importer/vessels_collection.xml"/>
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22 <tool file="biobank/importer/data_object.xml"/>
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23 <tool file="biobank/importer/illumina_bead_chip_measures.xml"/>
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24 </section>
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25
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26 <section name="BIOBANK library" id="bbSection.library">
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27 <tool file="biobank/library/import_to_library.xml"/>
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28 </section>
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29
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30 <section name="BIOBANK tools" id="bbSection.tools">
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31 <tool file="biobank/tools/all_enrollments.xml"/>
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32 <tool file="biobank/tools/build_miniped.xml"/>
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33 <tool file="biobank/tools/check_merge_individuals.xml"/>
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34 <tool file="biobank/tools/check_update_parents_data.xml"/>
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35 <tool file="biobank/tools/convert_sam.xml"/>
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36 <tool file="biobank/tools/drop_parental_info.xml"/>
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37 <tool file="biobank/tools/enrollments_by_platewells.xml"/>
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38 <tool file="biobank/tools/get_kinship_input.xml"/>
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39 <tool file="biobank/tools/get_parents_from_sibling.xml"/>
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40 <tool file="biobank/tools/get_studies_details.xml"/>
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41 <tool file="biobank/tools/get_titerplates_details.xml"/>
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42 <tool file="biobank/tools/global_stats.xml"/>
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43 <tool file="biobank/tools/gstudio_datasheet.xml"/>
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44 <tool file="biobank/tools/lookup_index.xml"/>
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45 <tool file="biobank/tools/map_to_collection.xml"/>
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46 <tool file="biobank/tools/map_vid.xml"/>
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47 <tool file="biobank/tools/markers_to_fastq.xml"/>
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48 <tool file="biobank/tools/plate_dsamples_details.xml"/>
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49 <tool file="biobank/tools/query.xml"/>
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50 <tool file="biobank/tools/select_sub_group.xml"/>
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51 <tool file="biobank/tools/snp_manager.xml"/>
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52 <tool file="biobank/tools/vessels_by_individual.xml"/>
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53 <tool file="biobank/tools/flowcell_samplesheet.xml"/>
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54 </section>
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55
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56 <section name="BIOBANK updater" id="bbSection.updater">
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57 <tool file="biobank/updater/change_source_item.xml"/>
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58 <tool file="biobank/updater/discard_from_collection.xml"/>
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59 <tool file="biobank/updater/merge_individuals.xml"/>
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60 <tool file="biobank/updater/update_parents_data.xml"/>
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61 </section>
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62
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63 <section name="BIOBANK utils" id="bbSection.utils">
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64 <tool file="biobank/utils/format_vessels_by_individual_output.xml"/>
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65 <tool file="biobank/utils/gdoize_ms.xml"/>
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66 <tool file="biobank/utils/before_prepare_seq_dsample_inputs.xml"/>
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67 <tool file="biobank/utils/prepare_seq_dsample_inputs.xml"/>
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68 <tool file="biobank/utils/prepare_seq_out_inputs.xml"/>
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69 <tool file="biobank/utils/delete_flowcell_results.xml"/>
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70 <tool file="biobank/utils/prepare_illumina_import_inputs.xml"/>
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71 <tool file="biobank/utils/check_tsv_header.xml"/>
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72 <tool file="biobank/utils/from_well_to_illumina_measures.xml"/>
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73 <tool file="biobank/utils/wells_barcode_to_label.xml"/>
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74 <tool file="biobank/utils/split_by_study.xml"/>
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75 <tool file="biobank/utils/prepare_individuals_import.xml"/>
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76 <tool file="biobank/utils/prepare_enrollments_import.xml"/>
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77 <tool file="biobank/utils/prepare_genome_variations_dsample_import.xml"/>
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78 <tool file="biobank/utils/prepare_aligned_seq_dsample_import.xml"/>
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79 </section>
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80
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81 </toolbox>
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