annotate toolfactory/tfworkflowsample.ga @ 36:ce2b1f8ea68d draft

passes flake8 tests finally :)
author fubar
date Mon, 10 Aug 2020 23:24:41 -0400
parents
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
36
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
1 {
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
2 "a_galaxy_workflow": "true",
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
3 "annotation": "",
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
4 "format-version": "0.1",
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
5 "name": "workflow to generate a bunch of sample toolfactory tools",
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
6 "steps": {
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
7 "0": {
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
8 "annotation": "",
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
9 "content_id": null,
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
10 "errors": null,
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
11 "id": 0,
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
12 "input_connections": {},
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
13 "inputs": [
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
14 {
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
15 "description": "",
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
16 "name": "rgToolFactory2.py"
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
17 }
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
18 ],
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
19 "label": "rgToolFactory2.py",
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
20 "name": "Input dataset",
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
21 "outputs": [],
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
22 "position": {
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
23 "bottom": 235.25,
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
24 "height": 81,
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
25 "left": 711.84375,
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
26 "right": 911.84375,
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
27 "top": 154.25,
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
28 "width": 200,
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
29 "x": 711.84375,
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
30 "y": 154.25
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
31 },
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
32 "tool_id": null,
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
33 "tool_state": "{\"optional\": false}",
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
34 "tool_version": null,
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
35 "type": "data_input",
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
36 "uuid": "b717b6ee-51d0-415d-876d-f19b42f67666",
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
37 "workflow_outputs": [
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
38 {
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
39 "label": null,
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
40 "output_name": "output",
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
41 "uuid": "09acd6fd-4e2b-44a8-8757-35eca8d0de89"
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
42 }
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
43 ]
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
44 },
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
45 "1": {
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
46 "annotation": "",
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
47 "content_id": null,
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
48 "errors": null,
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
49 "id": 1,
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
50 "input_connections": {},
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
51 "inputs": [
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
52 {
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
53 "description": "",
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
54 "name": "README.md"
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
55 }
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
56 ],
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
57 "label": "README.md",
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
58 "name": "Input dataset",
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
59 "outputs": [],
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
60 "position": {
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
61 "bottom": 760.25,
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
62 "height": 61,
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
63 "left": 711.84375,
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
64 "right": 911.84375,
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
65 "top": 699.25,
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
66 "width": 200,
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
67 "x": 711.84375,
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
68 "y": 699.25
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
69 },
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
70 "tool_id": null,
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
71 "tool_state": "{\"optional\": false}",
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
72 "tool_version": null,
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
73 "type": "data_input",
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
74 "uuid": "8aefae07-4fd1-44a6-bea2-5d377567ac27",
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
75 "workflow_outputs": [
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
76 {
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
77 "label": null,
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
78 "output_name": "output",
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
79 "uuid": "5f8453d0-abd1-41d9-a4a7-1f8b82f1f095"
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
80 }
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
81 ]
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
82 },
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
83 "2": {
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
84 "annotation": "",
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
85 "content_id": null,
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
86 "errors": null,
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
87 "id": 2,
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
88 "input_connections": {},
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
89 "inputs": [
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
90 {
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
91 "description": "",
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
92 "name": "testtext"
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
93 }
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
94 ],
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
95 "label": "testtext",
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
96 "name": "Input dataset",
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
97 "outputs": [],
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
98 "position": {
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
99 "bottom": 235.25,
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
100 "height": 61,
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
101 "left": 989.84375,
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
102 "right": 1189.84375,
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
103 "top": 174.25,
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
104 "width": 200,
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
105 "x": 989.84375,
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
106 "y": 174.25
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
107 },
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
108 "tool_id": null,
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
109 "tool_state": "{\"optional\": false}",
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
110 "tool_version": null,
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
111 "type": "data_input",
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
112 "uuid": "02a35533-a67b-44c0-bce8-96a8adddc5a9",
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
113 "workflow_outputs": [
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
114 {
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
115 "label": null,
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
116 "output_name": "output",
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
117 "uuid": "abe4a1b1-2c0b-44d1-95f8-4f9bb38e9daa"
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
118 }
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
119 ]
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
120 },
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
121 "3": {
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
122 "annotation": "",
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
123 "content_id": "rgTF2",
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
124 "errors": null,
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
125 "id": 3,
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
126 "input_connections": {
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
127 "ppass|history_inputs_0|input_files": {
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
128 "id": 1,
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
129 "output_name": "output"
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
130 }
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
131 },
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
132 "inputs": [],
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
133 "label": null,
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
134 "name": "toolfactory",
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
135 "outputs": [
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
136 {
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
137 "name": "ToolFactory_Outputs",
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
138 "type": "input"
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
139 },
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
140 {
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
141 "name": "new_tool",
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
142 "type": "tgz"
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
143 }
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
144 ],
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
145 "position": {
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
146 "bottom": 636.25,
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
147 "height": 222,
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
148 "left": 989.84375,
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
149 "right": 1189.84375,
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
150 "top": 414.25,
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
151 "width": 200,
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
152 "x": 989.84375,
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
153 "y": 414.25
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
154 },
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
155 "post_job_actions": {},
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
156 "tool_id": "rgTF2",
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
157 "tool_state": "{\"__input_ext\": \"txt\", \"chromInfo\": \"/home/ross/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"interexe\": {\"interpreter\": \"bash\", \"__current_case__\": 5, \"interpreter_version\": \"\", \"exe_package_version\": \"\", \"dynScript\": \"rev | tac\"}, \"makeMode\": {\"make_Tool\": \"yes\", \"__current_case__\": 0, \"tool_version\": \"0.01\", \"tool_desc\": \"tacrev\", \"help_text\": \"**What it Does**\", \"citations\": []}, \"ppass\": {\"parampass\": \"0\", \"__current_case__\": 2, \"history_inputs\": [{\"__index__\": 0, \"input_files\": {\"__class__\": \"ConnectedValue\"}, \"input_formats\": [\"txt\"], \"input_label\": \"input file\", \"input_help\": \"parameter_help\", \"input_CL\": \"1\"}], \"history_outputs\": [{\"__index__\": 0, \"history_name\": \"outfile\", \"history_format\": \"txt\", \"history_CL\": \"2\"}]}, \"tool_name\": \"tacrev\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
158 "tool_version": "2.00",
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
159 "type": "tool",
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
160 "uuid": "8fab16a0-5303-4e5c-8bf6-d6ebc70aa9af",
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
161 "workflow_outputs": [
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
162 {
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
163 "label": null,
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
164 "output_name": "ToolFactory_Outputs",
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
165 "uuid": "68d1a0b8-d897-48e9-a304-25d289e139e9"
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
166 },
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
167 {
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
168 "label": null,
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
169 "output_name": "new_tool",
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
170 "uuid": "8669863e-a1a5-4ed6-a412-c7f341f66176"
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
171 }
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
172 ]
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
173 },
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
174 "4": {
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
175 "annotation": "",
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
176 "content_id": "rgTF2",
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
177 "errors": null,
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
178 "id": 4,
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
179 "input_connections": {
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
180 "ppass|history_inputs_0|input_files": {
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
181 "id": 1,
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
182 "output_name": "output"
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
183 }
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
184 },
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
185 "inputs": [],
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
186 "label": null,
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
187 "name": "toolfactory",
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
188 "outputs": [
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
189 {
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
190 "name": "ToolFactory_Outputs",
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
191 "type": "input"
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
192 },
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
193 {
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
194 "name": "new_tool",
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
195 "type": "tgz"
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
196 }
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
197 ],
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
198 "position": {
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
199 "bottom": 916.25,
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
200 "height": 242,
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
201 "left": 989.84375,
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
202 "right": 1189.84375,
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
203 "top": 674.25,
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
204 "width": 200,
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
205 "x": 989.84375,
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
206 "y": 674.25
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
207 },
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
208 "post_job_actions": {},
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
209 "tool_id": "rgTF2",
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
210 "tool_state": "{\"__input_ext\": \"txt\", \"chromInfo\": \"/home/ross/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"interexe\": {\"interpreter\": \"python\", \"__current_case__\": 2, \"interpreter_version\": \"\", \"exe_package_version\": \"\", \"dynScript\": \"# reverse order of text by row\\nimport sys\\ninp = sys.argv[1]\\noutp = sys.argv[2]\\ni = open(inp,'r').readlines()\\no = open(outp,'w')\\nfor row in i:\\n rs = row.rstrip()\\n rs = list(rs)\\n rs.reverse()\\n o.write(''.join(rs))\\n o.write('\\\\n')\\no.close()\"}, \"makeMode\": {\"make_Tool\": \"yes\", \"__current_case__\": 0, \"tool_version\": \"0.01\", \"tool_desc\": \"pyrevpos\", \"help_text\": \"**What it Does**\", \"citations\": []}, \"ppass\": {\"parampass\": \"positional\", \"__current_case__\": 1, \"history_inputs\": [{\"__index__\": 0, \"input_files\": {\"__class__\": \"ConnectedValue\"}, \"input_formats\": [\"txt\"], \"input_label\": \"inputfile\", \"input_help\": \"parameter_help\", \"input_CL\": \"1\"}], \"history_outputs\": [{\"__index__\": 0, \"history_name\": \"output\", \"history_format\": \"txt\", \"history_CL\": \"2\"}], \"edit_params\": \"yes\", \"additional_parameters\": []}, \"tool_name\": \"pyrevpos\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
211 "tool_version": "2.00",
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
212 "type": "tool",
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
213 "uuid": "ea0f8bbe-6b0d-4aff-bf06-6192faf8fe22",
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
214 "workflow_outputs": [
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
215 {
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
216 "label": null,
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
217 "output_name": "ToolFactory_Outputs",
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
218 "uuid": "70755c1b-6f92-43a3-aacb-8cc508a89b74"
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
219 },
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
220 {
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
221 "label": null,
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
222 "output_name": "new_tool",
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
223 "uuid": "ea9482d9-7836-442d-b753-ce4a201fd8c9"
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
224 }
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
225 ]
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
226 },
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
227 "5": {
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
228 "annotation": "",
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
229 "content_id": "rgTF2",
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
230 "errors": null,
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
231 "id": 5,
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
232 "input_connections": {
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
233 "ppass|history_inputs_0|input_files": {
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
234 "id": 1,
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
235 "output_name": "output"
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
236 }
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
237 },
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
238 "inputs": [],
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
239 "label": null,
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
240 "name": "toolfactory",
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
241 "outputs": [
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
242 {
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
243 "name": "ToolFactory_Outputs",
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
244 "type": "input"
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
245 },
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
246 {
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
247 "name": "new_tool",
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
248 "type": "tgz"
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
249 }
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
250 ],
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
251 "position": {
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
252 "bottom": 1216.25,
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
253 "height": 262,
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
254 "left": 989.84375,
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
255 "right": 1189.84375,
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
256 "top": 954.25,
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
257 "width": 200,
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
258 "x": 989.84375,
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
259 "y": 954.25
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
260 },
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
261 "post_job_actions": {},
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
262 "tool_id": "rgTF2",
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
263 "tool_state": "{\"__input_ext\": \"txt\", \"chromInfo\": \"/home/ross/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"interexe\": {\"interpreter\": \"python\", \"__current_case__\": 2, \"interpreter_version\": \"\", \"exe_package_version\": \"\", \"dynScript\": \"# reverse order of text by row\\nimport sys\\nimport argparse\\nparser = argparse.ArgumentParser()\\na = parser.add_argument\\na('--infile',default='')\\na('--outfile',default=None)\\nargs = parser.parse_args()\\ninp = args.infile\\noutp = args.outfile\\ni = open(inp,'r').readlines()\\no = open(outp,'w')\\nfor row in i:\\n rs = row.rstrip()\\n rs = list(rs)\\n rs.reverse()\\n o.write(''.join(rs))\\n o.write('\\\\n')\\no.close()\"}, \"makeMode\": {\"make_Tool\": \"yes\", \"__current_case__\": 0, \"tool_version\": \"0.01\", \"tool_desc\": \"reverse argparse\", \"help_text\": \"**What it Does**\", \"citations\": []}, \"ppass\": {\"parampass\": \"argparse\", \"__current_case__\": 0, \"history_inputs\": [{\"__index__\": 0, \"input_files\": {\"__class__\": \"ConnectedValue\"}, \"input_formats\": [\"txt\"], \"input_label\": \"infile\", \"input_help\": \"parameter_help\", \"input_CL\": \"infile\"}], \"history_outputs\": [{\"__index__\": 0, \"history_name\": \"outfile\", \"history_format\": \"txt\", \"history_CL\": \"outfile\"}], \"edit_params\": \"yes\", \"additional_parameters\": []}, \"tool_name\": \"pyrevargparse\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
264 "tool_version": "2.00",
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
265 "type": "tool",
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
266 "uuid": "065b274a-ae73-43b0-b015-8b60d90db78f",
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
267 "workflow_outputs": [
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
268 {
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
269 "label": null,
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
270 "output_name": "ToolFactory_Outputs",
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
271 "uuid": "bec62d2d-b462-49bb-9646-28fea9136778"
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
272 },
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
273 {
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
274 "label": null,
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
275 "output_name": "new_tool",
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
276 "uuid": "2e1ed464-bcff-4354-8bf3-ed01167b280f"
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
277 }
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
278 ]
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
279 },
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
280 "6": {
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
281 "annotation": "",
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
282 "content_id": "rgTF2",
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
283 "errors": null,
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
284 "id": 6,
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
285 "input_connections": {
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
286 "ppass|history_inputs_0|input_files": {
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
287 "id": 1,
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
288 "output_name": "output"
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
289 }
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
290 },
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
291 "inputs": [],
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
292 "label": null,
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
293 "name": "toolfactory",
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
294 "outputs": [
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
295 {
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
296 "name": "ToolFactory_Outputs",
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
297 "type": "input"
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
298 },
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
299 {
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
300 "name": "new_tool",
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
301 "type": "tgz"
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
302 }
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
303 ],
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
304 "position": {
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
305 "bottom": 1496.25,
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
306 "height": 242,
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
307 "left": 989.84375,
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
308 "right": 1189.84375,
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
309 "top": 1254.25,
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
310 "width": 200,
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
311 "x": 989.84375,
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
312 "y": 1254.25
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
313 },
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
314 "post_job_actions": {},
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
315 "tool_id": "rgTF2",
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
316 "tool_state": "{\"__input_ext\": \"txt\", \"chromInfo\": \"/home/ross/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"interexe\": {\"interpreter\": \"python\", \"__current_case__\": 2, \"interpreter_version\": \"\", \"exe_package_version\": \"\", \"dynScript\": \"# reverse order of text by row\\nimport sys\\ninp = sys.argv[1]\\noutp = sys.argv[2]\\nappendme = sys.argv[3]\\ni = open(inp,'r').readlines()\\no = open(outp,'w')\\nfor row in i:\\n rs = row.rstrip()\\n rs = list(rs)\\n rs.reverse()\\n o.write(''.join(rs))\\n o.write(appendme)\\n o.write('\\\\n')\\no.close()\"}, \"makeMode\": {\"make_Tool\": \"yes\", \"__current_case__\": 0, \"tool_version\": \"0.01\", \"tool_desc\": \"pyrevpos\", \"help_text\": \"**What it Does**\", \"citations\": []}, \"ppass\": {\"parampass\": \"positional\", \"__current_case__\": 1, \"history_inputs\": [{\"__index__\": 0, \"input_files\": {\"__class__\": \"ConnectedValue\"}, \"input_formats\": [\"txt\"], \"input_label\": \"inputfile\", \"input_help\": \"parameter_help\", \"input_CL\": \"1\"}], \"history_outputs\": [{\"__index__\": 0, \"history_name\": \"output\", \"history_format\": \"txt\", \"history_CL\": \"2\"}], \"edit_params\": \"yes\", \"additional_parameters\": [{\"__index__\": 0, \"param_name\": \"appendme\", \"param_type\": \"text\", \"param_value\": \"added at the end\", \"param_label\": \"append string\", \"param_help\": \"parameter_help\", \"param_CL\": \"3\"}]}, \"tool_name\": \"pyrevaddpos\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
317 "tool_version": "2.00",
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
318 "type": "tool",
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
319 "uuid": "5954323f-4ca1-4957-8250-746703dfa7c5",
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
320 "workflow_outputs": [
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
321 {
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
322 "label": null,
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
323 "output_name": "ToolFactory_Outputs",
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
324 "uuid": "6466bf24-51b2-4fae-aac8-fc1d78faac89"
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
325 },
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
326 {
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
327 "label": null,
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
328 "output_name": "new_tool",
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
329 "uuid": "f37589e2-3582-4443-bce8-5759485a7220"
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
330 }
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
331 ]
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
332 },
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
333 "7": {
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
334 "annotation": "",
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
335 "content_id": "rgTF2",
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
336 "errors": null,
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
337 "id": 7,
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
338 "input_connections": {
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
339 "ppass|history_inputs_0|input_files": {
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
340 "id": 2,
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
341 "output_name": "output"
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
342 }
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
343 },
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
344 "inputs": [],
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
345 "label": null,
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
346 "name": "toolfactory",
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
347 "outputs": [
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
348 {
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
349 "name": "ToolFactory_Outputs",
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
350 "type": "input"
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
351 },
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
352 {
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
353 "name": "new_tool",
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
354 "type": "tgz"
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
355 }
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
356 ],
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
357 "position": {
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
358 "bottom": 376.25,
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
359 "height": 222,
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
360 "left": 1267.84375,
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
361 "right": 1467.84375,
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
362 "top": 154.25,
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
363 "width": 200,
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
364 "x": 1267.84375,
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
365 "y": 154.25
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
366 },
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
367 "post_job_actions": {},
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
368 "tool_id": "rgTF2",
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
369 "tool_state": "{\"__input_ext\": \"txt\", \"chromInfo\": \"/home/ross/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"interexe\": {\"interpreter\": \"system\", \"__current_case__\": 1, \"exe_package\": \"sed\", \"exe_package_version\": \"\"}, \"makeMode\": {\"make_Tool\": \"yes\", \"__current_case__\": 0, \"tool_version\": \"0.01\", \"tool_desc\": \"sed runner\", \"help_text\": \"sed '/old/new/g input.txt\", \"citations\": []}, \"ppass\": {\"parampass\": \"positional\", \"__current_case__\": 1, \"history_inputs\": [{\"__index__\": 0, \"input_files\": {\"__class__\": \"ConnectedValue\"}, \"input_formats\": [\"txt\"], \"input_label\": \"input text\", \"input_help\": \"parameter_help\", \"input_CL\": \"3\"}], \"history_outputs\": [{\"__index__\": 0, \"history_name\": \"output\", \"history_format\": \"txt\", \"history_CL\": \"STDOUT\"}], \"edit_params\": \"yes\", \"additional_parameters\": [{\"__index__\": 0, \"param_name\": \"sedstring\", \"param_type\": \"text\", \"param_value\": \"s/Old/New/g\", \"param_label\": \"parameter_label\", \"param_help\": \"parameter_help\", \"param_CL\": \"1\"}]}, \"tool_name\": \"sedtest\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
370 "tool_version": "2.00",
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
371 "type": "tool",
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
372 "uuid": "e26df7b6-3899-42fb-8efc-5f13d53668f8",
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
373 "workflow_outputs": [
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
374 {
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
375 "label": null,
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
376 "output_name": "ToolFactory_Outputs",
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
377 "uuid": "0a819390-acd4-4be6-aac9-ec3322302b0f"
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
378 },
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
379 {
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
380 "label": null,
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
381 "output_name": "new_tool",
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
382 "uuid": "f7555059-144d-4f64-a303-b70d189e6e35"
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
383 }
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
384 ]
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
385 },
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
386 "8": {
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
387 "annotation": "",
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
388 "content_id": "rgTF2",
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
389 "errors": null,
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
390 "id": 8,
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
391 "input_connections": {
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
392 "ppass|history_inputs_0|input_files": {
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
393 "id": 5,
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
394 "output_name": "new_tool"
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
395 }
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
396 },
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
397 "inputs": [],
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
398 "label": null,
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
399 "name": "toolfactory",
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
400 "outputs": [
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
401 {
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
402 "name": "ToolFactory_Outputs",
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
403 "type": "input"
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
404 },
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
405 {
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
406 "name": "new_tool",
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
407 "type": "tgz"
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
408 }
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
409 ],
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
410 "position": {
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
411 "bottom": 1271.25,
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
412 "height": 242,
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
413 "left": 1267.84375,
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
414 "right": 1467.84375,
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
415 "top": 1029.25,
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
416 "width": 200,
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
417 "x": 1267.84375,
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
418 "y": 1029.25
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
419 },
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
420 "post_job_actions": {},
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
421 "tool_id": "rgTF2",
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
422 "tool_state": "{\"__input_ext\": \"tgz\", \"chromInfo\": \"/home/ross/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"interexe\": {\"interpreter\": \"python\", \"__current_case__\": 2, \"interpreter_version\": \"\", \"exe_package_version\": \"\", \"dynScript\": \"import argparse\\nimport tarfile\\nimport os\\nimport tempfile\\nimport subprocess\\n\\n\\\"\\\"\\\"\\nplanemo test --no_cleanup --no_dependency_resolution --skip_venv --galaxy_root ~/galaxy ~/galaxy/tools/tool_makers/pyrevargparse/ &> pyrevargparse\\n\\\"\\\"\\\"\\n\\nparser = argparse.ArgumentParser()\\na = parser.add_argument\\na('--tooltgz',default='')\\na('--report',default=None)\\na('--toolout',default=None)\\na('--galaxy_root',default=None)\\nargs = parser.parse_args()\\ntoolname = args.toolout.split(os.sep)[-1]\\ntoolpath = os.path.join(args.galaxy_root,args.toolout)\\ntf = tarfile.open(args.tooltgz,\\\"r:gz\\\")\\ntf.extractall(toolpath)\\ncl = \\\"planemo test --skip_venv --galaxy_root %s %s\\\" % (args.galaxy_root,toolpath)\\ncll = cl.split(' ')\\nsto = open(args.report, 'w')\\np = subprocess.run(cll, shell=False, stdout=sto)\\nretval = p.returncode\\nsto.close()\\n\"}, \"makeMode\": {\"make_Tool\": \"yes\", \"__current_case__\": 0, \"tool_version\": \"0.01\", \"tool_desc\": \"Tool to test toolshed tool archives generated by the tool factory.\", \"help_text\": \"**What it Does**\\n\\nGiven a toolshed tgz file generated by a tool factory run, this will unpack it and run planemo test, returning the planemo stdout as a report\\nIt was generated using the tool factory.\", \"citations\": []}, \"ppass\": {\"parampass\": \"argparse\", \"__current_case__\": 0, \"history_inputs\": [{\"__index__\": 0, \"input_files\": {\"__class__\": \"ConnectedValue\"}, \"input_formats\": [\"tgz\"], \"input_label\": \"tool toolshed tgz archive from history\", \"input_help\": \"Run planemo test on a tool shed tool archive tgz format file generated by the ToolFactory or Planemo\", \"input_CL\": \"tooltgz\"}], \"history_outputs\": [{\"__index__\": 0, \"history_name\": \"report\", \"history_format\": \"txt\", \"history_CL\": \"report\"}], \"edit_params\": \"yes\", \"additional_parameters\": [{\"__index__\": 0, \"param_name\": \"toolout\", \"param_type\": \"text\", \"param_value\": \"tools/toolmakers/planemotest\", \"param_label\": \"output path under galaxy root\", \"param_help\": \"This is where the tgz file will be extracted and tested by planemo\", \"param_CL\": \"toolout\"}, {\"__index__\": 1, \"param_name\": \"galaxy_root\", \"param_type\": \"text\", \"param_value\": \"/home/ross/galaxy\", \"param_label\": \"your galaxy root to use for running planemo\", \"param_help\": \"This will form the galaxy_root parameter for running planemo using an existing Galaxy source tree, and the tgz will be extracted at a path relative to that root\", \"param_CL\": \"galaxy_root\"}]}, \"tool_name\": \"planemotest\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
423 "tool_version": "2.00",
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
424 "type": "tool",
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
425 "uuid": "c72a7aae-3801-431b-a331-be6938d34fbd",
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
426 "workflow_outputs": [
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
427 {
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
428 "label": null,
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
429 "output_name": "ToolFactory_Outputs",
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
430 "uuid": "75aa9815-5bd6-44a7-8210-889d3b7e5027"
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
431 },
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
432 {
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
433 "label": null,
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
434 "output_name": "new_tool",
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
435 "uuid": "744499de-5d7e-4415-b427-315057c81ebc"
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
436 }
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
437 ]
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
438 }
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
439 },
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
440 "tags": [],
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
441 "uuid": "490d9c7f-eea3-4616-a8b7-13510da0430b",
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
442 "version": 1
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
443 }