Mercurial > repos > eschen42 > mqppep_anova

annotate workflow/ppenrich_suite_wf.ga @ 13:b41a077af3aa draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
author eschen42
date Tue, 22 Mar 2022 20:47:40 +0000
parents
children 6679616d0c18
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
13
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
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1 {
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
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2 "a_galaxy_workflow": "true",
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
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3 "annotation": "phoshpoproteomic enrichment data pre-processing and ANOVA",
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
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4 "creator": [
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5 {
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6 "class": "Person",
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
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7 "identifier": "0000-0002-2882-0508",
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
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8 "name": "Art Eschenlauer"
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
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9 }
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
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10 ],
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11 "format-version": "0.1",
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
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12 "license": "MIT",
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
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13 "name": "ppenrich_suite_wf",
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
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14 "steps": {
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
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15 "0": {
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16 "annotation": "The Phospho (STY)Sites.txt file produced by MaxQuant (found in the txt folder).",
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17 "content_id": null,
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18 "errors": null,
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19 "id": 0,
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20 "input_connections": {},
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
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21 "inputs": [
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22 {
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23 "description": "The Phospho (STY)Sites.txt file produced by MaxQuant (found in the txt folder).",
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24 "name": "Phospho (STY)Sites.txt"
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25 }
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26 ],
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27 "label": "Phospho (STY)Sites.txt",
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
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28 "name": "Input dataset",
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29 "outputs": [],
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39 },
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41 "tool_state": "{\"optional\": false, \"format\": [\"tabular\"]}",
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43 "type": "data_input",
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44 "uuid": "21c3c29d-9e8c-4ece-b585-9e68fed7a93f",
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45 "workflow_outputs": []
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46 },
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47 "1": {
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48 "annotation": "FASTA file of all human canonical isoforms, derived from Swiss-Prot (e.g., merge of https://ftp.uniprot.org/pub/databases/uniprot/current_release/knowledgebase/complete/uniprot_sprot_varsplic.fasta.gz and https://ftp.uniprot.org/pub/databases/uniprot/current_release/knowledgebase/complete/uniprot_sprot.fasta.gz)",
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50 "errors": null,
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52 "input_connections": {},
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53 "inputs": [
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54 {
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55 "description": "FASTA file of all human canonical isoforms, derived from Swiss-Prot (e.g., merge of https://ftp.uniprot.org/pub/databases/uniprot/current_release/knowledgebase/complete/uniprot_sprot_varsplic.fasta.gz and https://ftp.uniprot.org/pub/databases/uniprot/current_release/knowledgebase/complete/uniprot_sprot.fasta.gz)",
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56 "name": "SwissProt_Human_Canonical_Isoform.fasta"
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57 }
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58 ],
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59 "label": "SwissProt_Human_Canonical_Isoform.fasta",
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60 "name": "Input dataset",
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61 "outputs": [],
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71 },
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73 "tool_state": "{\"optional\": false, \"format\": [\"fasta\"]}",
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75 "type": "data_input",
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76 "uuid": "5da7317c-4def-48f3-8eac-af95bd18b290",
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77 "workflow_outputs": []
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78 },
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79 "2": {
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80 "annotation": "Derived from https://networkin.info/download/networkin_human_predictions_3.1.tsv.xz (which is free for non-commercial use - for required citation, see https://networkin.info/)",
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82 "errors": null,
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83 "id": 2,
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84 "input_connections": {},
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85 "inputs": [
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86 {
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87 "description": "Derived from https://networkin.info/download/networkin_human_predictions_3.1.tsv.xz (which is free for non-commercial use - for required citation, see https://networkin.info/)",
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88 "name": "NetworKIN_cutoffscore2.0.tabular"
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89 }
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90 ],
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91 "label": "NetworKIN_cutoffscore2.0.tabular",
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92 "name": "Input dataset",
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93 "outputs": [],
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94 "position": {
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102 "y": 751.5
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103 },
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104 "tool_id": null,
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105 "tool_state": "{\"optional\": false, \"format\": [\"tabular\"]}",
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106 "tool_version": null,
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107 "type": "data_input",
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108 "uuid": "2edff8de-4379-45e2-b6b9-6ed4706bbf00",
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109 "workflow_outputs": []
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110 },
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111 "3": {
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112 "annotation": "Derived from http://hprd.org/serine_motifs, http://hprd.org/tyrosine_motifs, and http://pegasus.biochem.mpg.de/phosida/help/motifs.aspx",
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113 "content_id": null,
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114 "errors": null,
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115 "id": 3,
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116 "input_connections": {},
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117 "inputs": [
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118 {
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119 "description": "Derived from http://hprd.org/serine_motifs, http://hprd.org/tyrosine_motifs, and http://pegasus.biochem.mpg.de/phosida/help/motifs.aspx",
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120 "name": "pSTY_Motifs.tabular"
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121 }
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122 ],
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123 "label": "pSTY_Motifs.tabular",
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124 "name": "Input dataset",
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125 "outputs": [],
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126 "position": {
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135 },
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137 "tool_state": "{\"optional\": false, \"format\": [\"tabular\"]}",
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138 "tool_version": null,
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139 "type": "data_input",
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140 "uuid": "86ebaaf2-b050-4eca-a88b-23a4c1af39f5",
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141 "workflow_outputs": []
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142 },
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143 "4": {
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144 "annotation": "Derived from Kinase_Substrate_Dataset.gz found at https://www.phosphosite.org/staticDownloads (free for non-commercial use - see that link for citation.)",
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145 "content_id": null,
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146 "errors": null,
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147 "id": 4,
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148 "input_connections": {},
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149 "inputs": [
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150 {
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151 "description": "Derived from Kinase_Substrate_Dataset.gz found at https://www.phosphosite.org/staticDownloads (free for non-commercial use - see that link for citation.)",
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152 "name": "PSP_Kinase_Substrate_Dataset.tabular"
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153 }
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154 ],
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155 "label": "PSP_Kinase_Substrate_Dataset.tabular",
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156 "name": "Input dataset",
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157 "outputs": [],
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158 "position": {
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167 },
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169 "tool_state": "{\"optional\": false, \"format\": [\"tabular\"]}",
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170 "tool_version": null,
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171 "type": "data_input",
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172 "uuid": "92f16705-a19c-4fb9-b278-3ae8e11f09d8",
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173 "workflow_outputs": []
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174 },
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175 "5": {
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176 "annotation": "Derived from Regulatory_sites.gz found at https://www.phosphosite.org/staticDownloads (free for non-commercial use - see that link for citation.)",
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180 "input_connections": {},
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181 "inputs": [
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182 {
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183 "description": "Derived from Regulatory_sites.gz found at https://www.phosphosite.org/staticDownloads (free for non-commercial use - see that link for citation.)",
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184 "name": "PSP_Regulatory_sites.tabular"
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185 }
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186 ],
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188 "name": "Input dataset",
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189 "outputs": [],
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199 },
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203 "type": "data_input",
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204 "uuid": "5ab49d93-11e4-4e91-b30b-92269b319879",
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205 "workflow_outputs": []
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206 },
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207 "6": {
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208 "annotation": "List of alpha cutoff values for significance testing; text file having no header and a single line for each cutoff value.",
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211 "id": 6,
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212 "input_connections": {},
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213 "inputs": [
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214 {
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215 "description": "List of alpha cutoff values for significance testing; text file having no header and a single line for each cutoff value.",
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216 "name": "alpha_levels.tabular"
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217 }
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218 ],
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219 "label": "alpha_levels.tabular",
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220 "name": "Input dataset",
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221 "outputs": [],
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230 "y": 1420
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231 },
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232 "tool_id": null,
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233 "tool_state": "{\"optional\": false, \"format\": [\"tabular\"]}",
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234 "tool_version": null,
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235 "type": "data_input",
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236 "uuid": "481c627c-a4ce-45d7-b659-4f54692aafc7",
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237 "workflow_outputs": []
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238 },
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239 "7": {
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240 "annotation": "",
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241 "content_id": "mqppep_preproc",
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242 "errors": null,
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243 "id": 7,
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244 "input_connections": {
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245 "networkin": {
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246 "id": 2,
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247 "output_name": "output"
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248 },
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249 "p_sty_motifs": {
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250 "id": 3,
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251 "output_name": "output"
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252 },
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253 "phosphoSites": {
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254 "id": 0,
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255 "output_name": "output"
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256 },
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257 "protein_fasta": {
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258 "id": 1,
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diff changeset
259 "output_name": "output"
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260 },
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diff changeset
261 "psp_kinase_substrate": {
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262 "id": 4,
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263 "output_name": "output"
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264 },
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diff changeset
265 "psp_regulatory_sites": {
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266 "id": 5,
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diff changeset
267 "output_name": "output"
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268 }
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269 },
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270 "inputs": [],
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271 "label": null,
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272 "name": "MaxQuant Phosphopeptide Preprocessing",
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273 "outputs": [
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274 {
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275 "name": "phosphoPepIntensities",
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276 "type": "tabular"
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277 },
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278 {
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279 "name": "enrichGraph",
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280 "type": "pdf"
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281 },
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282 {
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283 "name": "locProbCutoffGraph",
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284 "type": "pdf"
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285 },
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286 {
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287 "name": "enrichGraph_svg",
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288 "type": "svg"
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289 },
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290 {
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291 "name": "locProbCutoffGraph_svg",
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292 "type": "svg"
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293 },
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294 {
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295 "name": "filteredData_tabular",
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296 "type": "tabular"
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297 },
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298 {
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299 "name": "quantData_tabular",
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300 "type": "tabular"
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301 },
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diff changeset
302 {
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303 "name": "mapped_phophopeptides",
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304 "type": "tabular"
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305 },
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diff changeset
306 {
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diff changeset
307 "name": "melted_phophopeptide_map",
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diff changeset
308 "type": "tabular"
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diff changeset
309 },
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diff changeset
310 {
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diff changeset
311 "name": "mqppep_output_sqlite",
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diff changeset
312 "type": "sqlite"
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313 },
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diff changeset
314 {
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315 "name": "preproc_tab",
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316 "type": "tabular"
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317 },
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diff changeset
318 {
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319 "name": "preproc_csv",
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320 "type": "csv"
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321 },
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diff changeset
322 {
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diff changeset
323 "name": "preproc_sqlite",
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324 "type": "sqlite"
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diff changeset
325 }
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diff changeset
326 ],
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327 "position": {
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328 "bottom": 1408.7000122070312,
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329 "height": 793.2000122070312,
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330 "left": 1138.5,
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331 "right": 1338.5,
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332 "top": 615.5,
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333 "width": 200,
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334 "x": 1138.5,
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335 "y": 615.5
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diff changeset
336 },
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diff changeset
337 "post_job_actions": {
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338 "RenameDatasetActionenrichGraph": {
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diff changeset
339 "action_arguments": {
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diff changeset
340 "newname": "#{phosphoSites}.enrichGraph_pdf"
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diff changeset
341 },
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diff changeset
342 "action_type": "RenameDatasetAction",
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diff changeset
343 "output_name": "enrichGraph"
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diff changeset
344 },
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diff changeset
345 "RenameDatasetActionenrichGraph_svg": {
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diff changeset
346 "action_arguments": {
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diff changeset
347 "newname": "#{phosphoSites}.enrichGraph_svg"
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diff changeset
348 },
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diff changeset
349 "action_type": "RenameDatasetAction",
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diff changeset
350 "output_name": "enrichGraph_svg"
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diff changeset
351 },
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352 "RenameDatasetActionfilteredData_tabular": {
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353 "action_arguments": {
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354 "newname": "#{phosphoSites}.filteredData"
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355 },
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356 "action_type": "RenameDatasetAction",
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357 "output_name": "filteredData_tabular"
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358 },
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359 "RenameDatasetActionlocProbCutoffGraph": {
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360 "action_arguments": {
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361 "newname": "#{phosphoSites}.locProbCutoffGraph_pdf"
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362 },
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363 "action_type": "RenameDatasetAction",
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364 "output_name": "locProbCutoffGraph"
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365 },
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366 "RenameDatasetActionlocProbCutoffGraph_svg": {
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367 "action_arguments": {
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368 "newname": "#{phosphoSites}.locProbCutoffGraph_svg"
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369 },
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370 "action_type": "RenameDatasetAction",
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371 "output_name": "locProbCutoffGraph_svg"
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372 },
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373 "RenameDatasetActionmapped_phophopeptides": {
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374 "action_arguments": {
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375 "newname": "#{phosphoSites}.ppep_map"
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376 },
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377 "action_type": "RenameDatasetAction",
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diff changeset
378 "output_name": "mapped_phophopeptides"
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379 },
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380 "RenameDatasetActionmelted_phophopeptide_map": {
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381 "action_arguments": {
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382 "newname": "#{phosphoSites}.melted"
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383 },
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384 "action_type": "RenameDatasetAction",
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385 "output_name": "melted_phophopeptide_map"
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386 },
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387 "RenameDatasetActionmqppep_output_sqlite": {
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388 "action_arguments": {
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389 "newname": "#{phosphoSites}.ppep_mapping_sqlite"
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390 },
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diff changeset
391 "action_type": "RenameDatasetAction",
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diff changeset
392 "output_name": "mqppep_output_sqlite"
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
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393 },
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394 "RenameDatasetActionphosphoPepIntensities": {
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395 "action_arguments": {
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396 "newname": "#{phosphoSites}.ppep_intensities"
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
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diff changeset
397 },
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diff changeset
398 "action_type": "RenameDatasetAction",
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diff changeset
399 "output_name": "phosphoPepIntensities"
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
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diff changeset
400 },
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diff changeset
401 "RenameDatasetActionpreproc_csv": {
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diff changeset
402 "action_arguments": {
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diff changeset
403 "newname": "#{phosphoSites}.preproc_csv"
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404 },
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diff changeset
405 "action_type": "RenameDatasetAction",
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diff changeset
406 "output_name": "preproc_csv"
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
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diff changeset
407 },
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diff changeset
408 "RenameDatasetActionpreproc_sqlite": {
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diff changeset
409 "action_arguments": {
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diff changeset
410 "newname": "#{phosphoSites}.preproc_sqlite"
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
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diff changeset
411 },
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diff changeset
412 "action_type": "RenameDatasetAction",
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diff changeset
413 "output_name": "preproc_sqlite"
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diff changeset
414 },
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diff changeset
415 "RenameDatasetActionpreproc_tab": {
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diff changeset
416 "action_arguments": {
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diff changeset
417 "newname": "#{phosphoSites}.preproc_tab"
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diff changeset
418 },
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diff changeset
419 "action_type": "RenameDatasetAction",
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diff changeset
420 "output_name": "preproc_tab"
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diff changeset
421 },
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diff changeset
422 "RenameDatasetActionquantData_tabular": {
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diff changeset
423 "action_arguments": {
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diff changeset
424 "newname": "#{phosphoSites}.quantData"
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diff changeset
425 },
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diff changeset
426 "action_type": "RenameDatasetAction",
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diff changeset
427 "output_name": "quantData_tabular"
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diff changeset
428 }
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
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diff changeset
429 },
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diff changeset
430 "tool_id": "mqppep_preproc",
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
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diff changeset
431 "tool_state": "{\"collapseFunc\": \"sum\", \"intervalCol\": \"1\", \"localProbCutoff\": \"0.75\", \"merge_function\": \"sum\", \"networkin\": {\"__class__\": \"ConnectedValue\"}, \"p_sty_motifs\": {\"__class__\": \"ConnectedValue\"}, \"phosphoCol\": \"^Number of Phospho [(]STY[)]$\", \"phosphoSites\": {\"__class__\": \"ConnectedValue\"}, \"protein_fasta\": {\"__class__\": \"ConnectedValue\"}, \"psp_kinase_substrate\": {\"__class__\": \"ConnectedValue\"}, \"psp_regulatory_sites\": {\"__class__\": \"ConnectedValue\"}, \"pst_not_py\": \"true\", \"species\": \"human\", \"startCol\": \"^Intensity[^_]\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
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diff changeset
432 "tool_version": null,
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
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parents:
diff changeset
433 "type": "tool",
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diff changeset
434 "uuid": "1e983dba-edca-4aed-a589-49b1651b4a85",
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diff changeset
435 "workflow_outputs": [
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diff changeset
436 {
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diff changeset
437 "label": "preproc_csv",
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438 "output_name": "preproc_csv",
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439 "uuid": "8cba5367-b25c-40e0-a324-552225b1aa1d"
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440 },
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441 {
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443 "output_name": "locProbCutoffGraph",
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444 "uuid": "641c5959-dab4-42d1-986d-8e6aaeb74ef6"
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445 },
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446 {
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450 },
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452 "label": "enrichGraph_svg",
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453 "output_name": "enrichGraph_svg",
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454 "uuid": "4492366c-945e-492f-8381-1c97c4da2264"
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455 },
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456 {
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457 "label": "locProbCutoffGraph_svg",
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458 "output_name": "locProbCutoffGraph_svg",
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459 "uuid": "06faf93c-5f04-4cb3-9e41-58e465f6180e"
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460 },
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461 {
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462 "label": "filteredData",
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463 "output_name": "filteredData_tabular",
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464 "uuid": "76e2e268-f728-45f0-9973-793fbde0dd0a"
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diff changeset
465 },
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diff changeset
466 {
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467 "label": "ppep_map",
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diff changeset
468 "output_name": "mapped_phophopeptides",
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
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469 "uuid": "d0fea028-2ea5-4862-8a92-c2088edfcbe1"
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diff changeset
470 },
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
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parents:
diff changeset
471 {
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diff changeset
472 "label": "ppep_mapping_sqlite",
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
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diff changeset
473 "output_name": "mqppep_output_sqlite",
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
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diff changeset
474 "uuid": "eb996931-c548-4f3b-aaaa-39cc711df516"
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
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diff changeset
475 },
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
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parents:
diff changeset
476 {
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
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diff changeset
477 "label": "preproc_tab",
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
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parents:
diff changeset
478 "output_name": "preproc_tab",
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
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diff changeset
479 "uuid": "c9410cf1-44a2-4aa6-b3df-06cef74f3a45"
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
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diff changeset
480 },
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
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parents:
diff changeset
481 {
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
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diff changeset
482 "label": "preproc_sqlite",
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
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diff changeset
483 "output_name": "preproc_sqlite",
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
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diff changeset
484 "uuid": "4eb22cc3-5879-4625-89c0-e0fddb01a197"
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diff changeset
485 },
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
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parents:
diff changeset
486 {
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
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parents:
diff changeset
487 "label": "ppep_intensities",
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents:
diff changeset
488 "output_name": "phosphoPepIntensities",
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents:
diff changeset
489 "uuid": "c704fd66-5ac3-4779-ad40-536955cd81e3"
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents:
diff changeset
490 },
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents:
diff changeset
491 {
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents:
diff changeset
492 "label": "enrichGraph_pdf",
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents:
diff changeset
493 "output_name": "enrichGraph",
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents:
diff changeset
494 "uuid": "5bf2a478-0431-4d32-84a9-7d46aad80ec5"
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents:
diff changeset
495 },
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents:
diff changeset
496 {
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents:
diff changeset
497 "label": "quantData",
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents:
diff changeset
498 "output_name": "quantData_tabular",
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents:
diff changeset
499 "uuid": "cc922a75-6e72-4e60-add2-4b6ed8f73cdb"
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents:
diff changeset
500 }
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents:
diff changeset
501 ]
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
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parents:
diff changeset
502 },
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents:
diff changeset
503 "8": {
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents:
diff changeset
504 "annotation": "Perform ANOVA. For imputing missing values, use median of non-missing values from the same treatment group.",
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
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parents:
diff changeset
505 "content_id": "mqppep_anova",
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents:
diff changeset
506 "errors": null,
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents:
diff changeset
507 "id": 8,
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents:
diff changeset
508 "input_connections": {
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents:
diff changeset
509 "alpha_file": {
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents:
diff changeset
510 "id": 6,
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents:
diff changeset
511 "output_name": "output"
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents:
diff changeset
512 },
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents:
diff changeset
513 "input_file": {
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents:
diff changeset
514 "id": 7,
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents:
diff changeset
515 "output_name": "preproc_tab"
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents:
diff changeset
516 }
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents:
diff changeset
517 },
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents:
diff changeset
518 "inputs": [],
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents:
diff changeset
519 "label": "MaxQuant Phosphopeptide ANOVA group-median imputed",
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents:
diff changeset
520 "name": "MaxQuant Phosphopeptide ANOVA",
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents:
diff changeset
521 "outputs": [
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents:
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613 "post_job_actions": {
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614 "RenameDatasetActionimputed_data_file": {
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diff changeset
616 "newname": "#{input_file}.intensities_randomly-imputed_QN_LT"
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617 },
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619 "output_name": "imputed_data_file"
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620 },
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622 "action_arguments": {
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623 "newname": "#{input_file}.intensities_randomly-imputed_report (download/unzip to view)"
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624 },
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626 "output_name": "report_file"
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628 },
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629 "tool_id": "mqppep_anova",
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630 "tool_state": "{\"alpha_file\": {\"__class__\": \"ConnectedValue\"}, \"first_data_column\": \"Intensity\", \"imputation\": {\"imputation_method\": \"random\", \"__current_case__\": 3, \"meanPercentile\": \"1\", \"sdPercentile\": \"0.2\"}, \"input_file\": {\"__class__\": \"ConnectedValue\"}, \"sample_grouping_regex\": \"(\\\\d+)\", \"sample_names_regex\": \"\\\\.(\\\\d+)[A-Z]$\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
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633 "workflow_outputs": [
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diff changeset
634 {
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635 "label": "intensities_randomly-imputed_QN_LT",
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638 },
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640 "label": "intensities_randomly-imputed_report",
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641 "output_name": "report_file",
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diff changeset
643 }
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diff changeset
644 ]
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645 }
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646 },
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diff changeset
647 "tags": [
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diff changeset
648 "ppenrich"
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diff changeset
649 ],
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651 "version": 3
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diff changeset
652 }