annotate proteomics_rnaseq_reduced_db_workflow.ga @ 1:20d9fb1ba210 default tip

Replace several tabular manipulations with regex_replace tool
author Jim Johnson <jj@umn.edu>
date Thu, 20 Mar 2014 21:50:05 -0500
parents 9d5e59373c84
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
1 {
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
2 "a_galaxy_workflow": "true",
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
3 "annotation": "Filter out proteins that have a transcript expression level, as quantified by RNA-Seq data, below a certain threshold.",
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
4 "format-version": "0.1",
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
5 "name": "Proteomics Reduced DB",
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
6 "steps": {
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
7 "0": {
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
8 "annotation": "",
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
9 "id": 0,
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
10 "input_connections": {},
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
11 "inputs": [
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
12 {
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
13 "description": "",
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
14 "name": "Ensembl Genome Reference Fasta"
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
15 }
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
16 ],
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
17 "name": "Input dataset",
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
18 "outputs": [],
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
19 "position": {
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
20 "left": 264,
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
21 "top": 438
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
22 },
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
23 "tool_errors": null,
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
24 "tool_id": null,
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
25 "tool_state": "{\"name\": \"Ensembl Genome Reference Fasta\"}",
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
26 "tool_version": null,
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
27 "type": "data_input",
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
28 "user_outputs": []
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
29 },
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
30 "1": {
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
31 "annotation": "",
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
32 "id": 1,
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
33 "input_connections": {},
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
34 "inputs": [
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
35 {
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
36 "description": "",
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
37 "name": "Ensembl GTF File (gene models)"
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
38 }
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
39 ],
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
40 "name": "Input dataset",
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
41 "outputs": [],
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
42 "position": {
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
43 "left": 261,
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
44 "top": 521
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
45 },
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
46 "tool_errors": null,
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
47 "tool_id": null,
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
48 "tool_state": "{\"name\": \"Ensembl GTF File (gene models)\"}",
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
49 "tool_version": null,
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
50 "type": "data_input",
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
51 "user_outputs": []
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
52 },
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
53 "2": {
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
54 "annotation": "",
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
55 "id": 2,
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
56 "input_connections": {},
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
57 "inputs": [
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
58 {
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
59 "description": "",
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
60 "name": "Ensembl Protein FASTA (reference proteome)"
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
61 }
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
62 ],
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
63 "name": "Input dataset",
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
64 "outputs": [],
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
65 "position": {
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
66 "left": 630,
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
67 "top": 286
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
68 },
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
69 "tool_errors": null,
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
70 "tool_id": null,
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
71 "tool_state": "{\"name\": \"Ensembl Protein FASTA (reference proteome)\"}",
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
72 "tool_version": null,
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
73 "type": "data_input",
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
74 "user_outputs": []
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
75 },
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
76 "3": {
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
77 "annotation": "",
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
78 "id": 3,
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
79 "input_connections": {},
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
80 "inputs": [
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
81 {
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
82 "description": "",
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
83 "name": "RNA-Seq left paired-end fastq"
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
84 }
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
85 ],
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
86 "name": "Input dataset",
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
87 "outputs": [],
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
88 "position": {
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
89 "left": 585,
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
90 "top": 618
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
91 },
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
92 "tool_errors": null,
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
93 "tool_id": null,
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
94 "tool_state": "{\"name\": \"RNA-Seq left paired-end fastq\"}",
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
95 "tool_version": null,
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
96 "type": "data_input",
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
97 "user_outputs": []
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
98 },
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
99 "4": {
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
100 "annotation": "",
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
101 "id": 4,
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
102 "input_connections": {},
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
103 "inputs": [
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
104 {
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
105 "description": "",
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
106 "name": "RNA-Seq right paired-end fastq"
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
107 }
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
108 ],
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
109 "name": "Input dataset",
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
110 "outputs": [],
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
111 "position": {
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
112 "left": 586,
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
113 "top": 703
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
114 },
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
115 "tool_errors": null,
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
116 "tool_id": null,
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
117 "tool_state": "{\"name\": \"RNA-Seq right paired-end fastq\"}",
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
118 "tool_version": null,
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
119 "type": "data_input",
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
120 "user_outputs": []
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
121 },
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
122 "5": {
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
123 "annotation": "",
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
124 "id": 5,
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
125 "input_connections": {
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
126 "reference|gtf": {
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
127 "id": 1,
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
128 "output_name": "output"
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
129 },
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
130 "reference|reference_fasta_file": {
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
131 "id": 0,
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
132 "output_name": "output"
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
133 }
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
134 },
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
135 "inputs": [],
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
136 "name": "RSEM prepare reference",
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
137 "outputs": [
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
138 {
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
139 "name": "reference_file",
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
140 "type": "rsem_ref"
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
141 }
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
142 ],
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
143 "position": {
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
144 "left": 516,
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
145 "top": 425
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
146 },
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
147 "post_job_actions": {},
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
148 "tool_errors": null,
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
149 "tool_id": "toolshed.g2.bx.psu.edu/repos/jjohnson/rsem/rsem_prepare_reference/1.1.17",
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
150 "tool_state": "{\"__page__\": 0, \"reference\": \"{\\\"ref_type\\\": \\\"genomic\\\", \\\"gtf\\\": null, \\\"reference_fasta_file\\\": null, \\\"__current_case__\\\": 1}\", \"reference_name\": \"\\\"primaryEnsemblGtfRef\\\"\", \"__rerun_remap_job_id__\": null, \"chromInfo\": \"\\\"/website/galaxy.msi.umn.edu/PRODUCTION/tool-data/shared/ucsc/chrom/GRCm38_canon.len\\\"\", \"polya\": \"{\\\"polya_use\\\": \\\"add\\\", \\\"polya_length\\\": \\\"125\\\", \\\"__current_case__\\\": 0}\", \"transcript_to_gene_map\": \"null\", \"ntog\": \"\\\"False\\\"\"}",
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
151 "tool_version": "1.1.17",
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
152 "type": "tool",
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
153 "user_outputs": []
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
154 },
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
155 "6": {
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
156 "annotation": "",
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
157 "id": 6,
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
158 "input_connections": {
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
159 "input": {
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
160 "id": 2,
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
161 "output_name": "output"
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
162 }
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
163 },
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
164 "inputs": [],
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
165 "name": "FASTA-to-Tabular",
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
166 "outputs": [
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
167 {
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
168 "name": "output",
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
169 "type": "tabular"
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
170 }
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
171 ],
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
172 "position": {
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
173 "left": 900,
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
174 "top": 273
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
175 },
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
176 "post_job_actions": {},
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
177 "tool_errors": null,
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
178 "tool_id": "fasta2tab",
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
179 "tool_state": "{\"__page__\": 0, \"keep_first\": \"\\\"0\\\"\", \"descr_columns\": \"\\\"1\\\"\", \"input\": \"null\", \"chromInfo\": \"\\\"/website/galaxy.msi.umn.edu/PRODUCTION/tool-data/shared/ucsc/chrom/GRCm38_canon.len\\\"\", \"__rerun_remap_job_id__\": null}",
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
180 "tool_version": "1.1.0",
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
181 "type": "tool",
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
182 "user_outputs": []
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
183 },
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
184 "7": {
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
185 "annotation": "",
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
186 "id": 7,
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
187 "input_connections": {
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
188 "input|fastq|fastq1": {
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
189 "id": 3,
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
190 "output_name": "output"
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
191 },
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
192 "input|fastq|fastq2": {
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
193 "id": 4,
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
194 "output_name": "output"
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
195 },
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
196 "reference|rsem_ref": {
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
197 "id": 5,
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
198 "output_name": "reference_file"
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
199 }
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
200 },
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
201 "inputs": [],
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
202 "name": "RSEM calculate expression",
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
203 "outputs": [
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
204 {
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
205 "name": "gene_abundances",
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
206 "type": "tabular"
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
207 },
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
208 {
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
209 "name": "isoform_abundances",
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
210 "type": "tabular"
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
211 },
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
212 {
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
213 "name": "transcript_bam",
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
214 "type": "bam"
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
215 },
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
216 {
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
217 "name": "transcript_sorted_bam",
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
218 "type": "bam"
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
219 },
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
220 {
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
221 "name": "genome_bam",
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
222 "type": "bam"
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
223 },
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
224 {
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
225 "name": "genome_sorted_bam",
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
226 "type": "bam"
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
227 },
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
228 {
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
229 "name": "log",
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
230 "type": "txt"
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
231 }
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
232 ],
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
233 "position": {
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
234 "left": 862,
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
235 "top": 524
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
236 },
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
237 "post_job_actions": {},
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
238 "tool_errors": null,
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
239 "tool_id": "toolshed.g2.bx.psu.edu/repos/jjohnson/rsem/rsem_calculate_expression/1.1.17",
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
240 "tool_state": "{\"__page__\": 0, \"reference\": \"{\\\"rsem_ref\\\": null, \\\"refSrc\\\": \\\"history\\\", \\\"__current_case__\\\": 1}\", \"rsem_options\": \"{\\\"fullparams\\\": \\\"default\\\", \\\"__current_case__\\\": 0}\", \"rsem_outputs\": \"{\\\"result_bams\\\": \\\"none\\\", \\\"__current_case__\\\": 0}\", \"__rerun_remap_job_id__\": null, \"seedlength\": \"\\\"25\\\"\", \"sample\": \"\\\"rsem_sample\\\"\", \"forward_prob\": \"\\\"0.5\\\"\", \"input\": \"{\\\"fastq\\\": {\\\"fastq2\\\": null, \\\"fastq1\\\": null, \\\"matepair\\\": \\\"paired\\\", \\\"__current_case__\\\": 1}, \\\"bowtie_options\\\": {\\\"fullparams\\\": \\\"default\\\", \\\"__current_case__\\\": 0}, \\\"fastq_select\\\": \\\"--phred33-quals\\\", \\\"__current_case__\\\": 0, \\\"format\\\": \\\"fastq\\\"}\", \"chromInfo\": \"\\\"/website/galaxy.msi.umn.edu/PRODUCTION/tool-data/shared/ucsc/chrom/GRCm38_canon.len\\\"\"}",
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
241 "tool_version": "1.1.17",
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
242 "type": "tool",
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
243 "user_outputs": []
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
244 },
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
245 "8": {
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
246 "annotation": "",
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
247 "id": 8,
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
248 "input_connections": {
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
249 "input": {
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
250 "id": 6,
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
251 "output_name": "output"
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
252 }
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
253 },
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
254 "inputs": [],
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
255 "name": "Cut",
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
256 "outputs": [
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
257 {
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
258 "name": "out_file1",
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
259 "type": "tabular"
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
260 }
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
261 ],
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
262 "position": {
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
263 "left": 1128,
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
264 "top": 401
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
265 },
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
266 "post_job_actions": {},
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
267 "tool_errors": null,
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
268 "tool_id": "Cut1",
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
269 "tool_state": "{\"__page__\": 0, \"__rerun_remap_job_id__\": null, \"delimiter\": \"\\\"T\\\"\", \"columnList\": \"\\\"c1\\\"\", \"input\": \"null\", \"chromInfo\": \"\\\"/website/galaxy.msi.umn.edu/PRODUCTION/tool-data/shared/ucsc/chrom/GRCm38_canon.len\\\"\"}",
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
270 "tool_version": "1.0.2",
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
271 "type": "tool",
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
272 "user_outputs": []
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
273 },
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
274 "9": {
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
275 "annotation": "",
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
276 "id": 9,
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
277 "input_connections": {
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
278 "input": {
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
279 "id": 7,
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
280 "output_name": "isoform_abundances"
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
281 }
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
282 },
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
283 "inputs": [],
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
284 "name": "Filter",
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
285 "outputs": [
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
286 {
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
287 "name": "out_file1",
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
288 "type": "input"
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
289 }
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
290 ],
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
291 "position": {
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
292 "left": 1485,
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
293 "top": 728
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
294 },
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
295 "post_job_actions": {},
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
296 "tool_errors": null,
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
297 "tool_id": "Filter1",
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
298 "tool_state": "{\"__page__\": 0, \"__rerun_remap_job_id__\": null, \"cond\": \"\\\"c3>0.000001\\\"\", \"input\": \"null\", \"header_lines\": \"\\\"0\\\"\", \"chromInfo\": \"\\\"/website/galaxy.msi.umn.edu/PRODUCTION/tool-data/shared/ucsc/chrom/GRCm38_canon.len\\\"\"}",
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
299 "tool_version": "1.1.0",
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
300 "type": "tool",
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
301 "user_outputs": []
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
302 },
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
303 "10": {
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
304 "annotation": "",
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
305 "id": 10,
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
306 "input_connections": {
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
307 "input": {
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
308 "id": 8,
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
309 "output_name": "out_file1"
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
310 }
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
311 },
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
312 "inputs": [],
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
313 "name": "Convert",
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
314 "outputs": [
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
315 {
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
316 "name": "out_file1",
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
317 "type": "tabular"
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
318 }
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
319 ],
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
320 "position": {
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
321 "left": 1341,
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
322 "top": 528
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
323 },
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
324 "post_job_actions": {},
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
325 "tool_errors": null,
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
326 "tool_id": "Convert characters1",
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
327 "tool_state": "{\"__page__\": 0, \"convert_from\": \"\\\"s\\\"\", \"__rerun_remap_job_id__\": null, \"chromInfo\": \"\\\"/website/galaxy.msi.umn.edu/PRODUCTION/tool-data/shared/ucsc/chrom/GRCm38_canon.len\\\"\", \"input\": \"null\"}",
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
328 "tool_version": "1.0.0",
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
329 "type": "tool",
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
330 "user_outputs": []
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
331 },
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
332 "11": {
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
333 "annotation": "",
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
334 "id": 11,
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
335 "input_connections": {
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
336 "input": {
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
337 "id": 9,
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
338 "output_name": "out_file1"
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
339 }
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
340 },
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
341 "inputs": [],
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
342 "name": "Compute",
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
343 "outputs": [
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
344 {
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
345 "name": "out_file1",
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
346 "type": "input"
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
347 }
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
348 ],
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
349 "position": {
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
350 "left": 1803,
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
351 "top": 682
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
352 },
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
353 "post_job_actions": {},
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
354 "tool_errors": null,
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
355 "tool_id": "Add_a_column1",
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
356 "tool_state": "{\"__page__\": 0, \"__rerun_remap_job_id__\": null, \"cond\": \"\\\"c3*1000000\\\"\", \"input\": \"null\", \"chromInfo\": \"\\\"/website/galaxy.msi.umn.edu/PRODUCTION/tool-data/shared/ucsc/chrom/GRCm38_canon.len\\\"\", \"round\": \"\\\"no\\\"\"}",
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
357 "tool_version": "1.1.0",
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
358 "type": "tool",
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
359 "user_outputs": []
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
360 },
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
361 "12": {
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
362 "annotation": "",
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
363 "id": 12,
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
364 "input_connections": {
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
365 "input": {
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
366 "id": 10,
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
367 "output_name": "out_file1"
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
368 }
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
369 },
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
370 "inputs": [],
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
371 "name": "Cut",
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
372 "outputs": [
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
373 {
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
374 "name": "out_file1",
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
375 "type": "tabular"
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
376 }
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
377 ],
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
378 "position": {
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
379 "left": 1587,
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
380 "top": 513
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
381 },
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
382 "post_job_actions": {},
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
383 "tool_errors": null,
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
384 "tool_id": "Cut1",
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
385 "tool_state": "{\"__page__\": 0, \"__rerun_remap_job_id__\": null, \"delimiter\": \"\\\"T\\\"\", \"columnList\": \"\\\"c5\\\"\", \"input\": \"null\", \"chromInfo\": \"\\\"/website/galaxy.msi.umn.edu/PRODUCTION/tool-data/shared/ucsc/chrom/GRCm38_canon.len\\\"\"}",
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
386 "tool_version": "1.0.2",
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
387 "type": "tool",
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
388 "user_outputs": []
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
389 },
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
390 "13": {
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
391 "annotation": "",
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
392 "id": 13,
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
393 "input_connections": {
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
394 "input": {
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
395 "id": 12,
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
396 "output_name": "out_file1"
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
397 }
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
398 },
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
399 "inputs": [],
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
400 "name": "Convert",
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
401 "outputs": [
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
402 {
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
403 "name": "out_file1",
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
404 "type": "tabular"
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
405 }
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
406 ],
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
407 "position": {
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
408 "left": 1808,
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
409 "top": 480
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
410 },
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
411 "post_job_actions": {},
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
412 "tool_errors": null,
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
413 "tool_id": "Convert characters1",
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
414 "tool_state": "{\"__page__\": 0, \"convert_from\": \"\\\"Co\\\"\", \"__rerun_remap_job_id__\": null, \"chromInfo\": \"\\\"/website/galaxy.msi.umn.edu/PRODUCTION/tool-data/shared/ucsc/chrom/GRCm38_canon.len\\\"\", \"input\": \"null\"}",
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
415 "tool_version": "1.0.0",
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
416 "type": "tool",
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
417 "user_outputs": []
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
418 },
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
419 "14": {
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
420 "annotation": "",
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
421 "id": 14,
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
422 "input_connections": {
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
423 "input": {
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
424 "id": 13,
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
425 "output_name": "out_file1"
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
426 }
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
427 },
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
428 "inputs": [],
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
429 "name": "Cut",
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
430 "outputs": [
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
431 {
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
432 "name": "out_file1",
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
433 "type": "tabular"
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
434 }
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
435 ],
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
436 "position": {
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
437 "left": 2006,
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
438 "top": 408
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
439 },
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
440 "post_job_actions": {},
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
441 "tool_errors": null,
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
442 "tool_id": "Cut1",
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
443 "tool_state": "{\"__page__\": 0, \"__rerun_remap_job_id__\": null, \"delimiter\": \"\\\"T\\\"\", \"columnList\": \"\\\"c2\\\"\", \"input\": \"null\", \"chromInfo\": \"\\\"/website/galaxy.msi.umn.edu/PRODUCTION/tool-data/shared/ucsc/chrom/GRCm38_canon.len\\\"\"}",
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
444 "tool_version": "1.0.2",
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
445 "type": "tool",
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
446 "user_outputs": []
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
447 },
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
448 "15": {
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
449 "annotation": "",
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
450 "id": 15,
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
451 "input_connections": {
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
452 "input1": {
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
453 "id": 6,
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
454 "output_name": "output"
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
455 },
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
456 "input2": {
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
457 "id": 14,
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
458 "output_name": "out_file1"
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
459 }
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
460 },
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
461 "inputs": [],
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
462 "name": "Paste",
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
463 "outputs": [
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
464 {
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
465 "name": "out_file1",
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
466 "type": "input"
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
467 }
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
468 ],
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
469 "position": {
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
470 "left": 2219,
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
471 "top": 318
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
472 },
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
473 "post_job_actions": {},
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
474 "tool_errors": null,
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
475 "tool_id": "Paste1",
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
476 "tool_state": "{\"input2\": \"null\", \"__page__\": 0, \"input1\": \"null\", \"__rerun_remap_job_id__\": null, \"delimiter\": \"\\\"T\\\"\", \"chromInfo\": \"\\\"/website/galaxy.msi.umn.edu/PRODUCTION/tool-data/shared/ucsc/chrom/GRCm38_canon.len\\\"\"}",
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
477 "tool_version": "1.0.0",
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
478 "type": "tool",
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
479 "user_outputs": []
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
480 },
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
481 "16": {
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
482 "annotation": "",
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
483 "id": 16,
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
484 "input_connections": {
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
485 "input1": {
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
486 "id": 15,
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
487 "output_name": "out_file1"
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
488 },
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
489 "input2": {
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
490 "id": 11,
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
491 "output_name": "out_file1"
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
492 }
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
493 },
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
494 "inputs": [],
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
495 "name": "Join two Datasets",
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
496 "outputs": [
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
497 {
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
498 "name": "out_file1",
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
499 "type": "input"
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
500 }
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
501 ],
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
502 "position": {
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
503 "left": 2417,
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
504 "top": 425
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
505 },
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
506 "post_job_actions": {},
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
507 "tool_errors": null,
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
508 "tool_id": "join1",
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
509 "tool_state": "{\"input2\": \"null\", \"__page__\": 0, \"field1\": \"{\\\"__class__\\\": \\\"UnvalidatedValue\\\", \\\"value\\\": \\\"3\\\"}\", \"partial\": \"\\\"\\\"\", \"field2\": \"{\\\"__class__\\\": \\\"UnvalidatedValue\\\", \\\"value\\\": \\\"1\\\"}\", \"__rerun_remap_job_id__\": null, \"fill_empty_columns\": \"{\\\"fill_empty_columns_switch\\\": \\\"no_fill\\\", \\\"__current_case__\\\": 0}\", \"unmatched\": \"\\\"\\\"\", \"input1\": \"null\", \"chromInfo\": \"\\\"/website/galaxy.msi.umn.edu/PRODUCTION/tool-data/shared/ucsc/chrom/GRCm38_canon.len\\\"\"}",
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
510 "tool_version": "2.0.2",
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
511 "type": "tool",
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
512 "user_outputs": []
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
513 },
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
514 "17": {
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
515 "annotation": "",
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
516 "id": 17,
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
517 "input_connections": {
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
518 "input": {
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
519 "id": 16,
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
520 "output_name": "out_file1"
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
521 }
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
522 },
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
523 "inputs": [],
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
524 "name": "Add column",
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
525 "outputs": [
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
526 {
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
527 "name": "out_file1",
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
528 "type": "input"
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
529 }
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
530 ],
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
531 "position": {
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
532 "left": 2619,
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
533 "top": 380
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
534 },
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
535 "post_job_actions": {},
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
536 "tool_errors": null,
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
537 "tool_id": "addValue",
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
538 "tool_state": "{\"__page__\": 0, \"__rerun_remap_job_id__\": null, \"exp\": \"\\\" \\\"\", \"iterate\": \"\\\"no\\\"\", \"input\": \"null\", \"chromInfo\": \"\\\"/website/galaxy.msi.umn.edu/PRODUCTION/tool-data/shared/ucsc/chrom/GRCm38_canon.len\\\"\"}",
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
539 "tool_version": "1.0.0",
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
540 "type": "tool",
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
541 "user_outputs": []
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
542 },
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
543 "18": {
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
544 "annotation": "",
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
545 "id": 18,
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
546 "input_connections": {
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
547 "input": {
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
548 "id": 17,
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
549 "output_name": "out_file1"
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
550 }
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
551 },
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
552 "inputs": [],
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
553 "name": "Add column",
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
554 "outputs": [
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
555 {
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
556 "name": "out_file1",
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
557 "type": "input"
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
558 }
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
559 ],
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
560 "position": {
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
561 "left": 2832,
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
562 "top": 302
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
563 },
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
564 "post_job_actions": {},
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
565 "tool_errors": null,
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
566 "tool_id": "addValue",
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
567 "tool_state": "{\"__page__\": 0, \"__rerun_remap_job_id__\": null, \"exp\": \"\\\"tpm:\\\"\", \"iterate\": \"\\\"no\\\"\", \"input\": \"null\", \"chromInfo\": \"\\\"/website/galaxy.msi.umn.edu/PRODUCTION/tool-data/shared/ucsc/chrom/GRCm38_canon.len\\\"\"}",
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
568 "tool_version": "1.0.0",
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
569 "type": "tool",
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
570 "user_outputs": []
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
571 },
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
572 "19": {
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
573 "annotation": "",
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
574 "id": 19,
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
575 "input_connections": {
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
576 "input1": {
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
577 "id": 18,
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
578 "output_name": "out_file1"
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
579 }
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
580 },
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
581 "inputs": [],
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
582 "name": "Merge Columns",
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
583 "outputs": [
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
584 {
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
585 "name": "out_file1",
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
586 "type": "tabular"
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
587 }
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
588 ],
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
589 "position": {
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
590 "left": 3026,
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
591 "top": 408
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
592 },
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
593 "post_job_actions": {},
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
594 "tool_errors": null,
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
595 "tool_id": "mergeCols1",
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
596 "tool_state": "{\"__page__\": 0, \"input1\": \"null\", \"__rerun_remap_job_id__\": null, \"col2\": \"{\\\"__class__\\\": \\\"UnvalidatedValue\\\", \\\"value\\\": \\\"9\\\"}\", \"col1\": \"{\\\"__class__\\\": \\\"UnvalidatedValue\\\", \\\"value\\\": \\\"1\\\"}\", \"chromInfo\": \"\\\"/website/galaxy.msi.umn.edu/PRODUCTION/tool-data/shared/ucsc/chrom/GRCm38_canon.len\\\"\", \"columns\": \"[{\\\"__index__\\\": 0, \\\"datacol\\\": {\\\"__class__\\\": \\\"UnvalidatedValue\\\", \\\"value\\\": \\\"10\\\"}}, {\\\"__index__\\\": 1, \\\"datacol\\\": {\\\"__class__\\\": \\\"UnvalidatedValue\\\", \\\"value\\\": \\\"8\\\"}}]\"}",
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
597 "tool_version": "1.0.1",
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
598 "type": "tool",
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
599 "user_outputs": []
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
600 },
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
601 "20": {
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
602 "annotation": "",
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
603 "id": 20,
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
604 "input_connections": {
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
605 "input": {
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
606 "id": 19,
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
607 "output_name": "out_file1"
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
608 }
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
609 },
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
610 "inputs": [],
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
611 "name": "Cut",
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
612 "outputs": [
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
613 {
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
614 "name": "out_file1",
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
615 "type": "tabular"
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
616 }
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
617 ],
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
618 "position": {
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
619 "left": 3246,
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
620 "top": 368
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
621 },
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
622 "post_job_actions": {},
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
623 "tool_errors": null,
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
624 "tool_id": "Cut1",
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
625 "tool_state": "{\"__page__\": 0, \"__rerun_remap_job_id__\": null, \"delimiter\": \"\\\"T\\\"\", \"columnList\": \"\\\"c11,c2\\\"\", \"input\": \"null\", \"chromInfo\": \"\\\"/website/galaxy.msi.umn.edu/PRODUCTION/tool-data/shared/ucsc/chrom/GRCm38_canon.len\\\"\"}",
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
626 "tool_version": "1.0.2",
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
627 "type": "tool",
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
628 "user_outputs": []
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
629 },
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
630 "21": {
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
631 "annotation": "",
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
632 "id": 21,
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
633 "input_connections": {
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
634 "input": {
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
635 "id": 20,
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
636 "output_name": "out_file1"
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
637 }
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
638 },
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
639 "inputs": [],
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
640 "name": "Tabular-to-FASTA",
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
641 "outputs": [
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
642 {
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
643 "name": "output",
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
644 "type": "fasta"
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
645 }
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
646 ],
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
647 "position": {
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
648 "left": 3455,
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
649 "top": 458
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
650 },
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
651 "post_job_actions": {},
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
652 "tool_errors": null,
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
653 "tool_id": "tab2fasta",
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
654 "tool_state": "{\"title_col\": \"{\\\"__class__\\\": \\\"UnvalidatedValue\\\", \\\"value\\\": [\\\"1\\\"]}\", \"__page__\": 0, \"seq_col\": \"{\\\"__class__\\\": \\\"UnvalidatedValue\\\", \\\"value\\\": \\\"2\\\"}\", \"__rerun_remap_job_id__\": null, \"input\": \"null\", \"chromInfo\": \"\\\"/website/galaxy.msi.umn.edu/PRODUCTION/tool-data/shared/ucsc/chrom/GRCm38_canon.len\\\"\"}",
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
655 "tool_version": "1.1.0",
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
656 "type": "tool",
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
657 "user_outputs": []
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
658 },
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
659 "22": {
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
660 "annotation": "",
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
661 "id": 22,
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
662 "input_connections": {
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
663 "input": {
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
664 "id": 21,
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
665 "output_name": "output"
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
666 }
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
667 },
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
668 "inputs": [],
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
669 "name": "FASTA Width",
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
670 "outputs": [
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
671 {
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
672 "name": "output",
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
673 "type": "input"
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
674 }
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
675 ],
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
676 "position": {
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
677 "left": 3653,
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
678 "top": 359
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
679 },
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
680 "post_job_actions": {},
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
681 "tool_errors": null,
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
682 "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/fasta_formatter/cshl_fasta_formatter/1.0.0",
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
683 "tool_state": "{\"__page__\": 0, \"input\": \"null\", \"__rerun_remap_job_id__\": null, \"chromInfo\": \"\\\"/website/galaxy.msi.umn.edu/PRODUCTION/tool-data/shared/ucsc/chrom/GRCm38_canon.len\\\"\", \"width\": \"\\\"80\\\"\"}",
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
684 "tool_version": "1.0.0",
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
685 "type": "tool",
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
686 "user_outputs": []
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
687 }
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
688 }
9d5e59373c84 Initial upload
Jim Johnson <jj@umn.edu>
parents:
diff changeset
689 }