Mercurial > repos > peterjc > rxlr_venn_workflow
annotate rxlr_venn_workflow.ga @ 5:4726b640f221 draft default tip
Uploaded revision to update the citation
author | peterjc |
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date | Fri, 25 Oct 2013 10:20:46 -0400 |
parents | 3c280e01b920 |
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rev | line source |
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0
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1 { |
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2 "a_galaxy_workflow": "true", |
5 | 3 "annotation": "Takes a protein FASTA file, runs three different RXLR motif methods, draws a Venn diagram comparing them, and creates a FASTA file of those proteins passing all three screens.<br />\n<br />\nThis workflow is <a href=\"http://toolshed.g2.bx.psu.edu/view/peterjc/rxlr_venn_workflow\" target=\"_blank\">available on the Galaxy Tool Shed</a> with a README file giving more information including sample data, and full citation details (Cock and Pritchard 2014).", |
0
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4 "format-version": "0.1", |
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5 "name": "3 RXLR methods, Venn Diagram, overlap FASTA", |
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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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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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20 "left": 200, |
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21 "top": 363 |
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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 "name": "RXLR Motifs", |
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41 "outputs": [ |
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42 { |
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43 "name": "tabular_file", |
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44 "type": "tabular" |
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45 } |
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46 ], |
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47 "position": { |
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48 "left": 420, |
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49 "top": 363 |
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50 }, |
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51 "post_job_actions": { |
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52 "HideDatasetActiontabular_file": { |
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53 "action_arguments": {}, |
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54 "action_type": "HideDatasetAction", |
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55 "output_name": "tabular_file" |
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56 } |
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57 }, |
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58 "tool_errors": null, |
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59 "tool_id": "rxlr_motifs", |
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60 "tool_state": "{\"__page__\": 0, \"fasta_file\": \"null\", \"__rerun_remap_job_id__\": null, \"chromInfo\": \"\\\"/opt/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\", \"model\": \"\\\"Whisson2007\\\"\"}", |
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61 "tool_version": "0.0.7", |
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62 "type": "tool", |
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63 "user_outputs": [] |
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64 }, |
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65 "2": { |
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66 "annotation": "", |
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67 "id": 2, |
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68 "input_connections": { |
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69 "fasta_file": { |
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70 "id": 0, |
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71 "output_name": "output" |
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72 } |
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73 }, |
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74 "inputs": [], |
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75 "name": "RXLR Motifs", |
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76 "outputs": [ |
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77 { |
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78 "name": "tabular_file", |
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79 "type": "tabular" |
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80 } |
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81 ], |
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82 "position": { |
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83 "left": 420, |
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84 "top": 483 |
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85 }, |
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86 "post_job_actions": { |
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87 "HideDatasetActiontabular_file": { |
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88 "action_arguments": {}, |
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89 "action_type": "HideDatasetAction", |
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90 "output_name": "tabular_file" |
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91 } |
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92 }, |
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93 "tool_errors": null, |
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94 "tool_id": "rxlr_motifs", |
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95 "tool_state": "{\"__page__\": 0, \"fasta_file\": \"null\", \"__rerun_remap_job_id__\": null, \"chromInfo\": \"\\\"/opt/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\", \"model\": \"\\\"Win2007\\\"\"}", |
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96 "tool_version": "0.0.7", |
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97 "type": "tool", |
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98 "user_outputs": [] |
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99 }, |
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100 "3": { |
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101 "annotation": "", |
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102 "id": 3, |
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103 "input_connections": { |
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104 "fasta_file": { |
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105 "id": 0, |
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106 "output_name": "output" |
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107 } |
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108 }, |
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109 "inputs": [], |
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110 "name": "RXLR Motifs", |
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111 "outputs": [ |
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112 { |
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113 "name": "tabular_file", |
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114 "type": "tabular" |
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115 } |
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116 ], |
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117 "position": { |
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118 "left": 420, |
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119 "top": 603 |
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120 }, |
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121 "post_job_actions": { |
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122 "HideDatasetActiontabular_file": { |
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123 "action_arguments": {}, |
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124 "action_type": "HideDatasetAction", |
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125 "output_name": "tabular_file" |
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126 } |
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127 }, |
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128 "tool_errors": null, |
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129 "tool_id": "rxlr_motifs", |
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130 "tool_state": "{\"__page__\": 0, \"fasta_file\": \"null\", \"__rerun_remap_job_id__\": null, \"chromInfo\": \"\\\"/opt/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\", \"model\": \"\\\"Bhattacharjee2006\\\"\"}", |
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131 "tool_version": "0.0.7", |
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132 "type": "tool", |
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Uploaded v0.0.1, includes README file and dependencies.
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207 }, |
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208 "action_type": "RenameDatasetAction", |
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|
212 "tool_errors": null, |
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Uploaded v0.0.1, includes README file and dependencies.
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|
213 "tool_id": "Filter1", |
4
3c280e01b920
Uploaded v0.0.2, bump tool version numbers to fix warning about Filter1 parameter, adding link to Tool Shed in annotation. No functional changes.
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0
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|
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0
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215 "tool_version": "1.1.0", |
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223 "input": { |
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225 "output_name": "tabular_file" |
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232 "name": "out_file1", |
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peterjc
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|
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247 "action_arguments": { |
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248 "newname": "Positive Bhattacharjee et al. (2006) results" |
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Uploaded v0.0.1, includes README file and dependencies.
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250 "action_type": "RenameDatasetAction", |
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251 "output_name": "out_file1" |
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252 } |
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253 }, |
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254 "tool_errors": null, |
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255 "tool_id": "Filter1", |
4
3c280e01b920
Uploaded v0.0.2, bump tool version numbers to fix warning about Filter1 parameter, adding link to Tool Shed in annotation. No functional changes.
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0
diff
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|
256 "tool_state": "{\"__page__\": 0, \"__rerun_remap_job_id__\": null, \"cond\": \"\\\"c2=='Y'\\\"\", \"input\": \"null\", \"header_lines\": \"\\\"0\\\"\", \"chromInfo\": \"\\\"/opt/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\"}", |
0
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257 "tool_version": "1.1.0", |
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258 "type": "tool", |
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260 }, |
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263 "id": 7, |
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264 "input_connections": { |
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267 "output_name": "output" |
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Uploaded v0.0.1, includes README file and dependencies.
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Uploaded v0.0.1, includes README file and dependencies.
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Uploaded v0.0.1, includes README file and dependencies.
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Uploaded v0.0.1, includes README file and dependencies.
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Uploaded v0.0.1, includes README file and dependencies.
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Uploaded v0.0.1, includes README file and dependencies.
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Uploaded v0.0.1, includes README file and dependencies.
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Uploaded v0.0.1, includes README file and dependencies.
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Uploaded v0.0.1, includes README file and dependencies.
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Uploaded v0.0.1, includes README file and dependencies.
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Uploaded v0.0.1, includes README file and dependencies.
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Uploaded v0.0.1, includes README file and dependencies.
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Uploaded v0.0.1, includes README file and dependencies.
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Uploaded v0.0.1, includes README file and dependencies.
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Uploaded v0.0.1, includes README file and dependencies.
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Uploaded v0.0.1, includes README file and dependencies.
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Uploaded v0.0.1, includes README file and dependencies.
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Uploaded v0.0.1, includes README file and dependencies.
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diff
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Uploaded v0.0.1, includes README file and dependencies.
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Uploaded v0.0.1, includes README file and dependencies.
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Uploaded v0.0.1, includes README file and dependencies.
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Uploaded v0.0.1, includes README file and dependencies.
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Uploaded v0.0.1, includes README file and dependencies.
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Uploaded v0.0.1, includes README file and dependencies.
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Uploaded v0.0.1, includes README file and dependencies.
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3c280e01b920
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peterjc
parents:
0
diff
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Uploaded v0.0.1, includes README file and dependencies.
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Uploaded v0.0.1, includes README file and dependencies.
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Uploaded v0.0.1, includes README file and dependencies.
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Uploaded v0.0.1, includes README file and dependencies.
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Uploaded v0.0.1, includes README file and dependencies.
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Uploaded v0.0.1, includes README file and dependencies.
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Uploaded v0.0.1, includes README file and dependencies.
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diff
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403 "output_name": "output_pos" |
0e7c07ff11f9
Uploaded v0.0.1, includes README file and dependencies.
peterjc
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404 }, |
0e7c07ff11f9
Uploaded v0.0.1, includes README file and dependencies.
peterjc
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405 "RenameDatasetActionoutput_pos": { |
0e7c07ff11f9
Uploaded v0.0.1, includes README file and dependencies.
peterjc
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406 "action_arguments": { |
0e7c07ff11f9
Uploaded v0.0.1, includes README file and dependencies.
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407 "newname": "Positive Whisson et al. (2007) and Win et al. (2007) results" |
0e7c07ff11f9
Uploaded v0.0.1, includes README file and dependencies.
peterjc
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408 }, |
0e7c07ff11f9
Uploaded v0.0.1, includes README file and dependencies.
peterjc
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409 "action_type": "RenameDatasetAction", |
0e7c07ff11f9
Uploaded v0.0.1, includes README file and dependencies.
peterjc
parents:
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410 "output_name": "output_pos" |
0e7c07ff11f9
Uploaded v0.0.1, includes README file and dependencies.
peterjc
parents:
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411 } |
0e7c07ff11f9
Uploaded v0.0.1, includes README file and dependencies.
peterjc
parents:
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412 }, |
0e7c07ff11f9
Uploaded v0.0.1, includes README file and dependencies.
peterjc
parents:
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413 "tool_errors": null, |
0e7c07ff11f9
Uploaded v0.0.1, includes README file and dependencies.
peterjc
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414 "tool_id": "seq_filter_by_id", |
4
3c280e01b920
Uploaded v0.0.2, bump tool version numbers to fix warning about Filter1 parameter, adding link to Tool Shed in annotation. No functional changes.
peterjc
parents:
0
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415 "tool_state": "{\"__page__\": 0, \"output_choice_cond\": \"{\\\"output_choice\\\": \\\"pos\\\", \\\"__current_case__\\\": 1}\", \"input_file\": \"null\", \"__rerun_remap_job_id__\": null, \"input_tabular\": \"null\", \"chromInfo\": \"\\\"/opt/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\", \"columns\": \"{\\\"__class__\\\": \\\"UnvalidatedValue\\\", \\\"value\\\": [\\\"1\\\"]}\"}", |
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0e7c07ff11f9
Uploaded v0.0.1, includes README file and dependencies.
peterjc
parents:
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416 "tool_version": "0.0.5", |
0e7c07ff11f9
Uploaded v0.0.1, includes README file and dependencies.
peterjc
parents:
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417 "type": "tool", |
0e7c07ff11f9
Uploaded v0.0.1, includes README file and dependencies.
peterjc
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418 "user_outputs": [] |
0e7c07ff11f9
Uploaded v0.0.1, includes README file and dependencies.
peterjc
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419 }, |
0e7c07ff11f9
Uploaded v0.0.1, includes README file and dependencies.
peterjc
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420 "10": { |
0e7c07ff11f9
Uploaded v0.0.1, includes README file and dependencies.
peterjc
parents:
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421 "annotation": "", |
0e7c07ff11f9
Uploaded v0.0.1, includes README file and dependencies.
peterjc
parents:
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422 "id": 10, |
0e7c07ff11f9
Uploaded v0.0.1, includes README file and dependencies.
peterjc
parents:
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423 "input_connections": { |
0e7c07ff11f9
Uploaded v0.0.1, includes README file and dependencies.
peterjc
parents:
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424 "input_file": { |
0e7c07ff11f9
Uploaded v0.0.1, includes README file and dependencies.
peterjc
parents:
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425 "id": 9, |
0e7c07ff11f9
Uploaded v0.0.1, includes README file and dependencies.
peterjc
parents:
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426 "output_name": "output_pos" |
0e7c07ff11f9
Uploaded v0.0.1, includes README file and dependencies.
peterjc
parents:
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|
427 }, |
0e7c07ff11f9
Uploaded v0.0.1, includes README file and dependencies.
peterjc
parents:
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428 "input_tabular": { |
0e7c07ff11f9
Uploaded v0.0.1, includes README file and dependencies.
peterjc
parents:
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429 "id": 6, |
0e7c07ff11f9
Uploaded v0.0.1, includes README file and dependencies.
peterjc
parents:
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430 "output_name": "out_file1" |
0e7c07ff11f9
Uploaded v0.0.1, includes README file and dependencies.
peterjc
parents:
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|
431 } |
0e7c07ff11f9
Uploaded v0.0.1, includes README file and dependencies.
peterjc
parents:
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432 }, |
0e7c07ff11f9
Uploaded v0.0.1, includes README file and dependencies.
peterjc
parents:
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|
433 "inputs": [], |
0e7c07ff11f9
Uploaded v0.0.1, includes README file and dependencies.
peterjc
parents:
diff
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|
434 "name": "Filter sequences by ID", |
0e7c07ff11f9
Uploaded v0.0.1, includes README file and dependencies.
peterjc
parents:
diff
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|
435 "outputs": [ |
0e7c07ff11f9
Uploaded v0.0.1, includes README file and dependencies.
peterjc
parents:
diff
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|
436 { |
0e7c07ff11f9
Uploaded v0.0.1, includes README file and dependencies.
peterjc
parents:
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|
437 "name": "output_pos", |
0e7c07ff11f9
Uploaded v0.0.1, includes README file and dependencies.
peterjc
parents:
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|
438 "type": "fasta" |
0e7c07ff11f9
Uploaded v0.0.1, includes README file and dependencies.
peterjc
parents:
diff
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|
439 }, |
0e7c07ff11f9
Uploaded v0.0.1, includes README file and dependencies.
peterjc
parents:
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|
440 { |
0e7c07ff11f9
Uploaded v0.0.1, includes README file and dependencies.
peterjc
parents:
diff
changeset
|
441 "name": "output_neg", |
0e7c07ff11f9
Uploaded v0.0.1, includes README file and dependencies.
peterjc
parents:
diff
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|
442 "type": "fasta" |
0e7c07ff11f9
Uploaded v0.0.1, includes README file and dependencies.
peterjc
parents:
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|
443 } |
0e7c07ff11f9
Uploaded v0.0.1, includes README file and dependencies.
peterjc
parents:
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444 ], |
0e7c07ff11f9
Uploaded v0.0.1, includes README file and dependencies.
peterjc
parents:
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|
445 "position": { |
0e7c07ff11f9
Uploaded v0.0.1, includes README file and dependencies.
peterjc
parents:
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|
446 "left": 1641, |
0e7c07ff11f9
Uploaded v0.0.1, includes README file and dependencies.
peterjc
parents:
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|
447 "top": 391 |
0e7c07ff11f9
Uploaded v0.0.1, includes README file and dependencies.
peterjc
parents:
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|
448 }, |
0e7c07ff11f9
Uploaded v0.0.1, includes README file and dependencies.
peterjc
parents:
diff
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|
449 "post_job_actions": { |
0e7c07ff11f9
Uploaded v0.0.1, includes README file and dependencies.
peterjc
parents:
diff
changeset
|
450 "HideDatasetActionoutput_neg": { |
0e7c07ff11f9
Uploaded v0.0.1, includes README file and dependencies.
peterjc
parents:
diff
changeset
|
451 "action_arguments": {}, |
0e7c07ff11f9
Uploaded v0.0.1, includes README file and dependencies.
peterjc
parents:
diff
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|
452 "action_type": "HideDatasetAction", |
0e7c07ff11f9
Uploaded v0.0.1, includes README file and dependencies.
peterjc
parents:
diff
changeset
|
453 "output_name": "output_neg" |
0e7c07ff11f9
Uploaded v0.0.1, includes README file and dependencies.
peterjc
parents:
diff
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|
454 }, |
0e7c07ff11f9
Uploaded v0.0.1, includes README file and dependencies.
peterjc
parents:
diff
changeset
|
455 "RenameDatasetActionoutput_pos": { |
0e7c07ff11f9
Uploaded v0.0.1, includes README file and dependencies.
peterjc
parents:
diff
changeset
|
456 "action_arguments": { |
0e7c07ff11f9
Uploaded v0.0.1, includes README file and dependencies.
peterjc
parents:
diff
changeset
|
457 "newname": "RXLR by all 3 methods" |
0e7c07ff11f9
Uploaded v0.0.1, includes README file and dependencies.
peterjc
parents:
diff
changeset
|
458 }, |
0e7c07ff11f9
Uploaded v0.0.1, includes README file and dependencies.
peterjc
parents:
diff
changeset
|
459 "action_type": "RenameDatasetAction", |
0e7c07ff11f9
Uploaded v0.0.1, includes README file and dependencies.
peterjc
parents:
diff
changeset
|
460 "output_name": "output_pos" |
0e7c07ff11f9
Uploaded v0.0.1, includes README file and dependencies.
peterjc
parents:
diff
changeset
|
461 } |
0e7c07ff11f9
Uploaded v0.0.1, includes README file and dependencies.
peterjc
parents:
diff
changeset
|
462 }, |
0e7c07ff11f9
Uploaded v0.0.1, includes README file and dependencies.
peterjc
parents:
diff
changeset
|
463 "tool_errors": null, |
0e7c07ff11f9
Uploaded v0.0.1, includes README file and dependencies.
peterjc
parents:
diff
changeset
|
464 "tool_id": "seq_filter_by_id", |
4
3c280e01b920
Uploaded v0.0.2, bump tool version numbers to fix warning about Filter1 parameter, adding link to Tool Shed in annotation. No functional changes.
peterjc
parents:
0
diff
changeset
|
465 "tool_state": "{\"__page__\": 0, \"output_choice_cond\": \"{\\\"output_choice\\\": \\\"pos\\\", \\\"__current_case__\\\": 1}\", \"input_file\": \"null\", \"__rerun_remap_job_id__\": null, \"input_tabular\": \"null\", \"chromInfo\": \"\\\"/opt/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\", \"columns\": \"{\\\"__class__\\\": \\\"UnvalidatedValue\\\", \\\"value\\\": [\\\"1\\\"]}\"}", |
0
0e7c07ff11f9
Uploaded v0.0.1, includes README file and dependencies.
peterjc
parents:
diff
changeset
|
466 "tool_version": "0.0.5", |
0e7c07ff11f9
Uploaded v0.0.1, includes README file and dependencies.
peterjc
parents:
diff
changeset
|
467 "type": "tool", |
0e7c07ff11f9
Uploaded v0.0.1, includes README file and dependencies.
peterjc
parents:
diff
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|
468 "user_outputs": [] |
0e7c07ff11f9
Uploaded v0.0.1, includes README file and dependencies.
peterjc
parents:
diff
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|
469 } |
0e7c07ff11f9
Uploaded v0.0.1, includes README file and dependencies.
peterjc
parents:
diff
changeset
|
470 } |
0e7c07ff11f9
Uploaded v0.0.1, includes README file and dependencies.
peterjc
parents:
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changeset
|
471 } |