Mercurial > repos > peterjc > secreted_protein_workflow

annotate secreted_protein_workflow.ga @ 0:3a6de5cb858d draft

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Uploaded first attempt at a workflow with dependencies on the Tool Shed
author peterjc
date Mon, 06 May 2013 11:11:11 -0400
parents
children 36b2c2b5051e
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3a6de5cb858d Uploaded first attempt at a workflow with dependencies on the Tool Shed
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1 {
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2 "a_galaxy_workflow": "true",
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3 "annotation": "Runs SignalP v3.0 and TMHMM v2.0 to look for secreted proteins.",
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4 "format-version": "0.1",
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5 "name": "Find secreted proteins with TMHMM and SignalP",
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6 "steps": {
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7 "0": {
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8 "annotation": "",
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9 "id": 0,
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10 "input_connections": {},
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11 "inputs": [
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12 {
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13 "description": "",
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14 "name": "Input Dataset"
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15 }
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16 ],
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17 "name": "Input dataset",
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18 "outputs": [],
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19 "position": {
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21 "top": 200
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22 },
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23 "tool_errors": null,
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24 "tool_id": null,
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25 "tool_state": "{\"name\": \"Input Dataset\"}",
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26 "tool_version": null,
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27 "type": "data_input",
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28 "user_outputs": []
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29 },
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30 "1": {
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31 "annotation": "",
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32 "id": 1,
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33 "input_connections": {
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34 "fasta_file": {
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35 "id": 0,
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36 "output_name": "output"
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37 }
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38 },
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39 "inputs": [
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40 {
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41 "description": "runtime parameter for tool SignalP 3.0",
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42 "name": "organism"
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43 }
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44 ],
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45 "name": "SignalP 3.0",
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46 "outputs": [
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47 {
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48 "name": "tabular_file",
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49 "type": "tabular"
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50 }
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51 ],
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52 "position": {
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55 },
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56 "post_job_actions": {
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57 "HideDatasetActiontabular_file": {
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58 "action_arguments": {},
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59 "action_type": "HideDatasetAction",
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60 "output_name": "tabular_file"
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61 }
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62 },
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63 "tool_errors": null,
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64 "tool_id": "signalp3",
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65 "tool_state": "{\"organism\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"fasta_file\": \"null\", \"chromInfo\": \"\\\"/opt/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\", \"truncate\": \"\\\"60\\\"\", \"__page__\": 0}",
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66 "tool_version": "0.0.8",
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67 "type": "tool",
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68 "user_outputs": []
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69 },
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70 "2": {
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71 "annotation": "Select proteins with predicted signal peptide (SignalP NN D-Score or HMM)",
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72 "id": 2,
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91 "post_job_actions": {
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92 "HideDatasetActionout_file1": {
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94 "action_type": "HideDatasetAction",
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98 "action_arguments": {
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99 "newname": "Filtered SignalP results"
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103 }
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104 },
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106 "tool_id": "Filter1",
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107 "tool_state": "{\"__page__\": 0, \"cond\": \"\\\"c14=='Y' or c15=='S'\\\"\", \"chromInfo\": \"\\\"/opt/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\", \"input\": \"null\"}",
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108 "tool_version": "1.1.0",
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109 "type": "tool",
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110 "user_outputs": []
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111 },
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112 "3": {
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113 "annotation": "Select those sequences with signal peptides.",
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114 "id": 3,
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115 "input_connections": {
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117 "id": 0,
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118 "output_name": "output"
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119 },
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120 "input_tabular": {
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121 "id": 2,
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122 "output_name": "out_file1"
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123 }
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124 },
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125 "inputs": [],
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126 "name": "Filter sequences by ID",
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127 "outputs": [
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128 {
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129 "name": "output_pos",
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130 "type": "fasta"
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131 },
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132 {
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133 "name": "output_neg",
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134 "type": "fasta"
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135 }
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136 ],
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143 "action_arguments": {},
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144 "action_type": "HideDatasetAction",
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145 "output_name": "output_neg"
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146 },
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147 "HideDatasetActionoutput_pos": {
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148 "action_arguments": {},
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149 "action_type": "HideDatasetAction",
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150 "output_name": "output_pos"
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151 }
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152 },
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153 "tool_errors": null,
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154 "tool_id": "seq_filter_by_id",
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155 "tool_state": "{\"__page__\": 0, \"output_choice_cond\": \"{\\\"output_choice\\\": \\\"pos\\\", \\\"__current_case__\\\": 1}\", \"input_file\": \"null\", \"input_tabular\": \"null\", \"chromInfo\": \"\\\"/opt/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\", \"columns\": \"{\\\"__class__\\\": \\\"UnvalidatedValue\\\", \\\"value\\\": [\\\"1\\\"]}\"}",
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156 "tool_version": "0.0.1",
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157 "type": "tool",
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158 "user_outputs": []
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159 },
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160 "4": {
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161 "annotation": "",
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202 }
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203 },
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207 {
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210 }
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211 ],
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215 },
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219 "action_type": "HideDatasetAction",
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220 "output_name": "out_file1"
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221 },
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225 },
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226 "action_type": "RenameDatasetAction",
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227 "output_name": "out_file1"
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228 }
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229 },
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232 "tool_state": "{\"__page__\": 0, \"cond\": \"\\\"c5== 0\\\"\", \"chromInfo\": \"\\\"/opt/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\", \"input\": \"null\"}",
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233 "tool_version": "1.1.0",
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236 },
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237 "6": {
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238 "annotation": "Select those sequences with no transmembrane helices (from those with signal peptides).",
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244 },
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247 "output_name": "out_file1"
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248 }
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249 },
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251 "name": "Filter sequences by ID",
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253 {
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254 "name": "output_pos",
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255 "type": "fasta"
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256 },
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257 {
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260 }
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261 ],
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271 },
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274 "newname": "Secreted proteins"
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275 },
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276 "action_type": "RenameDatasetAction",
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277 "output_name": "output_pos"
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278 }
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279 },
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282 "tool_state": "{\"__page__\": 0, \"output_choice_cond\": \"{\\\"output_choice\\\": \\\"pos\\\", \\\"__current_case__\\\": 1}\", \"input_file\": \"null\", \"input_tabular\": \"null\", \"chromInfo\": \"\\\"/opt/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\", \"columns\": \"{\\\"__class__\\\": \\\"UnvalidatedValue\\\", \\\"value\\\": [\\\"1\\\"]}\"}",
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283 "tool_version": "0.0.1",
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284 "type": "tool",
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286 }
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287 }
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288 }