annotate Galaxy-Workflow-creation_workflow_gandalf_2.0.ga @ 0:780ad1e582e1 draft

Uploaded
author urgi-team
date Thu, 12 Nov 2015 07:38:20 -0500
parents
children 025efd59ddd0
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
780ad1e582e1 Uploaded
urgi-team
parents:
diff changeset
1 {
780ad1e582e1 Uploaded
urgi-team
parents:
diff changeset
2 "a_galaxy_workflow": "true",
780ad1e582e1 Uploaded
urgi-team
parents:
diff changeset
3 "annotation": "",
780ad1e582e1 Uploaded
urgi-team
parents:
diff changeset
4 "format-version": "0.1",
780ad1e582e1 Uploaded
urgi-team
parents:
diff changeset
5 "name": "creation workflow gandalf 2.0",
780ad1e582e1 Uploaded
urgi-team
parents:
diff changeset
6 "steps": {
780ad1e582e1 Uploaded
urgi-team
parents:
diff changeset
7 "0": {
780ad1e582e1 Uploaded
urgi-team
parents:
diff changeset
8 "annotation": "",
780ad1e582e1 Uploaded
urgi-team
parents:
diff changeset
9 "id": 0,
780ad1e582e1 Uploaded
urgi-team
parents:
diff changeset
10 "input_connections": {},
780ad1e582e1 Uploaded
urgi-team
parents:
diff changeset
11 "inputs": [
780ad1e582e1 Uploaded
urgi-team
parents:
diff changeset
12 {
780ad1e582e1 Uploaded
urgi-team
parents:
diff changeset
13 "description": "",
780ad1e582e1 Uploaded
urgi-team
parents:
diff changeset
14 "name": "Input Dataset"
780ad1e582e1 Uploaded
urgi-team
parents:
diff changeset
15 }
780ad1e582e1 Uploaded
urgi-team
parents:
diff changeset
16 ],
780ad1e582e1 Uploaded
urgi-team
parents:
diff changeset
17 "name": "Input dataset",
780ad1e582e1 Uploaded
urgi-team
parents:
diff changeset
18 "outputs": [],
780ad1e582e1 Uploaded
urgi-team
parents:
diff changeset
19 "position": {
780ad1e582e1 Uploaded
urgi-team
parents:
diff changeset
20 "left": 288,
780ad1e582e1 Uploaded
urgi-team
parents:
diff changeset
21 "top": 200
780ad1e582e1 Uploaded
urgi-team
parents:
diff changeset
22 },
780ad1e582e1 Uploaded
urgi-team
parents:
diff changeset
23 "tool_errors": null,
780ad1e582e1 Uploaded
urgi-team
parents:
diff changeset
24 "tool_id": null,
780ad1e582e1 Uploaded
urgi-team
parents:
diff changeset
25 "tool_state": "{\"name\": \"Input Dataset\"}",
780ad1e582e1 Uploaded
urgi-team
parents:
diff changeset
26 "tool_version": null,
780ad1e582e1 Uploaded
urgi-team
parents:
diff changeset
27 "type": "data_input",
780ad1e582e1 Uploaded
urgi-team
parents:
diff changeset
28 "user_outputs": []
780ad1e582e1 Uploaded
urgi-team
parents:
diff changeset
29 },
780ad1e582e1 Uploaded
urgi-team
parents:
diff changeset
30 "1": {
780ad1e582e1 Uploaded
urgi-team
parents:
diff changeset
31 "annotation": "",
780ad1e582e1 Uploaded
urgi-team
parents:
diff changeset
32 "id": 1,
780ad1e582e1 Uploaded
urgi-team
parents:
diff changeset
33 "input_connections": {},
780ad1e582e1 Uploaded
urgi-team
parents:
diff changeset
34 "inputs": [
780ad1e582e1 Uploaded
urgi-team
parents:
diff changeset
35 {
780ad1e582e1 Uploaded
urgi-team
parents:
diff changeset
36 "description": "",
780ad1e582e1 Uploaded
urgi-team
parents:
diff changeset
37 "name": "Input Dataset"
780ad1e582e1 Uploaded
urgi-team
parents:
diff changeset
38 }
780ad1e582e1 Uploaded
urgi-team
parents:
diff changeset
39 ],
780ad1e582e1 Uploaded
urgi-team
parents:
diff changeset
40 "name": "Input dataset",
780ad1e582e1 Uploaded
urgi-team
parents:
diff changeset
41 "outputs": [],
780ad1e582e1 Uploaded
urgi-team
parents:
diff changeset
42 "position": {
780ad1e582e1 Uploaded
urgi-team
parents:
diff changeset
43 "left": 288,
780ad1e582e1 Uploaded
urgi-team
parents:
diff changeset
44 "top": 285
780ad1e582e1 Uploaded
urgi-team
parents:
diff changeset
45 },
780ad1e582e1 Uploaded
urgi-team
parents:
diff changeset
46 "tool_errors": null,
780ad1e582e1 Uploaded
urgi-team
parents:
diff changeset
47 "tool_id": null,
780ad1e582e1 Uploaded
urgi-team
parents:
diff changeset
48 "tool_state": "{\"name\": \"Input Dataset\"}",
780ad1e582e1 Uploaded
urgi-team
parents:
diff changeset
49 "tool_version": null,
780ad1e582e1 Uploaded
urgi-team
parents:
diff changeset
50 "type": "data_input",
780ad1e582e1 Uploaded
urgi-team
parents:
diff changeset
51 "user_outputs": []
780ad1e582e1 Uploaded
urgi-team
parents:
diff changeset
52 },
780ad1e582e1 Uploaded
urgi-team
parents:
diff changeset
53 "2": {
780ad1e582e1 Uploaded
urgi-team
parents:
diff changeset
54 "annotation": "",
780ad1e582e1 Uploaded
urgi-team
parents:
diff changeset
55 "id": 2,
780ad1e582e1 Uploaded
urgi-team
parents:
diff changeset
56 "input_connections": {},
780ad1e582e1 Uploaded
urgi-team
parents:
diff changeset
57 "inputs": [
780ad1e582e1 Uploaded
urgi-team
parents:
diff changeset
58 {
780ad1e582e1 Uploaded
urgi-team
parents:
diff changeset
59 "description": "",
780ad1e582e1 Uploaded
urgi-team
parents:
diff changeset
60 "name": "Input Dataset"
780ad1e582e1 Uploaded
urgi-team
parents:
diff changeset
61 }
780ad1e582e1 Uploaded
urgi-team
parents:
diff changeset
62 ],
780ad1e582e1 Uploaded
urgi-team
parents:
diff changeset
63 "name": "Input dataset",
780ad1e582e1 Uploaded
urgi-team
parents:
diff changeset
64 "outputs": [],
780ad1e582e1 Uploaded
urgi-team
parents:
diff changeset
65 "position": {
780ad1e582e1 Uploaded
urgi-team
parents:
diff changeset
66 "left": 288,
780ad1e582e1 Uploaded
urgi-team
parents:
diff changeset
67 "top": 370
780ad1e582e1 Uploaded
urgi-team
parents:
diff changeset
68 },
780ad1e582e1 Uploaded
urgi-team
parents:
diff changeset
69 "tool_errors": null,
780ad1e582e1 Uploaded
urgi-team
parents:
diff changeset
70 "tool_id": null,
780ad1e582e1 Uploaded
urgi-team
parents:
diff changeset
71 "tool_state": "{\"name\": \"Input Dataset\"}",
780ad1e582e1 Uploaded
urgi-team
parents:
diff changeset
72 "tool_version": null,
780ad1e582e1 Uploaded
urgi-team
parents:
diff changeset
73 "type": "data_input",
780ad1e582e1 Uploaded
urgi-team
parents:
diff changeset
74 "user_outputs": []
780ad1e582e1 Uploaded
urgi-team
parents:
diff changeset
75 },
780ad1e582e1 Uploaded
urgi-team
parents:
diff changeset
76 "3": {
780ad1e582e1 Uploaded
urgi-team
parents:
diff changeset
77 "annotation": "",
780ad1e582e1 Uploaded
urgi-team
parents:
diff changeset
78 "id": 3,
780ad1e582e1 Uploaded
urgi-team
parents:
diff changeset
79 "input_connections": {
780ad1e582e1 Uploaded
urgi-team
parents:
diff changeset
80 "input_file": {
780ad1e582e1 Uploaded
urgi-team
parents:
diff changeset
81 "id": 0,
780ad1e582e1 Uploaded
urgi-team
parents:
diff changeset
82 "output_name": "output"
780ad1e582e1 Uploaded
urgi-team
parents:
diff changeset
83 }
780ad1e582e1 Uploaded
urgi-team
parents:
diff changeset
84 },
780ad1e582e1 Uploaded
urgi-team
parents:
diff changeset
85 "inputs": [],
780ad1e582e1 Uploaded
urgi-team
parents:
diff changeset
86 "name": "mdust",
780ad1e582e1 Uploaded
urgi-team
parents:
diff changeset
87 "outputs": [
780ad1e582e1 Uploaded
urgi-team
parents:
diff changeset
88 {
780ad1e582e1 Uploaded
urgi-team
parents:
diff changeset
89 "name": "output_masked_fasta",
780ad1e582e1 Uploaded
urgi-team
parents:
diff changeset
90 "type": "fasta"
780ad1e582e1 Uploaded
urgi-team
parents:
diff changeset
91 },
780ad1e582e1 Uploaded
urgi-team
parents:
diff changeset
92 {
780ad1e582e1 Uploaded
urgi-team
parents:
diff changeset
93 "name": "output_tab",
780ad1e582e1 Uploaded
urgi-team
parents:
diff changeset
94 "type": "tabular"
780ad1e582e1 Uploaded
urgi-team
parents:
diff changeset
95 },
780ad1e582e1 Uploaded
urgi-team
parents:
diff changeset
96 {
780ad1e582e1 Uploaded
urgi-team
parents:
diff changeset
97 "name": "output_bed",
780ad1e582e1 Uploaded
urgi-team
parents:
diff changeset
98 "type": "bed"
780ad1e582e1 Uploaded
urgi-team
parents:
diff changeset
99 }
780ad1e582e1 Uploaded
urgi-team
parents:
diff changeset
100 ],
780ad1e582e1 Uploaded
urgi-team
parents:
diff changeset
101 "position": {
780ad1e582e1 Uploaded
urgi-team
parents:
diff changeset
102 "left": 571,
780ad1e582e1 Uploaded
urgi-team
parents:
diff changeset
103 "top": 394
780ad1e582e1 Uploaded
urgi-team
parents:
diff changeset
104 },
780ad1e582e1 Uploaded
urgi-team
parents:
diff changeset
105 "post_job_actions": {
780ad1e582e1 Uploaded
urgi-team
parents:
diff changeset
106 "RenameDatasetActionoutput_bed": {
780ad1e582e1 Uploaded
urgi-team
parents:
diff changeset
107 "action_arguments": {
780ad1e582e1 Uploaded
urgi-team
parents:
diff changeset
108 "newname": "#{input_file | basename}.bed"
780ad1e582e1 Uploaded
urgi-team
parents:
diff changeset
109 },
780ad1e582e1 Uploaded
urgi-team
parents:
diff changeset
110 "action_type": "RenameDatasetAction",
780ad1e582e1 Uploaded
urgi-team
parents:
diff changeset
111 "output_name": "output_bed"
780ad1e582e1 Uploaded
urgi-team
parents:
diff changeset
112 }
780ad1e582e1 Uploaded
urgi-team
parents:
diff changeset
113 },
780ad1e582e1 Uploaded
urgi-team
parents:
diff changeset
114 "tool_errors": null,
780ad1e582e1 Uploaded
urgi-team
parents:
diff changeset
115 "tool_id": "toolshed.g2.bx.psu.edu/repos/urgi-team/mdust/mdust/1.0",
780ad1e582e1 Uploaded
urgi-team
parents:
diff changeset
116 "tool_state": "{\"cutoff\": \"\\\"28\\\"\", \"input_file\": \"null\", \"__page__\": 0, \"__rerun_remap_job_id__\": null, \"wsize\": \"\\\"3\\\"\", \"output_type\": \"{\\\"output_type_selector\\\": \\\"bed\\\", \\\"__current_case__\\\": 1}\", \"masking_letter\": \"{\\\"masking_letter_selector\\\": \\\"N\\\", \\\"__current_case__\\\": 2}\", \"chromInfo\": \"\\\"/home/galaxy-dev/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\"}",
780ad1e582e1 Uploaded
urgi-team
parents:
diff changeset
117 "tool_version": "1.0",
780ad1e582e1 Uploaded
urgi-team
parents:
diff changeset
118 "type": "tool",
780ad1e582e1 Uploaded
urgi-team
parents:
diff changeset
119 "user_outputs": []
780ad1e582e1 Uploaded
urgi-team
parents:
diff changeset
120 },
780ad1e582e1 Uploaded
urgi-team
parents:
diff changeset
121 "4": {
780ad1e582e1 Uploaded
urgi-team
parents:
diff changeset
122 "annotation": "",
780ad1e582e1 Uploaded
urgi-team
parents:
diff changeset
123 "id": 4,
780ad1e582e1 Uploaded
urgi-team
parents:
diff changeset
124 "input_connections": {
780ad1e582e1 Uploaded
urgi-team
parents:
diff changeset
125 "fastq_input|fastq_input1": {
780ad1e582e1 Uploaded
urgi-team
parents:
diff changeset
126 "id": 1,
780ad1e582e1 Uploaded
urgi-team
parents:
diff changeset
127 "output_name": "output"
780ad1e582e1 Uploaded
urgi-team
parents:
diff changeset
128 },
780ad1e582e1 Uploaded
urgi-team
parents:
diff changeset
129 "fastq_input|fastq_input2": {
780ad1e582e1 Uploaded
urgi-team
parents:
diff changeset
130 "id": 2,
780ad1e582e1 Uploaded
urgi-team
parents:
diff changeset
131 "output_name": "output"
780ad1e582e1 Uploaded
urgi-team
parents:
diff changeset
132 },
780ad1e582e1 Uploaded
urgi-team
parents:
diff changeset
133 "reference_source|ref_file": {
780ad1e582e1 Uploaded
urgi-team
parents:
diff changeset
134 "id": 0,
780ad1e582e1 Uploaded
urgi-team
parents:
diff changeset
135 "output_name": "output"
780ad1e582e1 Uploaded
urgi-team
parents:
diff changeset
136 }
780ad1e582e1 Uploaded
urgi-team
parents:
diff changeset
137 },
780ad1e582e1 Uploaded
urgi-team
parents:
diff changeset
138 "inputs": [],
780ad1e582e1 Uploaded
urgi-team
parents:
diff changeset
139 "name": "Map with BWA-MEM",
780ad1e582e1 Uploaded
urgi-team
parents:
diff changeset
140 "outputs": [
780ad1e582e1 Uploaded
urgi-team
parents:
diff changeset
141 {
780ad1e582e1 Uploaded
urgi-team
parents:
diff changeset
142 "name": "bam_output",
780ad1e582e1 Uploaded
urgi-team
parents:
diff changeset
143 "type": "bam"
780ad1e582e1 Uploaded
urgi-team
parents:
diff changeset
144 }
780ad1e582e1 Uploaded
urgi-team
parents:
diff changeset
145 ],
780ad1e582e1 Uploaded
urgi-team
parents:
diff changeset
146 "position": {
780ad1e582e1 Uploaded
urgi-team
parents:
diff changeset
147 "left": 516,
780ad1e582e1 Uploaded
urgi-team
parents:
diff changeset
148 "top": 200
780ad1e582e1 Uploaded
urgi-team
parents:
diff changeset
149 },
780ad1e582e1 Uploaded
urgi-team
parents:
diff changeset
150 "post_job_actions": {
780ad1e582e1 Uploaded
urgi-team
parents:
diff changeset
151 "RenameDatasetActionbam_output": {
780ad1e582e1 Uploaded
urgi-team
parents:
diff changeset
152 "action_arguments": {
780ad1e582e1 Uploaded
urgi-team
parents:
diff changeset
153 "newname": "#{fastq_input1 | basename}.bam"
780ad1e582e1 Uploaded
urgi-team
parents:
diff changeset
154 },
780ad1e582e1 Uploaded
urgi-team
parents:
diff changeset
155 "action_type": "RenameDatasetAction",
780ad1e582e1 Uploaded
urgi-team
parents:
diff changeset
156 "output_name": "bam_output"
780ad1e582e1 Uploaded
urgi-team
parents:
diff changeset
157 }
780ad1e582e1 Uploaded
urgi-team
parents:
diff changeset
158 },
780ad1e582e1 Uploaded
urgi-team
parents:
diff changeset
159 "tool_errors": null,
780ad1e582e1 Uploaded
urgi-team
parents:
diff changeset
160 "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa_mem/0.4.1",
780ad1e582e1 Uploaded
urgi-team
parents:
diff changeset
161 "tool_state": "{\"__page__\": 0, \"__rerun_remap_job_id__\": null, \"rg\": \"{\\\"rg_selector\\\": \\\"set_picard\\\", \\\"read_group_sm_conditional\\\": {\\\"do_auto_name\\\": \\\"False\\\", \\\"SM\\\": \\\"SMstrand1\\\", \\\"__current_case__\\\": 1}, \\\"CN\\\": \\\"CNexemple\\\", \\\"PU\\\": \\\"\\\", \\\"read_group_lb_conditional\\\": {\\\"do_auto_name\\\": \\\"False\\\", \\\"LB\\\": \\\"LB1\\\", \\\"__current_case__\\\": 1}, \\\"read_group_id_conditional\\\": {\\\"do_auto_name\\\": \\\"False\\\", \\\"ID\\\": \\\"IDstrain1\\\", \\\"__current_case__\\\": 1}, \\\"__current_case__\\\": 0, \\\"DT\\\": \\\"\\\", \\\"PI\\\": \\\"\\\", \\\"DS\\\": \\\"\\\", \\\"PL\\\": \\\"ILLUMINA\\\"}\", \"fastq_input\": \"{\\\"iset_stats\\\": \\\"\\\", \\\"fastq_input2\\\": null, \\\"fastq_input_selector\\\": \\\"paired\\\", \\\"__current_case__\\\": 0, \\\"fastq_input1\\\": null}\", \"analysis_type\": \"{\\\"analysis_type_selector\\\": \\\"full\\\", \\\"algorithmic_options\\\": {\\\"algorithmic_options_selector\\\": \\\"do_not_set\\\", \\\"__current_case__\\\": 1}, \\\"io_options\\\": {\\\"a\\\": \\\"False\\\", \\\"C\\\": \\\"False\\\", \\\"__current_case__\\\": 0, \\\"h\\\": \\\"5\\\", \\\"M\\\": \\\"True\\\", \\\"T\\\": \\\"30\\\", \\\"io_options_selector\\\": \\\"set\\\", \\\"V\\\": \\\"False\\\", \\\"Y\\\": \\\"False\\\"}, \\\"__current_case__\\\": 2, \\\"scoring_options\\\": {\\\"scoring_options_selector\\\": \\\"do_not_set\\\", \\\"__current_case__\\\": 1}}\", \"reference_source\": \"{\\\"ref_file\\\": null, \\\"reference_source_selector\\\": \\\"history\\\", \\\"__current_case__\\\": 1}\", \"chromInfo\": \"\\\"/home/galaxy-dev/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\"}",
780ad1e582e1 Uploaded
urgi-team
parents:
diff changeset
162 "tool_version": "0.4.1",
780ad1e582e1 Uploaded
urgi-team
parents:
diff changeset
163 "type": "tool",
780ad1e582e1 Uploaded
urgi-team
parents:
diff changeset
164 "user_outputs": []
780ad1e582e1 Uploaded
urgi-team
parents:
diff changeset
165 },
780ad1e582e1 Uploaded
urgi-team
parents:
diff changeset
166 "5": {
780ad1e582e1 Uploaded
urgi-team
parents:
diff changeset
167 "annotation": "",
780ad1e582e1 Uploaded
urgi-team
parents:
diff changeset
168 "id": 5,
780ad1e582e1 Uploaded
urgi-team
parents:
diff changeset
169 "input_connections": {
780ad1e582e1 Uploaded
urgi-team
parents:
diff changeset
170 "input1": {
780ad1e582e1 Uploaded
urgi-team
parents:
diff changeset
171 "id": 4,
780ad1e582e1 Uploaded
urgi-team
parents:
diff changeset
172 "output_name": "bam_output"
780ad1e582e1 Uploaded
urgi-team
parents:
diff changeset
173 }
780ad1e582e1 Uploaded
urgi-team
parents:
diff changeset
174 },
780ad1e582e1 Uploaded
urgi-team
parents:
diff changeset
175 "inputs": [],
780ad1e582e1 Uploaded
urgi-team
parents:
diff changeset
176 "name": "mapQfilter",
780ad1e582e1 Uploaded
urgi-team
parents:
diff changeset
177 "outputs": [
780ad1e582e1 Uploaded
urgi-team
parents:
diff changeset
178 {
780ad1e582e1 Uploaded
urgi-team
parents:
diff changeset
179 "name": "output1",
780ad1e582e1 Uploaded
urgi-team
parents:
diff changeset
180 "type": "bam"
780ad1e582e1 Uploaded
urgi-team
parents:
diff changeset
181 }
780ad1e582e1 Uploaded
urgi-team
parents:
diff changeset
182 ],
780ad1e582e1 Uploaded
urgi-team
parents:
diff changeset
183 "position": {
780ad1e582e1 Uploaded
urgi-team
parents:
diff changeset
184 "left": 844,
780ad1e582e1 Uploaded
urgi-team
parents:
diff changeset
185 "top": 200
780ad1e582e1 Uploaded
urgi-team
parents:
diff changeset
186 },
780ad1e582e1 Uploaded
urgi-team
parents:
diff changeset
187 "post_job_actions": {
780ad1e582e1 Uploaded
urgi-team
parents:
diff changeset
188 "RenameDatasetActionoutput1": {
780ad1e582e1 Uploaded
urgi-team
parents:
diff changeset
189 "action_arguments": {
780ad1e582e1 Uploaded
urgi-team
parents:
diff changeset
190 "newname": "#{input1 | basename}.filteredbam"
780ad1e582e1 Uploaded
urgi-team
parents:
diff changeset
191 },
780ad1e582e1 Uploaded
urgi-team
parents:
diff changeset
192 "action_type": "RenameDatasetAction",
780ad1e582e1 Uploaded
urgi-team
parents:
diff changeset
193 "output_name": "output1"
780ad1e582e1 Uploaded
urgi-team
parents:
diff changeset
194 }
780ad1e582e1 Uploaded
urgi-team
parents:
diff changeset
195 },
780ad1e582e1 Uploaded
urgi-team
parents:
diff changeset
196 "tool_errors": null,
780ad1e582e1 Uploaded
urgi-team
parents:
diff changeset
197 "tool_id": "toolshed.g2.bx.psu.edu/repos/urgi-team/mapqfilter/mapQfilter/1.0",
780ad1e582e1 Uploaded
urgi-team
parents:
diff changeset
198 "tool_state": "{\"__page__\": 0, \"__rerun_remap_job_id__\": null, \"mapQ\": \"\\\"30\\\"\", \"chromInfo\": \"\\\"/home/galaxy-dev/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\", \"input1\": \"null\"}",
780ad1e582e1 Uploaded
urgi-team
parents:
diff changeset
199 "tool_version": "1.0",
780ad1e582e1 Uploaded
urgi-team
parents:
diff changeset
200 "type": "tool",
780ad1e582e1 Uploaded
urgi-team
parents:
diff changeset
201 "user_outputs": []
780ad1e582e1 Uploaded
urgi-team
parents:
diff changeset
202 },
780ad1e582e1 Uploaded
urgi-team
parents:
diff changeset
203 "6": {
780ad1e582e1 Uploaded
urgi-team
parents:
diff changeset
204 "annotation": "",
780ad1e582e1 Uploaded
urgi-team
parents:
diff changeset
205 "id": 6,
780ad1e582e1 Uploaded
urgi-team
parents:
diff changeset
206 "input_connections": {
780ad1e582e1 Uploaded
urgi-team
parents:
diff changeset
207 "inputFile": {
780ad1e582e1 Uploaded
urgi-team
parents:
diff changeset
208 "id": 5,
780ad1e582e1 Uploaded
urgi-team
parents:
diff changeset
209 "output_name": "output1"
780ad1e582e1 Uploaded
urgi-team
parents:
diff changeset
210 }
780ad1e582e1 Uploaded
urgi-team
parents:
diff changeset
211 },
780ad1e582e1 Uploaded
urgi-team
parents:
diff changeset
212 "inputs": [],
780ad1e582e1 Uploaded
urgi-team
parents:
diff changeset
213 "name": "MarkDuplicates",
780ad1e582e1 Uploaded
urgi-team
parents:
diff changeset
214 "outputs": [
780ad1e582e1 Uploaded
urgi-team
parents:
diff changeset
215 {
780ad1e582e1 Uploaded
urgi-team
parents:
diff changeset
216 "name": "metrics_file",
780ad1e582e1 Uploaded
urgi-team
parents:
diff changeset
217 "type": "txt"
780ad1e582e1 Uploaded
urgi-team
parents:
diff changeset
218 },
780ad1e582e1 Uploaded
urgi-team
parents:
diff changeset
219 {
780ad1e582e1 Uploaded
urgi-team
parents:
diff changeset
220 "name": "outFile",
780ad1e582e1 Uploaded
urgi-team
parents:
diff changeset
221 "type": "bam"
780ad1e582e1 Uploaded
urgi-team
parents:
diff changeset
222 }
780ad1e582e1 Uploaded
urgi-team
parents:
diff changeset
223 ],
780ad1e582e1 Uploaded
urgi-team
parents:
diff changeset
224 "position": {
780ad1e582e1 Uploaded
urgi-team
parents:
diff changeset
225 "left": 1072,
780ad1e582e1 Uploaded
urgi-team
parents:
diff changeset
226 "top": 200
780ad1e582e1 Uploaded
urgi-team
parents:
diff changeset
227 },
780ad1e582e1 Uploaded
urgi-team
parents:
diff changeset
228 "post_job_actions": {
780ad1e582e1 Uploaded
urgi-team
parents:
diff changeset
229 "RenameDatasetActionoutFile": {
780ad1e582e1 Uploaded
urgi-team
parents:
diff changeset
230 "action_arguments": {
780ad1e582e1 Uploaded
urgi-team
parents:
diff changeset
231 "newname": "#{inputFile | basename}.markedBAM"
780ad1e582e1 Uploaded
urgi-team
parents:
diff changeset
232 },
780ad1e582e1 Uploaded
urgi-team
parents:
diff changeset
233 "action_type": "RenameDatasetAction",
780ad1e582e1 Uploaded
urgi-team
parents:
diff changeset
234 "output_name": "outFile"
780ad1e582e1 Uploaded
urgi-team
parents:
diff changeset
235 }
780ad1e582e1 Uploaded
urgi-team
parents:
diff changeset
236 },
780ad1e582e1 Uploaded
urgi-team
parents:
diff changeset
237 "tool_errors": null,
780ad1e582e1 Uploaded
urgi-team
parents:
diff changeset
238 "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MarkDuplicates/1.126.0",
780ad1e582e1 Uploaded
urgi-team
parents:
diff changeset
239 "tool_state": "{\"duplicate_scoring_strategy\": \"\\\"SUM_OF_BASE_QUALITIES\\\"\", \"remove_duplicates\": \"\\\"True\\\"\", \"read_name_regex\": \"\\\"[a-zA-Z0-9]+:[0-9]:([0-9]+):([0-9]+):([0-9]+).*.\\\"\", \"__page__\": 0, \"__rerun_remap_job_id__\": null, \"validation_stringency\": \"\\\"LENIENT\\\"\", \"comments\": \"[]\", \"assume_sorted\": \"\\\"False\\\"\", \"optical_duplicate_pixel_distance\": \"\\\"100\\\"\", \"chromInfo\": \"\\\"/home/galaxy-dev/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\", \"inputFile\": \"null\"}",
780ad1e582e1 Uploaded
urgi-team
parents:
diff changeset
240 "tool_version": "1.126.0",
780ad1e582e1 Uploaded
urgi-team
parents:
diff changeset
241 "type": "tool",
780ad1e582e1 Uploaded
urgi-team
parents:
diff changeset
242 "user_outputs": []
780ad1e582e1 Uploaded
urgi-team
parents:
diff changeset
243 },
780ad1e582e1 Uploaded
urgi-team
parents:
diff changeset
244 "7": {
780ad1e582e1 Uploaded
urgi-team
parents:
diff changeset
245 "annotation": "",
780ad1e582e1 Uploaded
urgi-team
parents:
diff changeset
246 "id": 7,
780ad1e582e1 Uploaded
urgi-team
parents:
diff changeset
247 "input_connections": {
780ad1e582e1 Uploaded
urgi-team
parents:
diff changeset
248 "input1": {
780ad1e582e1 Uploaded
urgi-team
parents:
diff changeset
249 "id": 6,
780ad1e582e1 Uploaded
urgi-team
parents:
diff changeset
250 "output_name": "outFile"
780ad1e582e1 Uploaded
urgi-team
parents:
diff changeset
251 }
780ad1e582e1 Uploaded
urgi-team
parents:
diff changeset
252 },
780ad1e582e1 Uploaded
urgi-team
parents:
diff changeset
253 "inputs": [],
780ad1e582e1 Uploaded
urgi-team
parents:
diff changeset
254 "name": "flagstat",
780ad1e582e1 Uploaded
urgi-team
parents:
diff changeset
255 "outputs": [
780ad1e582e1 Uploaded
urgi-team
parents:
diff changeset
256 {
780ad1e582e1 Uploaded
urgi-team
parents:
diff changeset
257 "name": "output1",
780ad1e582e1 Uploaded
urgi-team
parents:
diff changeset
258 "type": "txt"
780ad1e582e1 Uploaded
urgi-team
parents:
diff changeset
259 }
780ad1e582e1 Uploaded
urgi-team
parents:
diff changeset
260 ],
780ad1e582e1 Uploaded
urgi-team
parents:
diff changeset
261 "position": {
780ad1e582e1 Uploaded
urgi-team
parents:
diff changeset
262 "left": 1400,
780ad1e582e1 Uploaded
urgi-team
parents:
diff changeset
263 "top": 200
780ad1e582e1 Uploaded
urgi-team
parents:
diff changeset
264 },
780ad1e582e1 Uploaded
urgi-team
parents:
diff changeset
265 "post_job_actions": {
780ad1e582e1 Uploaded
urgi-team
parents:
diff changeset
266 "RenameDatasetActionoutput1": {
780ad1e582e1 Uploaded
urgi-team
parents:
diff changeset
267 "action_arguments": {
780ad1e582e1 Uploaded
urgi-team
parents:
diff changeset
268 "newname": "#{inupt1| basename}.stats"
780ad1e582e1 Uploaded
urgi-team
parents:
diff changeset
269 },
780ad1e582e1 Uploaded
urgi-team
parents:
diff changeset
270 "action_type": "RenameDatasetAction",
780ad1e582e1 Uploaded
urgi-team
parents:
diff changeset
271 "output_name": "output1"
780ad1e582e1 Uploaded
urgi-team
parents:
diff changeset
272 }
780ad1e582e1 Uploaded
urgi-team
parents:
diff changeset
273 },
780ad1e582e1 Uploaded
urgi-team
parents:
diff changeset
274 "tool_errors": null,
780ad1e582e1 Uploaded
urgi-team
parents:
diff changeset
275 "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/samtools_flagstat/samtools_flagstat/1.0.1",
780ad1e582e1 Uploaded
urgi-team
parents:
diff changeset
276 "tool_state": "{\"__page__\": 0, \"__rerun_remap_job_id__\": null, \"input1\": \"null\", \"chromInfo\": \"\\\"/home/galaxy-dev/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\"}",
780ad1e582e1 Uploaded
urgi-team
parents:
diff changeset
277 "tool_version": "1.0.0",
780ad1e582e1 Uploaded
urgi-team
parents:
diff changeset
278 "type": "tool",
780ad1e582e1 Uploaded
urgi-team
parents:
diff changeset
279 "user_outputs": []
780ad1e582e1 Uploaded
urgi-team
parents:
diff changeset
280 },
780ad1e582e1 Uploaded
urgi-team
parents:
diff changeset
281 "8": {
780ad1e582e1 Uploaded
urgi-team
parents:
diff changeset
282 "annotation": "",
780ad1e582e1 Uploaded
urgi-team
parents:
diff changeset
283 "id": 8,
780ad1e582e1 Uploaded
urgi-team
parents:
diff changeset
284 "input_connections": {
780ad1e582e1 Uploaded
urgi-team
parents:
diff changeset
285 "input_bams_0|input_bam": {
780ad1e582e1 Uploaded
urgi-team
parents:
diff changeset
286 "id": 6,
780ad1e582e1 Uploaded
urgi-team
parents:
diff changeset
287 "output_name": "outFile"
780ad1e582e1 Uploaded
urgi-team
parents:
diff changeset
288 },
780ad1e582e1 Uploaded
urgi-team
parents:
diff changeset
289 "reference_source|ref_file": {
780ad1e582e1 Uploaded
urgi-team
parents:
diff changeset
290 "id": 0,
780ad1e582e1 Uploaded
urgi-team
parents:
diff changeset
291 "output_name": "output"
780ad1e582e1 Uploaded
urgi-team
parents:
diff changeset
292 }
780ad1e582e1 Uploaded
urgi-team
parents:
diff changeset
293 },
780ad1e582e1 Uploaded
urgi-team
parents:
diff changeset
294 "inputs": [],
780ad1e582e1 Uploaded
urgi-team
parents:
diff changeset
295 "name": "Freebayes4Workflow",
780ad1e582e1 Uploaded
urgi-team
parents:
diff changeset
296 "outputs": [
780ad1e582e1 Uploaded
urgi-team
parents:
diff changeset
297 {
780ad1e582e1 Uploaded
urgi-team
parents:
diff changeset
298 "name": "output_vcf_default",
780ad1e582e1 Uploaded
urgi-team
parents:
diff changeset
299 "type": "vcf"
780ad1e582e1 Uploaded
urgi-team
parents:
diff changeset
300 },
780ad1e582e1 Uploaded
urgi-team
parents:
diff changeset
301 {
780ad1e582e1 Uploaded
urgi-team
parents:
diff changeset
302 "name": "output_vcf_firstBAM",
780ad1e582e1 Uploaded
urgi-team
parents:
diff changeset
303 "type": "vcf"
780ad1e582e1 Uploaded
urgi-team
parents:
diff changeset
304 },
780ad1e582e1 Uploaded
urgi-team
parents:
diff changeset
305 {
780ad1e582e1 Uploaded
urgi-team
parents:
diff changeset
306 "name": "output_vcf_rename",
780ad1e582e1 Uploaded
urgi-team
parents:
diff changeset
307 "type": "vcf"
780ad1e582e1 Uploaded
urgi-team
parents:
diff changeset
308 },
780ad1e582e1 Uploaded
urgi-team
parents:
diff changeset
309 {
780ad1e582e1 Uploaded
urgi-team
parents:
diff changeset
310 "name": "output_failed_alleles_bed",
780ad1e582e1 Uploaded
urgi-team
parents:
diff changeset
311 "type": "bed"
780ad1e582e1 Uploaded
urgi-team
parents:
diff changeset
312 },
780ad1e582e1 Uploaded
urgi-team
parents:
diff changeset
313 {
780ad1e582e1 Uploaded
urgi-team
parents:
diff changeset
314 "name": "output_trace",
780ad1e582e1 Uploaded
urgi-team
parents:
diff changeset
315 "type": "txt"
780ad1e582e1 Uploaded
urgi-team
parents:
diff changeset
316 }
780ad1e582e1 Uploaded
urgi-team
parents:
diff changeset
317 ],
780ad1e582e1 Uploaded
urgi-team
parents:
diff changeset
318 "position": {
780ad1e582e1 Uploaded
urgi-team
parents:
diff changeset
319 "left": 1400,
780ad1e582e1 Uploaded
urgi-team
parents:
diff changeset
320 "top": 313
780ad1e582e1 Uploaded
urgi-team
parents:
diff changeset
321 },
780ad1e582e1 Uploaded
urgi-team
parents:
diff changeset
322 "post_job_actions": {},
780ad1e582e1 Uploaded
urgi-team
parents:
diff changeset
323 "tool_errors": null,
780ad1e582e1 Uploaded
urgi-team
parents:
diff changeset
324 "tool_id": "toolshed.g2.bx.psu.edu/repos/urgi-team/freebayes4workflow/freebayes4workflow/0.5",
780ad1e582e1 Uploaded
urgi-team
parents:
diff changeset
325 "tool_state": "{\"__page__\": 0, \"input_bams\": \"[{\\\"__index__\\\": 0, \\\"input_bam\\\": null}]\", \"__rerun_remap_job_id__\": null, \"rename_output\": \"{\\\"rename_output_selector\\\": \\\"firstBAM\\\", \\\"__current_case__\\\": 1}\", \"options_type\": \"{\\\"options_type_selector\\\": \\\"full\\\", \\\"allele_scope\\\": {\\\"no_partial_observations\\\": \\\"False\\\", \\\"I\\\": \\\"False\\\", \\\"n\\\": \\\"0\\\", \\\"min_repeat_length\\\": \\\"5\\\", \\\"i\\\": \\\"False\\\", \\\"min_repeat_entropy\\\": \\\"0\\\", \\\"u\\\": \\\"True\\\", \\\"__current_case__\\\": 0, \\\"X\\\": \\\"True\\\", \\\"haplotype_length\\\": \\\"3\\\", \\\"allele_scope_selector\\\": \\\"True\\\"}, \\\"reporting\\\": {\\\"reporting_selector\\\": \\\"False\\\", \\\"__current_case__\\\": 1}, \\\"genotype_likelihoods\\\": {\\\"genotype_likelihoods_selector\\\": \\\"False\\\", \\\"__current_case__\\\": 1}, \\\"O\\\": \\\"False\\\", \\\"population_model\\\": {\\\"population_model_selector\\\": \\\"False\\\", \\\"__current_case__\\\": 1}, \\\"reference_allele\\\": {\\\"reference_allele_selector\\\": \\\"False\\\", \\\"__current_case__\\\": 1}, \\\"optional_inputs\\\": {\\\"A\\\": null, \\\"output_trace_option\\\": \\\"False\\\", \\\"__current_case__\\\": 0, \\\"populations\\\": null, \\\"optional_inputs_selector\\\": \\\"True\\\", \\\"input_variant_type\\\": {\\\"input_variant_type_selector\\\": \\\"do_not_provide\\\", \\\"__current_case__\\\": 0}, \\\"report_monomorphic\\\": \\\"True\\\", \\\"observation_bias\\\": null, \\\"contamination_estimates\\\": null, \\\"samples\\\": null, \\\"output_failed_alleles_option\\\": \\\"False\\\", \\\"haplotype_basis_alleles\\\": null}, \\\"__current_case__\\\": 0, \\\"population_mappability_priors\\\": {\\\"population_mappability_priors_selector\\\": \\\"False\\\", \\\"__current_case__\\\": 1}, \\\"input_filters\\\": {\\\"input_filters_selector\\\": \\\"False\\\", \\\"__current_case__\\\": 1}, \\\"algorithmic_features\\\": {\\\"algorithmic_features_selector\\\": \\\"False\\\", \\\"__current_case__\\\": 1}}\", \"reference_source\": \"{\\\"ref_file\\\": null, \\\"reference_source_selector\\\": \\\"history\\\", \\\"__current_case__\\\": 1}\", \"chromInfo\": \"\\\"/home/galaxy-dev/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\", \"target_limit_type\": \"{\\\"target_limit_type_selector\\\": \\\"do_not_limit\\\", \\\"__current_case__\\\": 0}\"}",
780ad1e582e1 Uploaded
urgi-team
parents:
diff changeset
326 "tool_version": "0.5",
780ad1e582e1 Uploaded
urgi-team
parents:
diff changeset
327 "type": "tool",
780ad1e582e1 Uploaded
urgi-team
parents:
diff changeset
328 "user_outputs": []
780ad1e582e1 Uploaded
urgi-team
parents:
diff changeset
329 },
780ad1e582e1 Uploaded
urgi-team
parents:
diff changeset
330 "9": {
780ad1e582e1 Uploaded
urgi-team
parents:
diff changeset
331 "annotation": "",
780ad1e582e1 Uploaded
urgi-team
parents:
diff changeset
332 "id": 9,
780ad1e582e1 Uploaded
urgi-team
parents:
diff changeset
333 "input_connections": {
780ad1e582e1 Uploaded
urgi-team
parents:
diff changeset
334 "BedFile_List|BedFiles_0|inputBed": {
780ad1e582e1 Uploaded
urgi-team
parents:
diff changeset
335 "id": 3,
780ad1e582e1 Uploaded
urgi-team
parents:
diff changeset
336 "output_name": "output_bed"
780ad1e582e1 Uploaded
urgi-team
parents:
diff changeset
337 },
780ad1e582e1 Uploaded
urgi-team
parents:
diff changeset
338 "inputVCF": {
780ad1e582e1 Uploaded
urgi-team
parents:
diff changeset
339 "id": 8,
780ad1e582e1 Uploaded
urgi-team
parents:
diff changeset
340 "output_name": "output_vcf_firstBAM"
780ad1e582e1 Uploaded
urgi-team
parents:
diff changeset
341 }
780ad1e582e1 Uploaded
urgi-team
parents:
diff changeset
342 },
780ad1e582e1 Uploaded
urgi-team
parents:
diff changeset
343 "inputs": [],
780ad1e582e1 Uploaded
urgi-team
parents:
diff changeset
344 "name": "VCFFiltering",
780ad1e582e1 Uploaded
urgi-team
parents:
diff changeset
345 "outputs": [
780ad1e582e1 Uploaded
urgi-team
parents:
diff changeset
346 {
780ad1e582e1 Uploaded
urgi-team
parents:
diff changeset
347 "name": "outputVCF",
780ad1e582e1 Uploaded
urgi-team
parents:
diff changeset
348 "type": "vcf"
780ad1e582e1 Uploaded
urgi-team
parents:
diff changeset
349 },
780ad1e582e1 Uploaded
urgi-team
parents:
diff changeset
350 {
780ad1e582e1 Uploaded
urgi-team
parents:
diff changeset
351 "name": "output_html",
780ad1e582e1 Uploaded
urgi-team
parents:
diff changeset
352 "type": "html"
780ad1e582e1 Uploaded
urgi-team
parents:
diff changeset
353 }
780ad1e582e1 Uploaded
urgi-team
parents:
diff changeset
354 ],
780ad1e582e1 Uploaded
urgi-team
parents:
diff changeset
355 "position": {
780ad1e582e1 Uploaded
urgi-team
parents:
diff changeset
356 "left": 1904,
780ad1e582e1 Uploaded
urgi-team
parents:
diff changeset
357 "top": 265
780ad1e582e1 Uploaded
urgi-team
parents:
diff changeset
358 },
780ad1e582e1 Uploaded
urgi-team
parents:
diff changeset
359 "post_job_actions": {
780ad1e582e1 Uploaded
urgi-team
parents:
diff changeset
360 "RenameDatasetActionoutputVCF": {
780ad1e582e1 Uploaded
urgi-team
parents:
diff changeset
361 "action_arguments": {
780ad1e582e1 Uploaded
urgi-team
parents:
diff changeset
362 "newname": "#{inputVCF | basename}.filteredVCF"
780ad1e582e1 Uploaded
urgi-team
parents:
diff changeset
363 },
780ad1e582e1 Uploaded
urgi-team
parents:
diff changeset
364 "action_type": "RenameDatasetAction",
780ad1e582e1 Uploaded
urgi-team
parents:
diff changeset
365 "output_name": "outputVCF"
780ad1e582e1 Uploaded
urgi-team
parents:
diff changeset
366 },
780ad1e582e1 Uploaded
urgi-team
parents:
diff changeset
367 "RenameDatasetActionoutput_html": {
780ad1e582e1 Uploaded
urgi-team
parents:
diff changeset
368 "action_arguments": {
780ad1e582e1 Uploaded
urgi-team
parents:
diff changeset
369 "newname": "#{inputVCF | basename}.VCFFiltering.graphs"
780ad1e582e1 Uploaded
urgi-team
parents:
diff changeset
370 },
780ad1e582e1 Uploaded
urgi-team
parents:
diff changeset
371 "action_type": "RenameDatasetAction",
780ad1e582e1 Uploaded
urgi-team
parents:
diff changeset
372 "output_name": "output_html"
780ad1e582e1 Uploaded
urgi-team
parents:
diff changeset
373 }
780ad1e582e1 Uploaded
urgi-team
parents:
diff changeset
374 },
780ad1e582e1 Uploaded
urgi-team
parents:
diff changeset
375 "tool_errors": null,
780ad1e582e1 Uploaded
urgi-team
parents:
diff changeset
376 "tool_id": "toolshed.g2.bx.psu.edu/repos/urgi-team/vcfgandalftools/VCFFiltering/0.01",
780ad1e582e1 Uploaded
urgi-team
parents:
diff changeset
377 "tool_state": "{\"inputVCF\": \"null\", \"BedFile_List\": \"{\\\"BedFiles\\\": [{\\\"__index__\\\": 0, \\\"inputBed\\\": null}], \\\"is_BedFile\\\": \\\"True\\\", \\\"__current_case__\\\": 1}\", \"AF\": \"\\\"0.9\\\"\", \"__page__\": 0, \"DP_auto\": \"{\\\"is_DP_auto\\\": \\\"True\\\", \\\"__current_case__\\\": 0}\", \"__rerun_remap_job_id__\": null, \"AN\": \"\\\"2\\\"\", \"chromInfo\": \"\\\"/home/galaxy-dev/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\"}",
780ad1e582e1 Uploaded
urgi-team
parents:
diff changeset
378 "tool_version": "0.01",
780ad1e582e1 Uploaded
urgi-team
parents:
diff changeset
379 "type": "tool",
780ad1e582e1 Uploaded
urgi-team
parents:
diff changeset
380 "user_outputs": []
780ad1e582e1 Uploaded
urgi-team
parents:
diff changeset
381 }
780ad1e582e1 Uploaded
urgi-team
parents:
diff changeset
382 },
780ad1e582e1 Uploaded
urgi-team
parents:
diff changeset
383 "uuid": "7ffb6371-3f23-4cfe-8c68-70019963aa4a"
780ad1e582e1 Uploaded
urgi-team
parents:
diff changeset
384 }