Mercurial > repos > clairetn > detrprok_wf

comparison Galaxy-Workflow-Detrprok_wf.ga @ 1:20e004d0292b draft default tip

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author clairetn
date Mon, 20 May 2013 13:44:44 -0400
parents c265b11e7277
children
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0:c265b11e7277 1:20e004d0292b
1 { 1 {
2 "a_galaxy_workflow": "true", 2 "a_galaxy_workflow": "true",
3 "annotation": "", 3 "annotation": "",
4 "format-version": "0.1", 4 "format-version": "0.1",
5 "name": "Detrprok_current", 5 "name": "Detrprok_wf",
6 "steps": { 6 "steps": {
7 "0": { 7 "0": {
8 "annotation": "Select here annotation file containing coding genes, tRNAs, rRNAs and known ncRNAs. You can download it from GJI (http://genome.jgi.doe.gov) or NCBI. Caution: 1srt column should have exactly the same identifier as the genome sequence used for mapping.", 8 "annotation": "Select here annotation file containing coding genes, tRNAs, rRNAs and known ncRNAs. You can download it from GJI (http://genome.jgi.doe.gov) or NCBI (http://ftp.ncbi.nih.gov/genomes/Bacteria). Caution: 1srt column should have exactly the same identifier as the genome sequence used for mapping.",
9 "id": 0, 9 "id": 0,
10 "input_connections": {}, 10 "input_connections": {},
11 "inputs": [ 11 "inputs": [
12 { 12 {
13 "description": "Select here annotation file containing coding genes, tRNAs, rRNAs and known ncRNAs. You can download it from GJI (http://genome.jgi.doe.gov) or NCBI. Caution: 1srt column should have exactly the same identifier as the genome sequence used for mapping.", 13 "description": "Select here annotation file containing coding genes, tRNAs, rRNAs and known ncRNAs. You can download it from GJI (http://genome.jgi.doe.gov) or NCBI (http://ftp.ncbi.nih.gov/genomes/Bacteria). Caution: 1srt column should have exactly the same identifier as the genome sequence used for mapping.",
14 "name": "positions list of all genome known annotations" 14 "name": "genome annotations"
15 } 15 }
16 ], 16 ],
17 "name": "Input dataset", 17 "name": "Input dataset",
18 "outputs": [], 18 "outputs": [],
19 "position": { 19 "position": {
20 "left": 166, 20 "left": 200,
21 "top": 364 21 "top": 231.00001525878906
22 }, 22 },
23 "tool_errors": null, 23 "tool_errors": null,
24 "tool_id": null, 24 "tool_id": null,
25 "tool_state": "{\"name\": \"positions list of all genome known annotations\"}", 25 "tool_state": "{\"name\": \"genome annotations\"}",
26 "tool_version": null, 26 "tool_version": null,
27 "type": "data_input", 27 "type": "data_input",
28 "user_outputs": [] 28 "user_outputs": []
29 }, 29 },
30 "1": { 30 "1": {
38 } 38 }
39 ], 39 ],
40 "name": "Input dataset", 40 "name": "Input dataset",
41 "outputs": [], 41 "outputs": [],
42 "position": { 42 "position": {
43 "left": 215, 43 "left": 205,
44 "top": 484 44 "top": 403.00001525878906
45 }, 45 },
46 "tool_errors": null, 46 "tool_errors": null,
47 "tool_id": null, 47 "tool_id": null,
48 "tool_state": "{\"name\": \"read alignments on genome\"}", 48 "tool_state": "{\"name\": \"read alignments on genome\"}",
49 "tool_version": null, 49 "tool_version": null,
50 "type": "data_input", 50 "type": "data_input",
51 "user_outputs": [] 51 "user_outputs": []
52 }, 52 },
53 "2": { 53 "2": {
54 "annotation": "", 54 "annotation": "Select here the GFF file features that will be considered as initial annotations. Any term added here will cause pre-existing features with this term not to be predicted again by the workflow. Please use a comma separated list and use \"CDS\" rather than \"gene\" for protein coding genes. Suggested value: rRNA,tRNA,ncRNA,CDS",
55 "id": 2, 55 "id": 2,
56 "input_connections": { 56 "input_connections": {
57 "inputFile": { 57 "formatType|inputFileName": {
58 "id": 0, 58 "id": 0,
59 "output_name": "output" 59 "output_name": "output"
60 } 60 }
61 }, 61 },
62 "inputs": [], 62 "inputs": [
63 "name": "clean Gff", 63 {
64 "description": "runtime parameter for tool clean transcript file",
65 "name": "optionType"
66 }
67 ],
68 "name": "clean transcript file",
64 "outputs": [ 69 "outputs": [
65 { 70 {
66 "name": "outputFile", 71 "name": "outputFile",
67 "type": "gff3" 72 "type": "gtf"
68 } 73 }
69 ], 74 ],
70 "position": { 75 "position": {
71 "left": 361, 76 "left": 457,
72 "top": 327 77 "top": 218.00001525878906
73 }, 78 },
74 "post_job_actions": {}, 79 "post_job_actions": {
75 "tool_errors": null, 80 "RenameDatasetActionoutputFile": {
76 "tool_id": "toolshed.g2.bx.psu.edu/repos/yufei-luo/s_mart/cleanGff/1.0.0", 81 "action_arguments": {
77 "tool_state": "{\"__page__\": 0, \"type\": \"\\\"tRNA,rRNA,ncRNA,CDS\\\"\", \"inputFile\": \"null\"}", 82 "newname": "annotation selection"
83 },
84 "action_type": "RenameDatasetAction",
85 "output_name": "outputFile"
86 }
87 },
88 "tool_errors": null,
89 "tool_id": "toolshed.g2.bx.psu.edu/repos/yufei-luo/s_mart/CleanTranscriptFile/1.0.0",
90 "tool_state": "{\"optionType\": \"{\\\"type\\\": \\\"Yes\\\", \\\"value\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"__current_case__\\\": 0}\", \"formatType\": \"{\\\"inputFileName\\\": null, \\\"__current_case__\\\": 0, \\\"FormatInputFileName\\\": \\\"gff\\\"}\", \"chromInfo\": \"\\\"/srv/galaxy/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\", \"__page__\": 0}",
78 "tool_version": "1.0.0", 91 "tool_version": "1.0.0",
79 "type": "tool", 92 "type": "tool",
80 "user_outputs": [] 93 "user_outputs": []
81 }, 94 },
82 "3": { 95 "3": {
95 "name": "output1", 108 "name": "output1",
96 "type": "sam" 109 "type": "sam"
97 } 110 }
98 ], 111 ],
99 "position": { 112 "position": {
100 "left": 418, 113 "left": 428,
101 "top": 479 114 "top": 400.00001525878906
102 }, 115 },
103 "post_job_actions": { 116 "post_job_actions": {
104 "RenameDatasetActionoutput1": { 117 "RenameDatasetActionoutput1": {
105 "action_arguments": { 118 "action_arguments": {
106 "newname": "Read alignments in SAM format" 119 "newname": "Read alignments (SAM format)"
107 }, 120 },
108 "action_type": "RenameDatasetAction", 121 "action_type": "RenameDatasetAction",
109 "output_name": "output1" 122 "output_name": "output1"
110 } 123 }
111 }, 124 },
112 "tool_errors": null, 125 "tool_errors": null,
113 "tool_id": "bam_to_sam", 126 "tool_id": "bam_to_sam",
114 "tool_state": "{\"header\": \"\\\"False\\\"\", \"input1\": \"null\", \"chromInfo\": \"\\\"/share/apps/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\", \"__page__\": 0}", 127 "tool_state": "{\"header\": \"\\\"True\\\"\", \"input1\": \"null\", \"chromInfo\": \"\\\"/srv/galaxy/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\", \"__page__\": 0}",
115 "tool_version": "1.0.3", 128 "tool_version": "1.0.3",
116 "type": "tool", 129 "type": "tool",
117 "user_outputs": [] 130 "user_outputs": []
118 }, 131 },
119 "4": { 132 "4": {
120 "annotation": "Clusters annotated proximal genes into operons. \nParameter to be set: op_gap. \nGenes separated by a gap smaller than op_gap are clustered \n(suggested value: 10 to 150).", 133 "annotation": "Clusters annotated proximal genes into operons. Parameter to be set: op_gap. Genes separated by a gap smaller than op_gap are clustered (suggested value: 10 to 150).",
121 "id": 4, 134 "id": 4,
122 "input_connections": { 135 "input_connections": {
123 "formatType|inputFileName": { 136 "formatType|inputFileName": {
124 "id": 2, 137 "id": 2,
125 "output_name": "outputFile" 138 "output_name": "outputFile"
126 } 139 }
127 }, 140 },
128 "inputs": [ 141 "inputs": [
129 { 142 {
130 "description": "runtime parameter for tool Clusterize", 143 "description": "runtime parameter for tool clusterize",
131 "name": "distance" 144 "name": "distance"
132 } 145 }
133 ], 146 ],
134 "name": "Clusterize", 147 "name": "clusterize",
135 "outputs": [ 148 "outputs": [
136 { 149 {
137 "name": "outputFileGff", 150 "name": "outputFileGff",
138 "type": "gff3" 151 "type": "gff3"
139 }, 152 }
140 { 153 ],
141 "name": "outputFileLog", 154 "position": {
142 "type": "txt" 155 "left": 700,
143 } 156 "top": 200.00001525878906
144 ], 157 },
145 "position": { 158 "post_job_actions": {
146 "left": 547, 159 "RenameDatasetActionoutputFileGff": {
147 "top": 297 160 "action_arguments": {
148 }, 161 "newname": "Annotation with operon-like features"
149 "post_job_actions": {
150 "RenameDatasetActionoutputFileGff": {
151 "action_arguments": {
152 "newname": "Annotation with \"operon\""
153 }, 162 },
154 "action_type": "RenameDatasetAction", 163 "action_type": "RenameDatasetAction",
155 "output_name": "outputFileGff" 164 "output_name": "outputFileGff"
156 } 165 }
157 }, 166 },
158 "tool_errors": null, 167 "tool_errors": null,
159 "tool_id": "toolshed.g2.bx.psu.edu/repos/yufei-luo/s_mart/MergingDataClusterize/1.0.0", 168 "tool_id": "toolshed.g2.bx.psu.edu/repos/yufei-luo/s_mart/MergingDataClusterize/1.0.0",
160 "tool_state": "{\"normalize\": \"\\\"False\\\"\", \"__page__\": 0, \"formatType\": \"{\\\"inputFileName\\\": null, \\\"__current_case__\\\": 3, \\\"FormatInputFileName\\\": \\\"gff3\\\"}\", \"log\": \"\\\"False\\\"\", \"distance\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"colinear\": \"\\\"True\\\"\"}", 169 "tool_state": "{\"normalize\": \"\\\"False\\\"\", \"__page__\": 0, \"formatType\": \"{\\\"inputFileName\\\": null, \\\"__current_case__\\\": 1, \\\"FormatInputFileName\\\": \\\"gff\\\"}\", \"distance\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"colinear\": \"\\\"True\\\"\", \"chromInfo\": \"\\\"/srv/galaxy/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\"}",
161 "tool_version": "1.0.0", 170 "tool_version": "1.0.0",
162 "type": "tool", 171 "type": "tool",
163 "user_outputs": [] 172 "user_outputs": []
164 }, 173 },
165 "5": { 174 "5": {
166 "annotation": "Clusters overlapping or proximal reads to produce read clusters. \nParameter to be set: clust_gap. \nReads separated by a gap smaller than \nclust_gap are clustered (suggested value: 0 to 20 ; a value of 0 will cluster only overlapping reads while a value of 20 will cluster reads even if they are 20-nt apart).", 175 "annotation": "Clusters overlapping or proximal reads to produce read clusters. Parameter to be set: clust_gap. Reads separated by a gap smaller than clust_gap are clustered (suggested value: 0 to 20 ; a value of 0 will cluster only overlapping reads while a value of 20 will cluster reads even if they are 20-nt apart)",
167 "id": 5, 176 "id": 5,
168 "input_connections": { 177 "input_connections": {
169 "formatType|inputFileName": { 178 "formatType|inputFileName": {
170 "id": 3, 179 "id": 3,
171 "output_name": "output1" 180 "output_name": "output1"
172 } 181 }
173 }, 182 },
174 "inputs": [ 183 "inputs": [
175 { 184 {
176 "description": "runtime parameter for tool Clusterize", 185 "description": "runtime parameter for tool clusterize",
177 "name": "distance" 186 "name": "distance"
178 } 187 }
179 ], 188 ],
180 "name": "Clusterize", 189 "name": "clusterize",
181 "outputs": [ 190 "outputs": [
182 { 191 {
183 "name": "outputFileGff", 192 "name": "outputFileGff",
184 "type": "gff3" 193 "type": "gff3"
185 }, 194 }
186 { 195 ],
187 "name": "outputFileLog", 196 "position": {
188 "type": "txt" 197 "left": 662,
189 } 198 "top": 505.00001525878906
190 ], 199 },
191 "position": { 200 "post_job_actions": {
192 "left": 496, 201 "RenameDatasetActionoutputFileGff": {
193 "top": 596 202 "action_arguments": {
194 }, 203 "newname": "Read clusters (with exon)"
195 "post_job_actions": { 204 },
196 "RenameDatasetActionoutputFileGff": { 205 "action_type": "RenameDatasetAction",
206 "output_name": "outputFileGff"
207 }
208 },
209 "tool_errors": null,
210 "tool_id": "toolshed.g2.bx.psu.edu/repos/yufei-luo/s_mart/MergingDataClusterize/1.0.0",
211 "tool_state": "{\"normalize\": \"\\\"False\\\"\", \"__page__\": 0, \"formatType\": \"{\\\"inputFileName\\\": null, \\\"__current_case__\\\": 4, \\\"FormatInputFileName\\\": \\\"sam\\\"}\", \"distance\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"colinear\": \"\\\"True\\\"\", \"chromInfo\": \"\\\"/srv/galaxy/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\"}",
212 "tool_version": "1.0.0",
213 "type": "tool",
214 "user_outputs": []
215 },
216 "6": {
217 "annotation": "Technical step: suppresses unwanted \"exon\" features created by the previous clustering step.",
218 "id": 6,
219 "input_connections": {
220 "inputFile": {
221 "id": 4,
222 "output_name": "outputFileGff"
223 }
224 },
225 "inputs": [],
226 "name": "remove exon lines",
227 "outputs": [
228 {
229 "name": "outputFile",
230 "type": "gff3"
231 }
232 ],
233 "position": {
234 "left": 892,
235 "top": 221.00001525878906
236 },
237 "post_job_actions": {
238 "RenameDatasetActionoutputFile": {
239 "action_arguments": {
240 "newname": "Annotation with operon-like (without exon)"
241 },
242 "action_type": "RenameDatasetAction",
243 "output_name": "outputFile"
244 }
245 },
246 "tool_errors": null,
247 "tool_id": "toolshed.g2.bx.psu.edu/repos/yufei-luo/s_mart/removeExonLines/1.0.0",
248 "tool_state": "{\"__page__\": 0, \"chromInfo\": \"\\\"/srv/galaxy/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\", \"inputFile\": \"null\"}",
249 "tool_version": "1.0.0",
250 "type": "tool",
251 "user_outputs": []
252 },
253 "7": {
254 "annotation": "Technical step: suppresses unwanted \"exon\" features created by the previous clustering step.",
255 "id": 7,
256 "input_connections": {
257 "inputFile": {
258 "id": 5,
259 "output_name": "outputFileGff"
260 }
261 },
262 "inputs": [],
263 "name": "remove exon lines",
264 "outputs": [
265 {
266 "name": "outputFile",
267 "type": "gff3"
268 }
269 ],
270 "position": {
271 "left": 892,
272 "top": 505.00001525878906
273 },
274 "post_job_actions": {
275 "RenameDatasetActionoutputFile": {
197 "action_arguments": { 276 "action_arguments": {
198 "newname": "Read clusters" 277 "newname": "Read clusters"
199 }, 278 },
200 "action_type": "RenameDatasetAction", 279 "action_type": "RenameDatasetAction",
201 "output_name": "outputFileGff" 280 "output_name": "outputFile"
202 } 281 }
203 }, 282 },
204 "tool_errors": null, 283 "tool_errors": null,
205 "tool_id": "toolshed.g2.bx.psu.edu/repos/yufei-luo/s_mart/MergingDataClusterize/1.0.0", 284 "tool_id": "toolshed.g2.bx.psu.edu/repos/yufei-luo/s_mart/removeExonLines/1.0.0",
206 "tool_state": "{\"normalize\": \"\\\"False\\\"\", \"distance\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"formatType\": \"{\\\"inputFileName\\\": null, \\\"__current_case__\\\": 5, \\\"FormatInputFileName\\\": \\\"sam\\\"}\", \"log\": \"\\\"False\\\"\", \"__page__\": 0, \"colinear\": \"\\\"True\\\"\", \"chromInfo\": \"\\\"/share/apps/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\"}", 285 "tool_state": "{\"__page__\": 0, \"chromInfo\": \"\\\"/srv/galaxy/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\", \"inputFile\": \"null\"}",
207 "tool_version": "1.0.0", 286 "tool_version": "1.0.0",
208 "type": "tool", 287 "type": "tool",
209 "user_outputs": [] 288 "user_outputs": []
210 }, 289 },
211 "6": { 290 "8": {
212 "annotation": "Selects read clusters that overlap annotations in the same direction. \nParameter to be set: RNA_gap.\nA read cluster separated from an annotation by a gap smaller than RNA_gap is selected (suggested value: 25).", 291 "annotation": "Technical step: orders the features by increasing positions.",
213 "id": 6, 292 "id": 8,
293 "input_connections": {
294 "formatType|inputFileName": {
295 "id": 6,
296 "output_name": "outputFile"
297 }
298 },
299 "inputs": [],
300 "name": "collapse reads",
301 "outputs": [
302 {
303 "name": "outputFileGff",
304 "type": "gff3"
305 }
306 ],
307 "position": {
308 "left": 1072,
309 "top": 261.00001525878906
310 },
311 "post_job_actions": {
312 "RenameDatasetActionoutputFileGff": {
313 "action_arguments": {
314 "newname": "Annotation list with operon-like feature"
315 },
316 "action_type": "RenameDatasetAction",
317 "output_name": "outputFileGff"
318 }
319 },
320 "tool_errors": null,
321 "tool_id": "toolshed.g2.bx.psu.edu/repos/yufei-luo/s_mart/collapseReads/1.0.0",
322 "tool_state": "{\"__page__\": 0, \"formatType\": \"{\\\"inputFileName\\\": null, \\\"__current_case__\\\": 3, \\\"FormatInputFileName\\\": \\\"gff3\\\"}\", \"chromInfo\": \"\\\"/srv/galaxy/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\", \"strand\": \"\\\"False\\\"\"}",
323 "tool_version": "1.0.0",
324 "type": "tool",
325 "user_outputs": []
326 },
327 "9": {
328 "annotation": "Selects read clusters that form new independent annotations. Parameter to be set: RNA_gap. Read clusters at a distance from existing annotations larger than RNA_gap are selected (suggested value: 25).",
329 "id": 9,
214 "input_connections": { 330 "input_connections": {
215 "formatType2|inputFileName2": { 331 "formatType2|inputFileName2": {
216 "id": 4,
217 "output_name": "outputFileGff"
218 },
219 "formatType|inputFileName1": {
220 "id": 5,
221 "output_name": "outputFileGff"
222 }
223 },
224 "inputs": [
225 {
226 "description": "runtime parameter for tool Compare Overlapping Small Query",
227 "name": "OptionDistance"
228 }
229 ],
230 "name": "Compare Overlapping Small Query",
231 "outputs": [
232 {
233 "name": "outputFileGff",
234 "type": "gff3"
235 }
236 ],
237 "position": {
238 "left": 659,
239 "top": 417
240 },
241 "post_job_actions": {
242 "RenameDatasetActionoutputFileGff": {
243 "action_arguments": {
244 "newname": "Read clusters overlapping annotation"
245 },
246 "action_type": "RenameDatasetAction",
247 "output_name": "outputFileGff"
248 }
249 },
250 "tool_errors": null,
251 "tool_id": "toolshed.g2.bx.psu.edu/repos/yufei-luo/s_mart/CompareOverlappingSmallQuery/1.0.0",
252 "tool_state": "{\"OptionInclusionQuery\": \"\\\"False\\\"\", \"NotOverlapping\": \"\\\"False\\\"\", \"formatType\": \"{\\\"FormatInputFileName1\\\": \\\"gff3\\\", \\\"inputFileName1\\\": null, \\\"__current_case__\\\": 3}\", \"InvertMatch\": \"\\\"False\\\"\", \"__page__\": 0, \"OptionInclusionRef\": \"\\\"False\\\"\", \"OptionDistance\": \"{\\\"distance\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"Dist\\\": \\\"Yes\\\", \\\"__current_case__\\\": 0}\", \"formatType2\": \"{\\\"FormatInputFileName2\\\": \\\"gff\\\", \\\"inputFileName2\\\": null, \\\"__current_case__\\\": 1}\", \"OptionPcOverlapQuery\": \"{\\\"present\\\": \\\"No\\\", \\\"__current_case__\\\": 1}\", \"OptionMinOverlap\": \"{\\\"present\\\": \\\"No\\\", \\\"__current_case__\\\": 1}\", \"OptionCollinearOrAntiSens\": \"{\\\"__current_case__\\\": 0, \\\"OptionCA\\\": \\\"Collinear\\\"}\", \"OptionPcOverlapRef\": \"{\\\"present\\\": \\\"No\\\", \\\"__current_case__\\\": 1}\"}",
253 "tool_version": "1.0.0",
254 "type": "tool",
255 "user_outputs": []
256 },
257 "7": {
258 "annotation": "Selects read clusters that form new independent annotations. \nParameter to be set: RNA_gap.\nRead clusters at a distance from existing annotations larger than RNA_gap are selected. Caution: use same RNA_gap value as in previous step!",
259 "id": 7,
260 "input_connections": {
261 "formatType2|inputFileName2": {
262 "id": 4,
263 "output_name": "outputFileGff"
264 },
265 "formatType|inputFileName1": {
266 "id": 5,
267 "output_name": "outputFileGff"
268 }
269 },
270 "inputs": [
271 {
272 "description": "runtime parameter for tool Compare Overlapping Small Query",
273 "name": "OptionDistance"
274 }
275 ],
276 "name": "Compare Overlapping Small Query",
277 "outputs": [
278 {
279 "name": "outputFileGff",
280 "type": "gff3"
281 }
282 ],
283 "position": {
284 "left": 742,
285 "top": 588
286 },
287 "post_job_actions": {
288 "RenameDatasetActionoutputFileGff": {
289 "action_arguments": {
290 "newname": "Read clusters not overlapping annotation"
291 },
292 "action_type": "RenameDatasetAction",
293 "output_name": "outputFileGff"
294 }
295 },
296 "tool_errors": null,
297 "tool_id": "toolshed.g2.bx.psu.edu/repos/yufei-luo/s_mart/CompareOverlappingSmallQuery/1.0.0",
298 "tool_state": "{\"OptionInclusionQuery\": \"\\\"False\\\"\", \"NotOverlapping\": \"\\\"False\\\"\", \"formatType\": \"{\\\"FormatInputFileName1\\\": \\\"gff3\\\", \\\"inputFileName1\\\": null, \\\"__current_case__\\\": 3}\", \"InvertMatch\": \"\\\"True\\\"\", \"__page__\": 0, \"OptionInclusionRef\": \"\\\"False\\\"\", \"OptionDistance\": \"{\\\"distance\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"Dist\\\": \\\"Yes\\\", \\\"__current_case__\\\": 0}\", \"formatType2\": \"{\\\"FormatInputFileName2\\\": \\\"gff\\\", \\\"inputFileName2\\\": null, \\\"__current_case__\\\": 1}\", \"OptionPcOverlapQuery\": \"{\\\"present\\\": \\\"No\\\", \\\"__current_case__\\\": 1}\", \"OptionMinOverlap\": \"{\\\"present\\\": \\\"No\\\", \\\"__current_case__\\\": 1}\", \"OptionCollinearOrAntiSens\": \"{\\\"__current_case__\\\": 0, \\\"OptionCA\\\": \\\"Collinear\\\"}\", \"OptionPcOverlapRef\": \"{\\\"present\\\": \\\"No\\\", \\\"__current_case__\\\": 1}\"}",
299 "tool_version": "1.0.0",
300 "type": "tool",
301 "user_outputs": []
302 },
303 "8": {
304 "annotation": "Technical step: merging of annotations and their overlapping read clusters. This will be used to extend annotation.",
305 "id": 8,
306 "input_connections": {
307 "input1": {
308 "id": 4,
309 "output_name": "outputFileGff"
310 },
311 "queries_0|input2": {
312 "id": 6,
313 "output_name": "outputFileGff"
314 }
315 },
316 "inputs": [],
317 "name": "Concatenate datasets",
318 "outputs": [
319 {
320 "name": "out_file1",
321 "type": "input"
322 }
323 ],
324 "position": {
325 "left": 819,
326 "top": 294
327 },
328 "post_job_actions": {
329 "RenameDatasetActionout_file1": {
330 "action_arguments": {
331 "newname": "Annotations and read clusters overlapping them"
332 },
333 "action_type": "RenameDatasetAction",
334 "output_name": "out_file1"
335 }
336 },
337 "tool_errors": null,
338 "tool_id": "cat1",
339 "tool_state": "{\"__page__\": 0, \"input1\": \"null\", \"chromInfo\": \"\\\"/share/apps/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\", \"queries\": \"[{\\\"input2\\\": null, \\\"__index__\\\": 0}]\"}",
340 "tool_version": "1.0.0",
341 "type": "tool",
342 "user_outputs": []
343 },
344 "9": {
345 "annotation": "Extend annotations with overlapping or proximal read clusters in the same direction. \nParameter to be set: RNA_gap.\nRead cluster and annotations separated by a gap smaller than RNA_gap are clustered. Caution: use the same RNA_gap value as previous step!",
346 "id": 9,
347 "input_connections": {
348 "formatType|inputFileName": {
349 "id": 8, 332 "id": 8,
350 "output_name": "out_file1"
351 }
352 },
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538 "tool_version": "1.0.0",
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626 "16": {
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718 "output_name": "outputFileGff"
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740 }
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761 "name": "distance"
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768 "type": "gff3"
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770 {
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772 "type": "txt"
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779 "post_job_actions": {
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783 },
784 "action_type": "RenameDatasetAction",
785 "output_name": "outputFileGff"
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791 "tool_version": "1.0.0",
792 "type": "tool",
793 "user_outputs": []
794 },
795 "20": {
796 "annotation": "Clusters proximal small RNAs in the same direction.\nParameter to be set: RNA_merge.\nSmall RNAs located less than RNA_merge apart are merged (suggestion: 50).",
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798 "input_connections": {
799 "formatType|inputFileName": {
800 "id": 17,
801 "output_name": "outputFileGff"
802 }
803 },
804 "inputs": [],
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808 "name": "outputFileGff",
809 "type": "gff3"
810 },
811 {
812 "name": "outputFileLog",
813 "type": "txt"
814 }
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842 "output_name": "outputFileGff"
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851 }
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870 "type": "tool",
871 "user_outputs": []
872 },
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874 "annotation": "Technical step: suppresses unwanted \"exon\" features created by the use of the distance option in the previous clustering step.",
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878 "id": 19,
879 "output_name": "outputFileGff"
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881 },
882 "inputs": [],
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886 "name": "out_file1",
887 "type": "input"
888 }
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892 "top": 682
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894 "post_job_actions": {
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899 "action_type": "RenameDatasetAction",
900 "output_name": "out_file1"
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907 "type": "tool",
908 "user_outputs": []
909 },
910 "23": {
911 "annotation": "Technical step: suppresses unwanted \"exon\" features created by the use of the distance option in the previous clustering step.",
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915 "id": 20,
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924 "type": "input"
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930 },
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945 "user_outputs": []
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950 "input_connections": {
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986 "type": "tool",
987 "user_outputs": []
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992 "input_connections": {
993 "formatType|inputFileName": {
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1004 "name": "restrict from size",
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1008 "type": "gff3"
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1013 "top": 691
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1028 "type": "tool",
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1034 "input_connections": {
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1091 "name": "outputFileGff",
1092 "type": "gff3"
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1208 "top": 610
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1232 "output_name": "outputFile"
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1240 "type": "gff"
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1245 "top": 727
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1260 "type": "tool",
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1282 "top": 827
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