Mercurial > repos > iuc > ena_upload

annotate test-data/simple_test_case_v2.json @ 14:5cb6146337d8 draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ab38fa3d5ec06729c1efa86240ec57b8143b21ed
author iuc
date Wed, 12 Jun 2024 16:01:11 +0000
parents f803a68fc9e5
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
11
f803a68fc9e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit c7f54e6e3b1ffad5631ff7c150449cb79bd3686d
iuc
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1 {
f803a68fc9e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit c7f54e6e3b1ffad5631ff7c150449cb79bd3686d
iuc
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2 "identifier": "",
f803a68fc9e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit c7f54e6e3b1ffad5631ff7c150449cb79bd3686d
iuc
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3 "title": "Test Case ENA upload tool",
f803a68fc9e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit c7f54e6e3b1ffad5631ff7c150449cb79bd3686d
iuc
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4 "description": "This investigation matches the test case of the ENA upload tool",
f803a68fc9e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit c7f54e6e3b1ffad5631ff7c150449cb79bd3686d
iuc
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5 "submissionDate": "",
f803a68fc9e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit c7f54e6e3b1ffad5631ff7c150449cb79bd3686d
iuc
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6 "publicReleaseDate": "",
f803a68fc9e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit c7f54e6e3b1ffad5631ff7c150449cb79bd3686d
iuc
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7 "ontologySourceReferences": [],
f803a68fc9e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit c7f54e6e3b1ffad5631ff7c150449cb79bd3686d
iuc
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8 "filename": "Test Case ENA upload tool.txt",
f803a68fc9e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit c7f54e6e3b1ffad5631ff7c150449cb79bd3686d
iuc
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9 "comments": [
f803a68fc9e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit c7f54e6e3b1ffad5631ff7c150449cb79bd3686d
iuc
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10 {
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11 "name": "ISAjson export time",
f803a68fc9e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit c7f54e6e3b1ffad5631ff7c150449cb79bd3686d
iuc
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12 "value": "2023-11-08T16:27:49Z"
f803a68fc9e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit c7f54e6e3b1ffad5631ff7c150449cb79bd3686d
iuc
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13 },
f803a68fc9e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit c7f54e6e3b1ffad5631ff7c150449cb79bd3686d
iuc
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14 {
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iuc
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15 "name": "SEEK Project name",
f803a68fc9e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit c7f54e6e3b1ffad5631ff7c150449cb79bd3686d
iuc
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16 "value": "Test Project ENA upload Tool"
f803a68fc9e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit c7f54e6e3b1ffad5631ff7c150449cb79bd3686d
iuc
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17 },
f803a68fc9e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit c7f54e6e3b1ffad5631ff7c150449cb79bd3686d
iuc
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18 {
f803a68fc9e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit c7f54e6e3b1ffad5631ff7c150449cb79bd3686d
iuc
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19 "name": "SEEK Project ID",
f803a68fc9e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit c7f54e6e3b1ffad5631ff7c150449cb79bd3686d
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20 "value": "http://localhost:3000/single_pages/16"
f803a68fc9e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit c7f54e6e3b1ffad5631ff7c150449cb79bd3686d
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21 },
f803a68fc9e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit c7f54e6e3b1ffad5631ff7c150449cb79bd3686d
iuc
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22 {
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23 "name": "SEEK Investigation ID",
f803a68fc9e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit c7f54e6e3b1ffad5631ff7c150449cb79bd3686d
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24 "value": "27"
f803a68fc9e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit c7f54e6e3b1ffad5631ff7c150449cb79bd3686d
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25 }
f803a68fc9e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit c7f54e6e3b1ffad5631ff7c150449cb79bd3686d
iuc
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26 ],
f803a68fc9e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit c7f54e6e3b1ffad5631ff7c150449cb79bd3686d
iuc
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27 "publications": [],
f803a68fc9e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit c7f54e6e3b1ffad5631ff7c150449cb79bd3686d
iuc
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28 "people": [
f803a68fc9e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit c7f54e6e3b1ffad5631ff7c150449cb79bd3686d
iuc
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29 {
f803a68fc9e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit c7f54e6e3b1ffad5631ff7c150449cb79bd3686d
iuc
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30 "@id": "#people/4",
f803a68fc9e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit c7f54e6e3b1ffad5631ff7c150449cb79bd3686d
iuc
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31 "lastName": "De Pelseneer",
f803a68fc9e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit c7f54e6e3b1ffad5631ff7c150449cb79bd3686d
iuc
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32 "firstName": "Kevin",
f803a68fc9e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit c7f54e6e3b1ffad5631ff7c150449cb79bd3686d
iuc
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33 "midInitials": "",
f803a68fc9e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit c7f54e6e3b1ffad5631ff7c150449cb79bd3686d
iuc
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34 "email": "kevin.depelseneer@psb.ugent.be",
f803a68fc9e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit c7f54e6e3b1ffad5631ff7c150449cb79bd3686d
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35 "phone": "",
f803a68fc9e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit c7f54e6e3b1ffad5631ff7c150449cb79bd3686d
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36 "fax": "",
f803a68fc9e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit c7f54e6e3b1ffad5631ff7c150449cb79bd3686d
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37 "address": "",
f803a68fc9e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit c7f54e6e3b1ffad5631ff7c150449cb79bd3686d
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f803a68fc9e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit c7f54e6e3b1ffad5631ff7c150449cb79bd3686d
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39 "roles": [
f803a68fc9e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit c7f54e6e3b1ffad5631ff7c150449cb79bd3686d
iuc
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40 {
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41 "termAccession": "",
f803a68fc9e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit c7f54e6e3b1ffad5631ff7c150449cb79bd3686d
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42 "termSource": "",
f803a68fc9e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit c7f54e6e3b1ffad5631ff7c150449cb79bd3686d
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43 "annotationValue": ""
f803a68fc9e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit c7f54e6e3b1ffad5631ff7c150449cb79bd3686d
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44 }
f803a68fc9e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit c7f54e6e3b1ffad5631ff7c150449cb79bd3686d
iuc
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45 ],
f803a68fc9e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit c7f54e6e3b1ffad5631ff7c150449cb79bd3686d
iuc
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46 "comments": [
f803a68fc9e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit c7f54e6e3b1ffad5631ff7c150449cb79bd3686d
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47 {
f803a68fc9e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit c7f54e6e3b1ffad5631ff7c150449cb79bd3686d
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48 "@id": "",
f803a68fc9e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit c7f54e6e3b1ffad5631ff7c150449cb79bd3686d
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49 "value": "",
f803a68fc9e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit c7f54e6e3b1ffad5631ff7c150449cb79bd3686d
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50 "name": ""
f803a68fc9e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit c7f54e6e3b1ffad5631ff7c150449cb79bd3686d
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51 }
f803a68fc9e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit c7f54e6e3b1ffad5631ff7c150449cb79bd3686d
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52 ]
f803a68fc9e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit c7f54e6e3b1ffad5631ff7c150449cb79bd3686d
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53 }
f803a68fc9e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit c7f54e6e3b1ffad5631ff7c150449cb79bd3686d
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54 ],
f803a68fc9e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit c7f54e6e3b1ffad5631ff7c150449cb79bd3686d
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55 "studies": [
f803a68fc9e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit c7f54e6e3b1ffad5631ff7c150449cb79bd3686d
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56 {
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57 "identifier": "",
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58 "title": "Study - Test Case ENA",
f803a68fc9e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit c7f54e6e3b1ffad5631ff7c150449cb79bd3686d
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59 "description": "",
f803a68fc9e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit c7f54e6e3b1ffad5631ff7c150449cb79bd3686d
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60 "submissionDate": "",
f803a68fc9e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit c7f54e6e3b1ffad5631ff7c150449cb79bd3686d
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61 "publicReleaseDate": "",
f803a68fc9e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit c7f54e6e3b1ffad5631ff7c150449cb79bd3686d
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62 "filename": "Study - Test Case ENA.txt",
f803a68fc9e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit c7f54e6e3b1ffad5631ff7c150449cb79bd3686d
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63 "comments": [
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64 {
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65 "@id": "#study_comment/25_13_49",
f803a68fc9e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit c7f54e6e3b1ffad5631ff7c150449cb79bd3686d
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66 "name": "ena_sample_alias_prefix",
f803a68fc9e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit c7f54e6e3b1ffad5631ff7c150449cb79bd3686d
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67 "value": "sample_alias_"
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68 },
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69 {
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70 "@id": "#study_comment/25_ae7461a0-6081-013c-9ed3-7a163e608de1",
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71 "name": "SEEK Study ID",
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72 "value": "25"
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73 },
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74 {
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75 "@id": "#study_comment/25_ae7467e0-6081-013c-9ed4-7a163e608de1",
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76 "name": "SEEK creation date",
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77 "value": "2023-10-20T11:12:23Z"
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78 }
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79 ],
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80 "publications": [],
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82 {
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83 "@id": "#people/4",
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84 "lastName": "De Pelseneer",
f803a68fc9e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit c7f54e6e3b1ffad5631ff7c150449cb79bd3686d
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85 "firstName": "Kevin",
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86 "midInitials": "",
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87 "email": "kevin.depelseneer@psb.ugent.be",
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630 "@id": "#protocol/_25"
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640 "outputs": [
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642 "@id": "#sample/224"
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645 },
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647 "@id": "#process/sample_collection/225",
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648 "name": "",
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649 "executesProtocol": {
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650 "@id": "#protocol/_25"
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651 },
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652 "parameterValues": [],
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653 "performer": "",
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654 "date": "",
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655 "inputs": [
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656 {
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657 "@id": "#source/226"
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658 }
f803a68fc9e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit c7f54e6e3b1ffad5631ff7c150449cb79bd3686d
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659 ],
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660 "outputs": [
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661 {
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662 "@id": "#sample/225"
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663 }
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714 "name": "ena_experiment_alias_prefix",
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715 "value": "experiment_alias_"
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717 {
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718 "@id": "#assay_comment/25_48_49_14_57",
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719 "name": "ena_run_alias_prefix",
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720 "value": "run_alias_"
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721 },
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722 {
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723 "@id": "#assay_comment/48_49",
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724 "name": "linked_assays",
f803a68fc9e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit c7f54e6e3b1ffad5631ff7c150449cb79bd3686d
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725 "value": "[{\"id\":48,\"title\":\"Assay 1 - Test case ENA upload tool\"},{\"id\":49,\"title\":\"Assay 2 - Test case ENA upload tool\"}]"
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729 "characteristicCategories": [
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734 "termAccession": "",
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735 "termSource": ""
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738 {
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739 "@id": "#characteristic_category/library_name_673",
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741 "annotationValue": "library_name",
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742 "termAccession": "",
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746 {
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747 "@id": "#characteristic_category/accession_681",
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748 "characteristicType": {
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749 "annotationValue": "accession",
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750 "termAccession": "",
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751 "termSource": ""
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754 {
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755 "@id": "#characteristic_category/submission_date_682",
f803a68fc9e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit c7f54e6e3b1ffad5631ff7c150449cb79bd3686d
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756 "characteristicType": {
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1518 "outputs": [
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1519 {
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1520 "@id": "#data_file/235"
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1523 "previousProcess": {
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1524 "@id": "#process/library_construction/235"
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1525 },
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1526 "nextProcess": {}
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1529 "dataFiles": [
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1530 {
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1531 "@id": "#data_file/233",
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1532 "name": "RD file 1a",
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1533 "type": "Raw Data File",
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1534 "comments": [
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1536 "name": "file_name",
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1537 "value": "ENA_TEST2.R1.fastq.gz"
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1539 {
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1540 "name": "file_type",
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1541 "value": "fastq"
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1542 },
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1543 {
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1544 "name": "file checksum",
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1545 "value": ""
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1547 {
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1548 "name": "accession",
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1549 "value": ""
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1551 {
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1552 "name": "submission date",
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1553 "value": ""
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1555 {
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1556 "name": "status",
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1557 "value": "add"
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1560 },
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1561 {
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1562 "@id": "#data_file/234",
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1563 "name": "RD file 1b",
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1564 "type": "Raw Data File",
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1565 "comments": [
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1566 {
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1567 "name": "file_name",
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1568 "value": "ENA_TEST2.R2.fastq.gz"
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1569 },
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1570 {
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1571 "name": "file_type",
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1572 "value": "fastq"
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1574 {
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1575 "name": "file checksum",
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1576 "value": ""
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1578 {
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1579 "name": "accession",
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1580 "value": ""
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1582 {
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1583 "name": "submission date",
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1584 "value": ""
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1586 {
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1587 "name": "status",
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1588 "value": "add"
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1592 {
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1593 "@id": "#data_file/235",
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1594 "name": "RD file 3",
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1595 "type": "Raw Data File",
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1596 "comments": [
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1597 {
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1598 "name": "file_name",
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1599 "value": "ENA_TEST1.R1.fastq.gz"
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1602 "name": "file_type",
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1603 "value": "fastq"
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1605 {
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1606 "name": "file checksum",
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1607 "value": ""
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diff changeset
1610 "name": "accession",
f803a68fc9e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit c7f54e6e3b1ffad5631ff7c150449cb79bd3686d
iuc
parents:
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1611 "value": ""
f803a68fc9e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit c7f54e6e3b1ffad5631ff7c150449cb79bd3686d
iuc
parents:
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1612 },
f803a68fc9e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit c7f54e6e3b1ffad5631ff7c150449cb79bd3686d
iuc
parents:
diff changeset
1613 {
f803a68fc9e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit c7f54e6e3b1ffad5631ff7c150449cb79bd3686d
iuc
parents:
diff changeset
1614 "name": "submission date",
f803a68fc9e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit c7f54e6e3b1ffad5631ff7c150449cb79bd3686d
iuc
parents:
diff changeset
1615 "value": ""
f803a68fc9e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit c7f54e6e3b1ffad5631ff7c150449cb79bd3686d
iuc
parents:
diff changeset
1616 },
f803a68fc9e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit c7f54e6e3b1ffad5631ff7c150449cb79bd3686d
iuc
parents:
diff changeset
1617 {
f803a68fc9e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit c7f54e6e3b1ffad5631ff7c150449cb79bd3686d
iuc
parents:
diff changeset
1618 "name": "status",
f803a68fc9e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit c7f54e6e3b1ffad5631ff7c150449cb79bd3686d
iuc
parents:
diff changeset
1619 "value": "add"
f803a68fc9e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit c7f54e6e3b1ffad5631ff7c150449cb79bd3686d
iuc
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1620 }
f803a68fc9e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit c7f54e6e3b1ffad5631ff7c150449cb79bd3686d
iuc
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1621 ]
f803a68fc9e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit c7f54e6e3b1ffad5631ff7c150449cb79bd3686d
iuc
parents:
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1622 }
f803a68fc9e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit c7f54e6e3b1ffad5631ff7c150449cb79bd3686d
iuc
parents:
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1623 ],
f803a68fc9e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit c7f54e6e3b1ffad5631ff7c150449cb79bd3686d
iuc
parents:
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1624 "unitCategories": []
f803a68fc9e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit c7f54e6e3b1ffad5631ff7c150449cb79bd3686d
iuc
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1625 }
f803a68fc9e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit c7f54e6e3b1ffad5631ff7c150449cb79bd3686d
iuc
parents:
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1626 ],
f803a68fc9e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit c7f54e6e3b1ffad5631ff7c150449cb79bd3686d
iuc
parents:
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1627 "factors": [],
f803a68fc9e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit c7f54e6e3b1ffad5631ff7c150449cb79bd3686d
iuc
parents:
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1628 "unitCategories": []
f803a68fc9e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit c7f54e6e3b1ffad5631ff7c150449cb79bd3686d
iuc
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1629 }
f803a68fc9e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit c7f54e6e3b1ffad5631ff7c150449cb79bd3686d
iuc
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1630 ]
f803a68fc9e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit c7f54e6e3b1ffad5631ff7c150449cb79bd3686d
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1631 }