Mercurial > repos > mikel-egana-aranguren > sadi_docker_workflow

annotate Galaxy-Workflow-SADI-Docker_use_case.ga @ 1:47db0b303a50 default tip

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Added annotations to workflow
author Mikel Egana <mikel.egana.aranguren@gmail.com>
date Mon, 07 Sep 2015 19:18:27 +0200
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1 {
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2 "a_galaxy_workflow": "true",
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3 "annotation": "The workflow answers the following question: Given a set of UniProt proteins, which ones are related to PubMed abstracts containing the term ``brain'', and what are they KEGG entries? The workflow starts from a simple list of UniProt identifiers, and retrieves different datasets from a regular SADI service (to obtain KEGG entries) and a set of 3 OpenLifeData2SADI services (to obtain PubMed abstracts). The results are then merged and queried to obtain the KEGG entries of proteins that are related to PubMed abstracts that contain the term",
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4 "format-version": "0.1",
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5 "name": "SADI-Docker use case",
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6 "steps": {
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7 "0": {
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8 "annotation": "Convert white spaces to tabs, so that Galaxy recognises the list of UniProt IDs as a column",
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9 "id": 0,
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10 "input_connections": {},
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11 "inputs": [],
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12 "label": null,
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13 "name": "Convert",
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14 "outputs": [
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15 {
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16 "name": "out_file1",
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17 "type": "tabular"
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18 }
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19 ],
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20 "position": {
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21 "left": 204.9895977973938,
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22 "top": 202.90626764297485
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23 },
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24 "post_job_actions": {},
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25 "tool_errors": null,
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26 "tool_id": "Convert characters1",
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27 "tool_state": "{\"__page__\": 0, \"__rerun_remap_job_id__\": null, \"condense\": \"\\\"True\\\"\", \"strip\": \"\\\"True\\\"\", \"input\": \"null\", \"convert_from\": \"\\\"s\\\"\"}",
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28 "tool_version": "1.0.0",
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29 "type": "tool",
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30 "user_outputs": [],
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31 "uuid": "658762bb-9052-4dd2-bb6b-e77613a6dcfe"
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32 },
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33 "1": {
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34 "annotation": "Convert UniProt identifiers to URIs: Add a column with the first part of the URI",
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35 "id": 1,
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36 "input_connections": {
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37 "input": {
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38 "id": 0,
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39 "output_name": "out_file1"
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40 }
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41 },
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42 "inputs": [],
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43 "label": null,
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44 "name": "Add column",
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45 "outputs": [
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46 {
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47 "name": "out_file1",
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48 "type": "input"
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49 }
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50 ],
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51 "position": {
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52 "left": 199.9895977973938,
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53 "top": 335.9097466468811
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54 },
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55 "post_job_actions": {},
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56 "tool_errors": null,
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57 "tool_id": "addValue",
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58 "tool_state": "{\"__page__\": 0, \"input\": \"null\", \"__rerun_remap_job_id__\": null, \"exp\": \"\\\"http://openlifedata.org/uniprot:\\\"\", \"iterate\": \"\\\"no\\\"\"}",
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59 "tool_version": "1.0.0",
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60 "type": "tool",
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61 "user_outputs": [],
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62 "uuid": "c2421757-1d5d-435c-ac9e-fb036ccd4448"
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63 },
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64 "2": {
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65 "annotation": "Convert UniProt identifiers to URIs",
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66 "id": 2,
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67 "input_connections": {
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68 "input1": {
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69 "id": 1,
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70 "output_name": "out_file1"
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71 }
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72 },
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73 "inputs": [],
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74 "label": null,
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75 "name": "Merge Columns",
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76 "outputs": [
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77 {
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78 "name": "out_file1",
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79 "type": "tabular"
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80 }
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81 ],
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82 "position": {
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83 "left": 201.96875429153442,
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84 "top": 473.91322565078735
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85 },
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86 "post_job_actions": {},
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87 "tool_errors": null,
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88 "tool_id": "mergeCols1",
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89 "tool_state": "{\"__page__\": 0, \"input1\": \"null\", \"__rerun_remap_job_id__\": null, \"col2\": \"\\\"\\\"\", \"col1\": \"\\\"\\\"\", \"columns\": \"[]\"}",
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90 "tool_version": "1.0.1",
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91 "type": "tool",
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92 "user_outputs": [],
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93 "uuid": "63b4d2ff-0e1d-449d-aad5-a2ccd033d36a"
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94 },
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95 "3": {
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96 "annotation": "Obtain the UniProt URIs",
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97 "id": 3,
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98 "input_connections": {
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99 "input": {
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100 "id": 2,
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101 "output_name": "out_file1"
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102 }
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103 },
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104 "inputs": [],
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105 "label": null,
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106 "name": "Cut",
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107 "outputs": [
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108 {
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109 "name": "out_file1",
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110 "type": "tabular"
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111 }
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112 ],
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113 "position": {
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114 "left": 202.99307680130005,
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115 "top": 592.906298160553
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116 },
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117 "post_job_actions": {},
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118 "tool_errors": null,
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119 "tool_id": "Cut1",
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120 "tool_state": "{\"columnList\": \"\\\"c3\\\"\", \"input\": \"null\", \"delimiter\": \"\\\"T\\\"\", \"__rerun_remap_job_id__\": null, \"__page__\": 0}",
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121 "tool_version": "1.0.2",
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122 "type": "tool",
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123 "user_outputs": [],
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124 "uuid": "f3912f69-b561-4dd5-91f0-1e492e19bb9c"
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125 },
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126 "4": {
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127 "annotation": "Add a column with the URI of the SADI service input OWL class",
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128 "id": 4,
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129 "input_connections": {
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130 "input": {
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131 "id": 3,
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132 "output_name": "out_file1"
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133 }
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134 },
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135 "inputs": [],
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136 "label": null,
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137 "name": "Add column",
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138 "outputs": [
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139 {
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140 "name": "out_file1",
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141 "type": "input"
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142 }
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143 ],
47db0b303a50 Added annotations to workflow
Mikel Egana <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
144 "position": {
47db0b303a50 Added annotations to workflow
Mikel Egana <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
145 "left": 448.9826703071594,
47db0b303a50 Added annotations to workflow
Mikel Egana <mikel.egana.aranguren@gmail.com>
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diff changeset
146 "top": 480.9097466468811
47db0b303a50 Added annotations to workflow
Mikel Egana <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
147 },
47db0b303a50 Added annotations to workflow
Mikel Egana <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
148 "post_job_actions": {},
47db0b303a50 Added annotations to workflow
Mikel Egana <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
149 "tool_errors": null,
47db0b303a50 Added annotations to workflow
Mikel Egana <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
150 "tool_id": "addValue",
47db0b303a50 Added annotations to workflow
Mikel Egana <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
151 "tool_state": "{\"__page__\": 0, \"input\": \"null\", \"__rerun_remap_job_id__\": null, \"exp\": \"\\\"http://purl.oclc.org/SADI/LSRN/UniProt_Record\\\"\", \"iterate\": \"\\\"no\\\"\"}",
47db0b303a50 Added annotations to workflow
Mikel Egana <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
152 "tool_version": "1.0.0",
47db0b303a50 Added annotations to workflow
Mikel Egana <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
153 "type": "tool",
47db0b303a50 Added annotations to workflow
Mikel Egana <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
154 "user_outputs": [],
47db0b303a50 Added annotations to workflow
Mikel Egana <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
155 "uuid": "c01e5509-2a60-4ad4-848c-b31f9ccfc841"
47db0b303a50 Added annotations to workflow
Mikel Egana <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
156 },
47db0b303a50 Added annotations to workflow
Mikel Egana <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
157 "5": {
47db0b303a50 Added annotations to workflow
Mikel Egana <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
158 "annotation": "Add a column with the URI of the SADI service input OWL class",
47db0b303a50 Added annotations to workflow
Mikel Egana <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
159 "id": 5,
47db0b303a50 Added annotations to workflow
Mikel Egana <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
160 "input_connections": {
47db0b303a50 Added annotations to workflow
Mikel Egana <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
161 "input": {
47db0b303a50 Added annotations to workflow
Mikel Egana <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
162 "id": 3,
47db0b303a50 Added annotations to workflow
Mikel Egana <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
163 "output_name": "out_file1"
47db0b303a50 Added annotations to workflow
Mikel Egana <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
164 }
47db0b303a50 Added annotations to workflow
Mikel Egana <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
165 },
47db0b303a50 Added annotations to workflow
Mikel Egana <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
166 "inputs": [],
47db0b303a50 Added annotations to workflow
Mikel Egana <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
167 "label": null,
47db0b303a50 Added annotations to workflow
Mikel Egana <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
168 "name": "Add column",
47db0b303a50 Added annotations to workflow
Mikel Egana <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
169 "outputs": [
47db0b303a50 Added annotations to workflow
Mikel Egana <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
170 {
47db0b303a50 Added annotations to workflow
Mikel Egana <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
171 "name": "out_file1",
47db0b303a50 Added annotations to workflow
Mikel Egana <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
172 "type": "input"
47db0b303a50 Added annotations to workflow
Mikel Egana <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
173 }
47db0b303a50 Added annotations to workflow
Mikel Egana <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
174 ],
47db0b303a50 Added annotations to workflow
Mikel Egana <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
175 "position": {
47db0b303a50 Added annotations to workflow
Mikel Egana <mikel.egana.aranguren@gmail.com>
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diff changeset
176 "left": 449.9896283149719,
47db0b303a50 Added annotations to workflow
Mikel Egana <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
177 "top": 636.9166741371155
47db0b303a50 Added annotations to workflow
Mikel Egana <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
178 },
47db0b303a50 Added annotations to workflow
Mikel Egana <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
179 "post_job_actions": {},
47db0b303a50 Added annotations to workflow
Mikel Egana <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
180 "tool_errors": null,
47db0b303a50 Added annotations to workflow
Mikel Egana <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
181 "tool_id": "addValue",
47db0b303a50 Added annotations to workflow
Mikel Egana <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
182 "tool_state": "{\"__page__\": 0, \"input\": \"null\", \"__rerun_remap_job_id__\": null, \"exp\": \"\\\"http://openlifedata.org/uniprot_vocabulary:Resource\\\"\", \"iterate\": \"\\\"no\\\"\"}",
47db0b303a50 Added annotations to workflow
Mikel Egana <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
183 "tool_version": "1.0.0",
47db0b303a50 Added annotations to workflow
Mikel Egana <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
184 "type": "tool",
47db0b303a50 Added annotations to workflow
Mikel Egana <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
185 "user_outputs": [],
47db0b303a50 Added annotations to workflow
Mikel Egana <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
186 "uuid": "98b1f088-3de5-4dbd-a655-63a630517e1a"
47db0b303a50 Added annotations to workflow
Mikel Egana <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
187 },
47db0b303a50 Added annotations to workflow
Mikel Egana <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
188 "6": {
47db0b303a50 Added annotations to workflow
Mikel Egana <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
189 "annotation": "Convert to RDF, adding the triple rdf:type input OWL class",
47db0b303a50 Added annotations to workflow
Mikel Egana <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
190 "id": 6,
47db0b303a50 Added annotations to workflow
Mikel Egana <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
191 "input_connections": {
47db0b303a50 Added annotations to workflow
Mikel Egana <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
192 "input_file": {
47db0b303a50 Added annotations to workflow
Mikel Egana <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
193 "id": 4,
47db0b303a50 Added annotations to workflow
Mikel Egana <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
194 "output_name": "out_file1"
47db0b303a50 Added annotations to workflow
Mikel Egana <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
195 }
47db0b303a50 Added annotations to workflow
Mikel Egana <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
196 },
47db0b303a50 Added annotations to workflow
Mikel Egana <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
197 "inputs": [],
47db0b303a50 Added annotations to workflow
Mikel Egana <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
198 "label": null,
47db0b303a50 Added annotations to workflow
Mikel Egana <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
199 "name": "SADI - Tab-to-RDF",
47db0b303a50 Added annotations to workflow
Mikel Egana <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
200 "outputs": [
47db0b303a50 Added annotations to workflow
Mikel Egana <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
201 {
47db0b303a50 Added annotations to workflow
Mikel Egana <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
202 "name": "output_file",
47db0b303a50 Added annotations to workflow
Mikel Egana <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
203 "type": "rdf"
47db0b303a50 Added annotations to workflow
Mikel Egana <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
204 }
47db0b303a50 Added annotations to workflow
Mikel Egana <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
205 ],
47db0b303a50 Added annotations to workflow
Mikel Egana <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
206 "position": {
47db0b303a50 Added annotations to workflow
Mikel Egana <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
207 "left": 449.9896283149719,
47db0b303a50 Added annotations to workflow
Mikel Egana <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
208 "top": 340.9097466468811
47db0b303a50 Added annotations to workflow
Mikel Egana <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
209 },
47db0b303a50 Added annotations to workflow
Mikel Egana <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
210 "post_job_actions": {},
47db0b303a50 Added annotations to workflow
Mikel Egana <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
211 "tool_errors": null,
47db0b303a50 Added annotations to workflow
Mikel Egana <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
212 "tool_id": "SADI-Docker-tab2rdf",
47db0b303a50 Added annotations to workflow
Mikel Egana <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
213 "tool_state": "{\"__page__\": 0, \"triples\": \"[{\\\"__index__\\\": 0, \\\"o_col\\\": \\\"\\\", \\\"o_type\\\": \\\"False\\\", \\\"s_col\\\": \\\"\\\", \\\"p_val\\\": \\\"http://www.w3.org/1999/02/22-rdf-syntax-ns#type\\\"}]\", \"input_file\": \"null\", \"output_format\": \"\\\"ntriples\\\"\", \"namespace\": \"{\\\"choose_namespace\\\": \\\"none\\\", \\\"__current_case__\\\": 1}\", \"__rerun_remap_job_id__\": null}",
47db0b303a50 Added annotations to workflow
Mikel Egana <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
214 "tool_version": "0.1",
47db0b303a50 Added annotations to workflow
Mikel Egana <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
215 "type": "tool",
47db0b303a50 Added annotations to workflow
Mikel Egana <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
216 "user_outputs": [],
47db0b303a50 Added annotations to workflow
Mikel Egana <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
217 "uuid": "a05b8d4f-1b5f-4930-bd77-dfb5163b4556"
47db0b303a50 Added annotations to workflow
Mikel Egana <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
218 },
47db0b303a50 Added annotations to workflow
Mikel Egana <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
219 "7": {
47db0b303a50 Added annotations to workflow
Mikel Egana <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
220 "annotation": "Convert to RDF, adding the triple rdf:type input OWL class",
47db0b303a50 Added annotations to workflow
Mikel Egana <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
221 "id": 7,
47db0b303a50 Added annotations to workflow
Mikel Egana <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
222 "input_connections": {
47db0b303a50 Added annotations to workflow
Mikel Egana <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
223 "input_file": {
47db0b303a50 Added annotations to workflow
Mikel Egana <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
224 "id": 5,
47db0b303a50 Added annotations to workflow
Mikel Egana <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
225 "output_name": "out_file1"
47db0b303a50 Added annotations to workflow
Mikel Egana <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
226 }
47db0b303a50 Added annotations to workflow
Mikel Egana <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
227 },
47db0b303a50 Added annotations to workflow
Mikel Egana <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
228 "inputs": [],
47db0b303a50 Added annotations to workflow
Mikel Egana <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
229 "label": null,
47db0b303a50 Added annotations to workflow
Mikel Egana <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
230 "name": "SADI - Tab-to-RDF",
47db0b303a50 Added annotations to workflow
Mikel Egana <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
231 "outputs": [
47db0b303a50 Added annotations to workflow
Mikel Egana <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
232 {
47db0b303a50 Added annotations to workflow
Mikel Egana <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
233 "name": "output_file",
47db0b303a50 Added annotations to workflow
Mikel Egana <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
234 "type": "rdf"
47db0b303a50 Added annotations to workflow
Mikel Egana <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
235 }
47db0b303a50 Added annotations to workflow
Mikel Egana <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
236 ],
47db0b303a50 Added annotations to workflow
Mikel Egana <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
237 "position": {
47db0b303a50 Added annotations to workflow
Mikel Egana <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
238 "left": 447.9757122993469,
47db0b303a50 Added annotations to workflow
Mikel Egana <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
239 "top": 766.9166741371155
47db0b303a50 Added annotations to workflow
Mikel Egana <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
240 },
47db0b303a50 Added annotations to workflow
Mikel Egana <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
241 "post_job_actions": {},
47db0b303a50 Added annotations to workflow
Mikel Egana <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
242 "tool_errors": null,
47db0b303a50 Added annotations to workflow
Mikel Egana <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
243 "tool_id": "SADI-Docker-tab2rdf",
47db0b303a50 Added annotations to workflow
Mikel Egana <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
244 "tool_state": "{\"__page__\": 0, \"triples\": \"[{\\\"__index__\\\": 0, \\\"o_col\\\": \\\"\\\", \\\"o_type\\\": \\\"False\\\", \\\"s_col\\\": \\\"\\\", \\\"p_val\\\": \\\"http://www.w3.org/1999/02/22-rdf-syntax-ns#type\\\"}]\", \"input_file\": \"null\", \"output_format\": \"\\\"ntriples\\\"\", \"namespace\": \"{\\\"choose_namespace\\\": \\\"none\\\", \\\"__current_case__\\\": 1}\", \"__rerun_remap_job_id__\": null}",
47db0b303a50 Added annotations to workflow
Mikel Egana <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
245 "tool_version": "0.1",
47db0b303a50 Added annotations to workflow
Mikel Egana <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
246 "type": "tool",
47db0b303a50 Added annotations to workflow
Mikel Egana <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
247 "user_outputs": [],
47db0b303a50 Added annotations to workflow
Mikel Egana <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
248 "uuid": "217c654d-5353-4d93-a6de-c5c5bb205e64"
47db0b303a50 Added annotations to workflow
Mikel Egana <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
249 },
47db0b303a50 Added annotations to workflow
Mikel Egana <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
250 "8": {
47db0b303a50 Added annotations to workflow
Mikel Egana <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
251 "annotation": "Convert to RDF/XML syntax",
47db0b303a50 Added annotations to workflow
Mikel Egana <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
252 "id": 8,
47db0b303a50 Added annotations to workflow
Mikel Egana <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
253 "input_connections": {
47db0b303a50 Added annotations to workflow
Mikel Egana <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
254 "input_file": {
47db0b303a50 Added annotations to workflow
Mikel Egana <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
255 "id": 6,
47db0b303a50 Added annotations to workflow
Mikel Egana <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
256 "output_name": "output_file"
47db0b303a50 Added annotations to workflow
Mikel Egana <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
257 }
47db0b303a50 Added annotations to workflow
Mikel Egana <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
258 },
47db0b303a50 Added annotations to workflow
Mikel Egana <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
259 "inputs": [],
47db0b303a50 Added annotations to workflow
Mikel Egana <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
260 "label": null,
47db0b303a50 Added annotations to workflow
Mikel Egana <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
261 "name": "SADI - RDF Format (Rapper)",
47db0b303a50 Added annotations to workflow
Mikel Egana <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
262 "outputs": [
47db0b303a50 Added annotations to workflow
Mikel Egana <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
263 {
47db0b303a50 Added annotations to workflow
Mikel Egana <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
264 "name": "output_file",
47db0b303a50 Added annotations to workflow
Mikel Egana <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
265 "type": "rdf"
47db0b303a50 Added annotations to workflow
Mikel Egana <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
266 }
47db0b303a50 Added annotations to workflow
Mikel Egana <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
267 ],
47db0b303a50 Added annotations to workflow
Mikel Egana <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
268 "position": {
47db0b303a50 Added annotations to workflow
Mikel Egana <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
269 "left": 438.9826703071594,
47db0b303a50 Added annotations to workflow
Mikel Egana <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
270 "top": 200.90973138809204
47db0b303a50 Added annotations to workflow
Mikel Egana <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
271 },
47db0b303a50 Added annotations to workflow
Mikel Egana <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
272 "post_job_actions": {},
47db0b303a50 Added annotations to workflow
Mikel Egana <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
273 "tool_errors": null,
47db0b303a50 Added annotations to workflow
Mikel Egana <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
274 "tool_id": "SADI-Docker-rapper",
47db0b303a50 Added annotations to workflow
Mikel Egana <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
275 "tool_state": "{\"__page__\": 0, \"output_format\": \"\\\"rdfxml\\\"\", \"__rerun_remap_job_id__\": null, \"input_format\": \"\\\"ntriples\\\"\", \"input_file\": \"null\"}",
47db0b303a50 Added annotations to workflow
Mikel Egana <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
276 "tool_version": "0.1",
47db0b303a50 Added annotations to workflow
Mikel Egana <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
277 "type": "tool",
47db0b303a50 Added annotations to workflow
Mikel Egana <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
278 "user_outputs": [],
47db0b303a50 Added annotations to workflow
Mikel Egana <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
279 "uuid": "b5e1600e-a4ef-4ed6-a839-46bd1bcc59b3"
47db0b303a50 Added annotations to workflow
Mikel Egana <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
280 },
47db0b303a50 Added annotations to workflow
Mikel Egana <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
281 "9": {
47db0b303a50 Added annotations to workflow
Mikel Egana <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
282 "annotation": "Convert to RDF/XML syntax",
47db0b303a50 Added annotations to workflow
Mikel Egana <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
283 "id": 9,
47db0b303a50 Added annotations to workflow
Mikel Egana <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
284 "input_connections": {
47db0b303a50 Added annotations to workflow
Mikel Egana <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
285 "input_file": {
47db0b303a50 Added annotations to workflow
Mikel Egana <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
286 "id": 7,
47db0b303a50 Added annotations to workflow
Mikel Egana <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
287 "output_name": "output_file"
47db0b303a50 Added annotations to workflow
Mikel Egana <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
288 }
47db0b303a50 Added annotations to workflow
Mikel Egana <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
289 },
47db0b303a50 Added annotations to workflow
Mikel Egana <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
290 "inputs": [],
47db0b303a50 Added annotations to workflow
Mikel Egana <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
291 "label": null,
47db0b303a50 Added annotations to workflow
Mikel Egana <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
292 "name": "SADI - RDF Format (Rapper)",
47db0b303a50 Added annotations to workflow
Mikel Egana <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
293 "outputs": [
47db0b303a50 Added annotations to workflow
Mikel Egana <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
294 {
47db0b303a50 Added annotations to workflow
Mikel Egana <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
295 "name": "output_file",
47db0b303a50 Added annotations to workflow
Mikel Egana <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
296 "type": "rdf"
47db0b303a50 Added annotations to workflow
Mikel Egana <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
297 }
47db0b303a50 Added annotations to workflow
Mikel Egana <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
298 ],
47db0b303a50 Added annotations to workflow
Mikel Egana <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
299 "position": {
47db0b303a50 Added annotations to workflow
Mikel Egana <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
300 "left": 446.98611879348755,
47db0b303a50 Added annotations to workflow
Mikel Egana <mikel.egana.aranguren@gmail.com>
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diff changeset
301 "top": 913.9132561683655
47db0b303a50 Added annotations to workflow
Mikel Egana <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
302 },
47db0b303a50 Added annotations to workflow
Mikel Egana <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
303 "post_job_actions": {},
47db0b303a50 Added annotations to workflow
Mikel Egana <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
304 "tool_errors": null,
47db0b303a50 Added annotations to workflow
Mikel Egana <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
305 "tool_id": "SADI-Docker-rapper",
47db0b303a50 Added annotations to workflow
Mikel Egana <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
306 "tool_state": "{\"__page__\": 0, \"output_format\": \"\\\"rdfxml\\\"\", \"__rerun_remap_job_id__\": null, \"input_format\": \"\\\"ntriples\\\"\", \"input_file\": \"null\"}",
47db0b303a50 Added annotations to workflow
Mikel Egana <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
307 "tool_version": "0.1",
47db0b303a50 Added annotations to workflow
Mikel Egana <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
308 "type": "tool",
47db0b303a50 Added annotations to workflow
Mikel Egana <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
309 "user_outputs": [],
47db0b303a50 Added annotations to workflow
Mikel Egana <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
310 "uuid": "995db5b3-4e12-48c8-bda0-f961861f008c"
47db0b303a50 Added annotations to workflow
Mikel Egana <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
311 },
47db0b303a50 Added annotations to workflow
Mikel Egana <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
312 "10": {
47db0b303a50 Added annotations to workflow
Mikel Egana <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
313 "annotation": "Execute SADI service to obtain KEGG entries",
47db0b303a50 Added annotations to workflow
Mikel Egana <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
314 "id": 10,
47db0b303a50 Added annotations to workflow
Mikel Egana <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
315 "input_connections": {
47db0b303a50 Added annotations to workflow
Mikel Egana <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
316 "input": {
47db0b303a50 Added annotations to workflow
Mikel Egana <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
317 "id": 8,
47db0b303a50 Added annotations to workflow
Mikel Egana <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
318 "output_name": "output_file"
47db0b303a50 Added annotations to workflow
Mikel Egana <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
319 }
47db0b303a50 Added annotations to workflow
Mikel Egana <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
320 },
47db0b303a50 Added annotations to workflow
Mikel Egana <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
321 "inputs": [],
47db0b303a50 Added annotations to workflow
Mikel Egana <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
322 "label": null,
47db0b303a50 Added annotations to workflow
Mikel Egana <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
323 "name": "SADI client",
47db0b303a50 Added annotations to workflow
Mikel Egana <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
324 "outputs": [
47db0b303a50 Added annotations to workflow
Mikel Egana <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
325 {
47db0b303a50 Added annotations to workflow
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parents:
diff changeset
326 "name": "output",
47db0b303a50 Added annotations to workflow
Mikel Egana <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
327 "type": "rdf"
47db0b303a50 Added annotations to workflow
Mikel Egana <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
328 }
47db0b303a50 Added annotations to workflow
Mikel Egana <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
329 ],
47db0b303a50 Added annotations to workflow
Mikel Egana <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
330 "position": {
47db0b303a50 Added annotations to workflow
Mikel Egana <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
331 "left": 775.9965863227844,
47db0b303a50 Added annotations to workflow
Mikel Egana <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
332 "top": 202.90626764297485
47db0b303a50 Added annotations to workflow
Mikel Egana <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
333 },
47db0b303a50 Added annotations to workflow
Mikel Egana <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
334 "post_job_actions": {},
47db0b303a50 Added annotations to workflow
Mikel Egana <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
335 "tool_errors": null,
47db0b303a50 Added annotations to workflow
Mikel Egana <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
336 "tool_id": "SADI-Docker-sadi_client",
47db0b303a50 Added annotations to workflow
Mikel Egana <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
337 "tool_state": "{\"url\": \"\\\"http://sadiframework.org/services/getKEGGIDFromUniProt\\\"\", \"input\": \"null\", \"__rerun_remap_job_id__\": null, \"__page__\": 0}",
47db0b303a50 Added annotations to workflow
Mikel Egana <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
338 "tool_version": "0.1",
47db0b303a50 Added annotations to workflow
Mikel Egana <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
339 "type": "tool",
47db0b303a50 Added annotations to workflow
Mikel Egana <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
340 "user_outputs": [],
47db0b303a50 Added annotations to workflow
Mikel Egana <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
341 "uuid": "01c2bbe7-a5e1-4bad-8c93-b01c6d0a5c8f"
47db0b303a50 Added annotations to workflow
Mikel Egana <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
342 },
47db0b303a50 Added annotations to workflow
Mikel Egana <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
343 "11": {
47db0b303a50 Added annotations to workflow
Mikel Egana <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
344 "annotation": "Execute SADI service to obtain HGNC entries",
47db0b303a50 Added annotations to workflow
Mikel Egana <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
345 "id": 11,
47db0b303a50 Added annotations to workflow
Mikel Egana <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
346 "input_connections": {
47db0b303a50 Added annotations to workflow
Mikel Egana <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
347 "input": {
47db0b303a50 Added annotations to workflow
Mikel Egana <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
348 "id": 9,
47db0b303a50 Added annotations to workflow
Mikel Egana <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
349 "output_name": "output_file"
47db0b303a50 Added annotations to workflow
Mikel Egana <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
350 }
47db0b303a50 Added annotations to workflow
Mikel Egana <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
351 },
47db0b303a50 Added annotations to workflow
Mikel Egana <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
352 "inputs": [],
47db0b303a50 Added annotations to workflow
Mikel Egana <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
353 "label": null,
47db0b303a50 Added annotations to workflow
Mikel Egana <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
354 "name": "SADI client",
47db0b303a50 Added annotations to workflow
Mikel Egana <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
355 "outputs": [
47db0b303a50 Added annotations to workflow
Mikel Egana <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
356 {
47db0b303a50 Added annotations to workflow
Mikel Egana <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
357 "name": "output",
47db0b303a50 Added annotations to workflow
Mikel Egana <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
358 "type": "rdf"
47db0b303a50 Added annotations to workflow
Mikel Egana <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
359 }
47db0b303a50 Added annotations to workflow
Mikel Egana <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
360 ],
47db0b303a50 Added annotations to workflow
Mikel Egana <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
361 "position": {
47db0b303a50 Added annotations to workflow
Mikel Egana <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
362 "left": 788.9826703071594,
47db0b303a50 Added annotations to workflow
Mikel Egana <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
363 "top": 579.9201531410217
47db0b303a50 Added annotations to workflow
Mikel Egana <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
364 },
47db0b303a50 Added annotations to workflow
Mikel Egana <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
365 "post_job_actions": {},
47db0b303a50 Added annotations to workflow
Mikel Egana <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
366 "tool_errors": null,
47db0b303a50 Added annotations to workflow
Mikel Egana <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
367 "tool_id": "SADI-Docker-sadi_client",
47db0b303a50 Added annotations to workflow
Mikel Egana <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
368 "tool_state": "{\"url\": \"\\\"http://biordf.org/cgi-bin/SADI/OpenLifeData2SADI/SADI/hgnc/uniprot_vocabulary_Resource_hgnc_vocabulary_x-uniprot-inverse_hgnc_vocabulary_Resource\\\"\", \"input\": \"null\", \"__rerun_remap_job_id__\": null, \"__page__\": 0}",
47db0b303a50 Added annotations to workflow
Mikel Egana <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
369 "tool_version": "0.1",
47db0b303a50 Added annotations to workflow
Mikel Egana <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
370 "type": "tool",
47db0b303a50 Added annotations to workflow
Mikel Egana <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
371 "user_outputs": [],
47db0b303a50 Added annotations to workflow
Mikel Egana <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
372 "uuid": "ccdd413c-36be-48c3-96fc-4f233208a6b8"
47db0b303a50 Added annotations to workflow
Mikel Egana <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
373 },
47db0b303a50 Added annotations to workflow
Mikel Egana <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
374 "12": {
47db0b303a50 Added annotations to workflow
Mikel Egana <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
375 "annotation": "Execute SADI service to obtain OMIM entries",
47db0b303a50 Added annotations to workflow
Mikel Egana <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
376 "id": 12,
47db0b303a50 Added annotations to workflow
Mikel Egana <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
377 "input_connections": {
47db0b303a50 Added annotations to workflow
Mikel Egana <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
378 "input": {
47db0b303a50 Added annotations to workflow
Mikel Egana <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
379 "id": 11,
47db0b303a50 Added annotations to workflow
Mikel Egana <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
380 "output_name": "output"
47db0b303a50 Added annotations to workflow
Mikel Egana <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
381 }
47db0b303a50 Added annotations to workflow
Mikel Egana <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
382 },
47db0b303a50 Added annotations to workflow
Mikel Egana <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
383 "inputs": [],
47db0b303a50 Added annotations to workflow
Mikel Egana <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
384 "label": null,
47db0b303a50 Added annotations to workflow
Mikel Egana <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
385 "name": "SADI client",
47db0b303a50 Added annotations to workflow
Mikel Egana <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
386 "outputs": [
47db0b303a50 Added annotations to workflow
Mikel Egana <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
387 {
47db0b303a50 Added annotations to workflow
Mikel Egana <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
388 "name": "output",
47db0b303a50 Added annotations to workflow
Mikel Egana <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
389 "type": "rdf"
47db0b303a50 Added annotations to workflow
Mikel Egana <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
390 }
47db0b303a50 Added annotations to workflow
Mikel Egana <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
391 ],
47db0b303a50 Added annotations to workflow
Mikel Egana <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
392 "position": {
47db0b303a50 Added annotations to workflow
Mikel Egana <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
393 "left": 793.9826703071594,
47db0b303a50 Added annotations to workflow
Mikel Egana <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
394 "top": 753.9132561683655
47db0b303a50 Added annotations to workflow
Mikel Egana <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
395 },
47db0b303a50 Added annotations to workflow
Mikel Egana <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
396 "post_job_actions": {},
47db0b303a50 Added annotations to workflow
Mikel Egana <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
397 "tool_errors": null,
47db0b303a50 Added annotations to workflow
Mikel Egana <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
398 "tool_id": "SADI-Docker-sadi_client",
47db0b303a50 Added annotations to workflow
Mikel Egana <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
399 "tool_state": "{\"url\": \"\\\"http://biordf.org/cgi-bin/SADI/OpenLifeData2SADI/SADI/hgnc/hgnc_vocabulary_Resource_hgnc_vocabulary_x-omim_omim_vocabulary_Gene\\\"\", \"input\": \"null\", \"__rerun_remap_job_id__\": null, \"__page__\": 0}",
47db0b303a50 Added annotations to workflow
Mikel Egana <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
400 "tool_version": "0.1",
47db0b303a50 Added annotations to workflow
Mikel Egana <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
401 "type": "tool",
47db0b303a50 Added annotations to workflow
Mikel Egana <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
402 "user_outputs": [],
47db0b303a50 Added annotations to workflow
Mikel Egana <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
403 "uuid": "b7af50a8-a92a-44d9-bf1e-ca90cb69905d"
47db0b303a50 Added annotations to workflow
Mikel Egana <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
404 },
47db0b303a50 Added annotations to workflow
Mikel Egana <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
405 "13": {
47db0b303a50 Added annotations to workflow
Mikel Egana <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
406 "annotation": "Execute SADI service to obtain PubMed entries",
47db0b303a50 Added annotations to workflow
Mikel Egana <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
407 "id": 13,
47db0b303a50 Added annotations to workflow
Mikel Egana <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
408 "input_connections": {
47db0b303a50 Added annotations to workflow
Mikel Egana <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
409 "input": {
47db0b303a50 Added annotations to workflow
Mikel Egana <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
410 "id": 12,
47db0b303a50 Added annotations to workflow
Mikel Egana <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
411 "output_name": "output"
47db0b303a50 Added annotations to workflow
Mikel Egana <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
412 }
47db0b303a50 Added annotations to workflow
Mikel Egana <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
413 },
47db0b303a50 Added annotations to workflow
Mikel Egana <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
414 "inputs": [],
47db0b303a50 Added annotations to workflow
Mikel Egana <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
415 "label": null,
47db0b303a50 Added annotations to workflow
Mikel Egana <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
416 "name": "SADI client",
47db0b303a50 Added annotations to workflow
Mikel Egana <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
417 "outputs": [
47db0b303a50 Added annotations to workflow
Mikel Egana <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
418 {
47db0b303a50 Added annotations to workflow
Mikel Egana <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
419 "name": "output",
47db0b303a50 Added annotations to workflow
Mikel Egana <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
420 "type": "rdf"
47db0b303a50 Added annotations to workflow
Mikel Egana <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
421 }
47db0b303a50 Added annotations to workflow
Mikel Egana <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
422 ],
47db0b303a50 Added annotations to workflow
Mikel Egana <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
423 "position": {
47db0b303a50 Added annotations to workflow
Mikel Egana <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
424 "left": 799.9896283149719,
47db0b303a50 Added annotations to workflow
Mikel Egana <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
425 "top": 914.9201531410217
47db0b303a50 Added annotations to workflow
Mikel Egana <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
426 },
47db0b303a50 Added annotations to workflow
Mikel Egana <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
427 "post_job_actions": {},
47db0b303a50 Added annotations to workflow
Mikel Egana <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
428 "tool_errors": null,
47db0b303a50 Added annotations to workflow
Mikel Egana <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
429 "tool_id": "SADI-Docker-sadi_client",
47db0b303a50 Added annotations to workflow
Mikel Egana <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
430 "tool_state": "{\"url\": \"\\\"http://biordf.org/cgi-bin/SADI/OpenLifeData2SADI/SADI/omim/omim_vocabulary_Gene_omim_vocabulary_article_pubmed_vocabulary_PubMedRecord\\\"\", \"input\": \"null\", \"__rerun_remap_job_id__\": null, \"__page__\": 0}",
47db0b303a50 Added annotations to workflow
Mikel Egana <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
431 "tool_version": "0.1",
47db0b303a50 Added annotations to workflow
Mikel Egana <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
432 "type": "tool",
47db0b303a50 Added annotations to workflow
Mikel Egana <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
433 "user_outputs": [],
47db0b303a50 Added annotations to workflow
Mikel Egana <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
434 "uuid": "3dcb6fc4-4021-4ea6-8e88-31c71d68699d"
47db0b303a50 Added annotations to workflow
Mikel Egana <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
435 },
47db0b303a50 Added annotations to workflow
Mikel Egana <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
436 "14": {
47db0b303a50 Added annotations to workflow
Mikel Egana <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
437 "annotation": "Merge all the inputs and outputs in single RDF graph: SADI only decorates inputs with new triples, so we can keep track of the whole process via URIs",
47db0b303a50 Added annotations to workflow
Mikel Egana <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
438 "id": 14,
47db0b303a50 Added annotations to workflow
Mikel Egana <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
439 "input_connections": {
47db0b303a50 Added annotations to workflow
Mikel Egana <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
440 "input_files_0|input_file": {
47db0b303a50 Added annotations to workflow
Mikel Egana <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
441 "id": 13,
47db0b303a50 Added annotations to workflow
Mikel Egana <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
442 "output_name": "output"
47db0b303a50 Added annotations to workflow
Mikel Egana <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
443 },
47db0b303a50 Added annotations to workflow
Mikel Egana <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
444 "input_files_1|input_file": {
47db0b303a50 Added annotations to workflow
Mikel Egana <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
445 "id": 12,
47db0b303a50 Added annotations to workflow
Mikel Egana <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
446 "output_name": "output"
47db0b303a50 Added annotations to workflow
Mikel Egana <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
447 },
47db0b303a50 Added annotations to workflow
Mikel Egana <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
448 "input_files_2|input_file": {
47db0b303a50 Added annotations to workflow
Mikel Egana <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
449 "id": 11,
47db0b303a50 Added annotations to workflow
Mikel Egana <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
450 "output_name": "output"
47db0b303a50 Added annotations to workflow
Mikel Egana <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
451 },
47db0b303a50 Added annotations to workflow
Mikel Egana <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
452 "input_files_3|input_file": {
47db0b303a50 Added annotations to workflow
Mikel Egana <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
453 "id": 10,
47db0b303a50 Added annotations to workflow
Mikel Egana <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
454 "output_name": "output"
47db0b303a50 Added annotations to workflow
Mikel Egana <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
455 },
47db0b303a50 Added annotations to workflow
Mikel Egana <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
456 "input_files_4|input_file": {
47db0b303a50 Added annotations to workflow
Mikel Egana <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
457 "id": 9,
47db0b303a50 Added annotations to workflow
Mikel Egana <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
458 "output_name": "output_file"
47db0b303a50 Added annotations to workflow
Mikel Egana <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
459 },
47db0b303a50 Added annotations to workflow
Mikel Egana <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
460 "input_files_5|input_file": {
47db0b303a50 Added annotations to workflow
Mikel Egana <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
461 "id": 8,
47db0b303a50 Added annotations to workflow
Mikel Egana <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
462 "output_name": "output_file"
47db0b303a50 Added annotations to workflow
Mikel Egana <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
463 }
47db0b303a50 Added annotations to workflow
Mikel Egana <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
464 },
47db0b303a50 Added annotations to workflow
Mikel Egana <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
465 "inputs": [],
47db0b303a50 Added annotations to workflow
Mikel Egana <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
466 "label": null,
47db0b303a50 Added annotations to workflow
Mikel Egana <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
467 "name": "SADI - Merge RDF Graphs",
47db0b303a50 Added annotations to workflow
Mikel Egana <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
468 "outputs": [
47db0b303a50 Added annotations to workflow
Mikel Egana <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
469 {
47db0b303a50 Added annotations to workflow
Mikel Egana <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
470 "name": "output_file",
47db0b303a50 Added annotations to workflow
Mikel Egana <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
471 "type": "rdf"
47db0b303a50 Added annotations to workflow
Mikel Egana <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
472 }
47db0b303a50 Added annotations to workflow
Mikel Egana <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
473 ],
47db0b303a50 Added annotations to workflow
Mikel Egana <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
474 "position": {
47db0b303a50 Added annotations to workflow
Mikel Egana <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
475 "left": 1125.9965252876282,
47db0b303a50 Added annotations to workflow
Mikel Egana <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
476 "top": 318.91319513320923
47db0b303a50 Added annotations to workflow
Mikel Egana <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
477 },
47db0b303a50 Added annotations to workflow
Mikel Egana <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
478 "post_job_actions": {},
47db0b303a50 Added annotations to workflow
Mikel Egana <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
479 "tool_errors": null,
47db0b303a50 Added annotations to workflow
Mikel Egana <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
480 "tool_id": "SADI-Docker-mergeRDFgraphs",
47db0b303a50 Added annotations to workflow
Mikel Egana <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
481 "tool_state": "{\"__page__\": 0, \"__rerun_remap_job_id__\": null, \"input_files\": \"[{\\\"__index__\\\": 0, \\\"input_file\\\": null}, {\\\"__index__\\\": 1, \\\"input_file\\\": null}, {\\\"__index__\\\": 2, \\\"input_file\\\": null}, {\\\"__index__\\\": 3, \\\"input_file\\\": null}, {\\\"__index__\\\": 4, \\\"input_file\\\": null}, {\\\"__index__\\\": 5, \\\"input_file\\\": null}]\"}",
47db0b303a50 Added annotations to workflow
Mikel Egana <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
482 "tool_version": "0.1",
47db0b303a50 Added annotations to workflow
Mikel Egana <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
483 "type": "tool",
47db0b303a50 Added annotations to workflow
Mikel Egana <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
484 "user_outputs": [],
47db0b303a50 Added annotations to workflow
Mikel Egana <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
485 "uuid": "7c24dd55-3032-4329-9fa3-734c963d8ed2"
47db0b303a50 Added annotations to workflow
Mikel Egana <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
486 },
47db0b303a50 Added annotations to workflow
Mikel Egana <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
487 "15": {
47db0b303a50 Added annotations to workflow
Mikel Egana <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
488 "annotation": "Query the merged RDF graph with the actual question",
47db0b303a50 Added annotations to workflow
Mikel Egana <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
489 "id": 15,
47db0b303a50 Added annotations to workflow
Mikel Egana <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
490 "input_connections": {
47db0b303a50 Added annotations to workflow
Mikel Egana <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
491 "ontology": {
47db0b303a50 Added annotations to workflow
Mikel Egana <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
492 "id": 14,
47db0b303a50 Added annotations to workflow
Mikel Egana <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
493 "output_name": "output_file"
47db0b303a50 Added annotations to workflow
Mikel Egana <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
494 }
47db0b303a50 Added annotations to workflow
Mikel Egana <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
495 },
47db0b303a50 Added annotations to workflow
Mikel Egana <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
496 "inputs": [],
47db0b303a50 Added annotations to workflow
Mikel Egana <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
497 "label": null,
47db0b303a50 Added annotations to workflow
Mikel Egana <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
498 "name": "SADI - Execute an SPARQL query against an RDF file",
47db0b303a50 Added annotations to workflow
Mikel Egana <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
499 "outputs": [
47db0b303a50 Added annotations to workflow
Mikel Egana <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
500 {
47db0b303a50 Added annotations to workflow
Mikel Egana <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
501 "name": "output",
47db0b303a50 Added annotations to workflow
Mikel Egana <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
502 "type": "html"
47db0b303a50 Added annotations to workflow
Mikel Egana <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
503 }
47db0b303a50 Added annotations to workflow
Mikel Egana <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
504 ],
47db0b303a50 Added annotations to workflow
Mikel Egana <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
505 "position": {
47db0b303a50 Added annotations to workflow
Mikel Egana <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
506 "left": 1439.993106842041,
47db0b303a50 Added annotations to workflow
Mikel Egana <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
507 "top": 461.92015266418457
47db0b303a50 Added annotations to workflow
Mikel Egana <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
508 },
47db0b303a50 Added annotations to workflow
Mikel Egana <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
509 "post_job_actions": {},
47db0b303a50 Added annotations to workflow
Mikel Egana <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
510 "tool_errors": null,
47db0b303a50 Added annotations to workflow
Mikel Egana <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
511 "tool_id": "SADI-Docker-SPARQLGalaxy",
47db0b303a50 Added annotations to workflow
Mikel Egana <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
512 "tool_state": "{\"out_format\": \"\\\"html\\\"\", \"__page__\": 0, \"pasted_query\": \"\\\"PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> \\\\nPREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>\\\\nPREFIX sadi: <http://sadiframework.org/ontologies/predicates.owl#>\\\\nPREFIX lsrn: <http://purl.oclc.org/SADI/LSRN/>\\\\n\\\\nSELECT ?protein ?label ?KEGG\\\\nWHERE { \\\\n?protein rdf:type lsrn:UniProt_Record . \\\\n?protein sadi:isEncodedBy ?KEGG . \\\\n?protein ?prot2hgnc ?hgnc . \\\\n?hgnc ?hgnc2omim ?omim . \\\\n?omim ?omim2pubmed ?pubmed . \\\\n?pubmed rdfs:label ?label . \\\\nFILTER (regex (?label, 'brain'))\\\\n}\\\"\", \"ontology\": \"null\", \"__rerun_remap_job_id__\": null}",
47db0b303a50 Added annotations to workflow
Mikel Egana <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
513 "tool_version": "0.1",
47db0b303a50 Added annotations to workflow
Mikel Egana <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
514 "type": "tool",
47db0b303a50 Added annotations to workflow
Mikel Egana <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
515 "user_outputs": [],
47db0b303a50 Added annotations to workflow
Mikel Egana <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
516 "uuid": "9a453f8c-370e-4ab7-8e45-73cbba721db9"
47db0b303a50 Added annotations to workflow
Mikel Egana <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
517 }
47db0b303a50 Added annotations to workflow
Mikel Egana <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
518 },
47db0b303a50 Added annotations to workflow
Mikel Egana <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
519 "uuid": "8796e5be-1c91-4f91-9946-02a09a79401d"
47db0b303a50 Added annotations to workflow
Mikel Egana <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
520 }