Mercurial > repos > peterjc > blast_top_hit_species

comparison blast_top_hit_species.ga @ 0:2e96bf82b463 draft

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Uploaded first attempt at Tool Shed package
author peterjc
date Mon, 30 Mar 2015 11:07:48 -0400
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-1:000000000000 0:2e96bf82b463
1 {
2 "a_galaxy_workflow": "true",
3 "annotation": "",
4 "format-version": "0.1",
5 "name": "Species of top BLAST hits",
6 "steps": {
7 "0": {
8 "annotation": "",
9 "id": 0,
10 "input_connections": {},
11 "inputs": [
12 {
13 "description": "",
14 "name": "Transcriptome FASTA file"
15 }
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18 "name": "Input dataset",
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22 "top": 119
23 },
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25 "tool_id": null,
26 "tool_state": "{\"name\": \"Transcriptome FASTA file\"}",
27 "tool_version": null,
28 "type": "data_input",
29 "user_outputs": [],
30 "uuid": "e445b44b-02a7-4fd1-8944-cd680f967062"
31 },
32 "1": {
33 "annotation": "This workflow is deliberately a simple/crude assessment, and there is no need to run BLASTX on all the sequences - a sample of 1000 should be enough.",
34 "id": 1,
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37 "id": 0,
38 "output_name": "output"
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43 "name": "Sub-sample sequences files",
44 "outputs": [
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47 "type": "input"
48 }
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54 "post_job_actions": {
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61 }
62 },
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64 "tool_id": "toolshed.g2.bx.psu.edu/repos/peterjc/sample_seqs/sample_seqs/0.2.1",
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71 "2": {
72 "annotation": "We only want one line per query, so limit this to the best scoring target sequence. Assumes current NCBI nr database is available locally as \"nr\".",
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74 "input_connections": {
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76 "id": 1,
77 "output_name": "output_file"
78 }
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80 "inputs": [],
81 "label": null,
82 "name": "NCBI BLAST+ blastx",
83 "outputs": [
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86 "type": "tabular"
87 }
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92 },
93 "post_job_actions": {
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111 "annotation": "Having a tabular file of all 1000 sequences is used in the \"join\" step to count the sequences giving no BLAST hit.",
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115 "id": 1,
116 "output_name": "output_file"
117 }
118 },
119 "inputs": [],
120 "label": null,
121 "name": "FASTA-to-Tabular",
122 "outputs": [
123 {
124 "name": "output",
125 "type": "tabular"
126 }
127 ],
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131 },
132 "post_job_actions": {
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135 "action_type": "HideDatasetAction",
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149 "tool_version": "1.1.0",
150 "type": "tool",
151 "user_outputs": [],
152 "uuid": "31f11208-b2bd-4d9d-9745-dc1a6ed7ccf9"
153 },
154 "4": {
155 "annotation": "Some BLAST matches will give multiple HSPs, and thus multiple lines in the tabular output. We only want one line per query.",
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158 "input": {
159 "id": 2,
160 "output_name": "output1"
161 }
162 },
163 "inputs": [],
164 "label": null,
165 "name": "Unique",
166 "outputs": [
167 {
168 "name": "outfile",
169 "type": "input"
170 }
171 ],
172 "position": {
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174 "top": 376
175 },
176 "post_job_actions": {
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179 "action_type": "HideDatasetAction",
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184 "newname": "One HSP per BLAST hit"
185 },
186 "action_type": "RenameDatasetAction",
187 "output_name": "outfile"
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192 "tool_state": "{\"__page__\": 0, \"ignore_case\": \"\\\"False\\\"\", \"adv_opts\": \"{\\\"column_end\\\": {\\\"__class__\\\": \\\"UnvalidatedValue\\\", \\\"value\\\": \\\"2\\\"}, \\\"column_start\\\": {\\\"__class__\\\": \\\"UnvalidatedValue\\\", \\\"value\\\": \\\"1\\\"}, \\\"adv_opts_selector\\\": \\\"advanced\\\", \\\"__current_case__\\\": 1}\", \"__rerun_remap_job_id__\": null, \"is_numeric\": \"\\\"False\\\"\", \"input\": \"null\", \"chromInfo\": \"\\\"/mnt/galaxy/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\"}",
193 "tool_version": "0.3",
194 "type": "tool",
195 "user_outputs": [],
196 "uuid": "acf948e3-71dc-4f35-8357-3998bd0abdd8"
197 },
198 "5": {
199 "annotation": "We don't need all the columns in this join, but the key is to assign \"None\" to the sequences with no BLAST hits.",
200 "id": 5,
201 "input_connections": {
202 "input1": {
203 "id": 3,
204 "output_name": "output"
205 },
206 "input2": {
207 "id": 4,
208 "output_name": "outfile"
209 }
210 },
211 "inputs": [],
212 "label": null,
213 "name": "Join two Datasets",
214 "outputs": [
215 {
216 "name": "out_file1",
217 "type": "input"
218 }
219 ],
220 "position": {
221 "left": 827,
222 "top": 263
223 },
224 "post_job_actions": {
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227 "action_type": "HideDatasetAction",
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232 "newname": "Top BLAST hits or None"
233 },
234 "action_type": "RenameDatasetAction",
235 "output_name": "out_file1"
236 }
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243 "user_outputs": [],
244 "uuid": "4c280b0e-b4a6-4ae4-8a81-d6e93932ef71"
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246 "6": {
247 "annotation": "Here we make a tally table of the BLAST species name column",
248 "id": 6,
249 "input_connections": {
250 "input": {
251 "id": 5,
252 "output_name": "out_file1"
253 }
254 },
255 "inputs": [],
256 "label": null,
257 "name": "Count",
258 "outputs": [
259 {
260 "name": "out_file1",
261 "type": "tabular"
262 }
263 ],
264 "position": {
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266 "top": 398
267 },
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271 "action_type": "HideDatasetAction",
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275 "action_arguments": {
276 "newname": "Top BLAST hit species counts (unsorted)"
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278 "action_type": "RenameDatasetAction",
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285 "tool_version": "1.0.0",
286 "type": "tool",
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290 "7": {
291 "annotation": "Sorting the counts makes the results easier to interpret directly.",
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294 "input": {
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297 }
298 },
299 "inputs": [],
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305 "type": "input"
306 }
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312 "post_job_actions": {
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