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25
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1 {
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2 "a_galaxy_workflow": "true",
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3 "annotation": "1 bigWig, 1 \nBED --> clustered heatmap",
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4 "format-version": "0.1",
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5 "name": "Clustered heatmap of signals around the TSSs",
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6 "steps": {
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7 "0": {
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8 "annotation": "Gene list must:\na) match the genome of the score file\nb) be in INTERVAL or BED format with the STRAND being specified",
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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": "Gene list must:\na) match the genome of the score file\nb) be in INTERVAL or BED format with the STRAND being specified",
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14 "name": "Genes"
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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": 175,
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21 "top": 186.5
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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\": \"Genes\"}",
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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": "must be in bigWig format, score can be anything: read coverages, GC content...",
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32 "id": 1,
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33 "input_connections": {},
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34 "inputs": [
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35 {
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36 "description": "must be in bigWig format, score can be anything: read coverages, GC content...",
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37 "name": "score file"
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38 }
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39 ],
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40 "name": "Input dataset",
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41 "outputs": [],
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42 "position": {
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43 "left": 168,
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44 "top": 304.5
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45 },
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46 "tool_errors": null,
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47 "tool_id": null,
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48 "tool_state": "{\"name\": \"score file\"}",
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49 "tool_version": null,
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50 "type": "data_input",
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51 "user_outputs": []
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52 },
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53 "2": {
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54 "annotation": "computes the matrix for the heatmap",
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55 "id": 2,
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56 "input_connections": {
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57 "regionsFiles_0|regionsFile": {
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58 "id": 0,
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59 "output_name": "output"
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60 },
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61 "scoreFile": {
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62 "id": 1,
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63 "output_name": "output"
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64 }
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65 },
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66 "inputs": [
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67 {
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68 "description": "runtime parameter for tool computeMatrix",
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69 "name": "mode"
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70 },
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71 {
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72 "description": "runtime parameter for tool computeMatrix",
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73 "name": "mode"
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74 }
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75 ],
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76 "name": "computeMatrix",
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77 "outputs": [
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78 {
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79 "name": "outFileName",
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80 "type": "bgzip"
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81 },
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82 {
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83 "name": "outFileNameData",
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84 "type": "tabular"
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85 },
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86 {
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87 "name": "outFileSortedRegions",
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88 "type": "bed"
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89 },
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90 {
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91 "name": "outFileNameMatrix",
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92 "type": "tabular"
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93 }
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94 ],
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95 "position": {
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96 "left": 490.6166687011719,
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97 "top": 485.11669921875
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98 },
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99 "post_job_actions": {
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100 "HideDatasetActionoutFileNameData": {
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101 "action_arguments": {},
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102 "action_type": "HideDatasetAction",
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103 "output_name": "outFileNameData"
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104 },
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105 "HideDatasetActionoutFileNameMatrix": {
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106 "action_arguments": {},
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107 "action_type": "HideDatasetAction",
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108 "output_name": "outFileNameMatrix"
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109 },
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110 "HideDatasetActionoutFileSortedRegions": {
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111 "action_arguments": {},
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112 "action_type": "HideDatasetAction",
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113 "output_name": "outFileSortedRegions"
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114 }
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115 },
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116 "tool_errors": null,
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117 "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/deeptools/deeptools_computeMatrix/1.0.3",
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118 "tool_state": "{\"__page__\": 0, \"scoreFile\": \"null\", \"__rerun_remap_job_id__\": null, \"mode\": \"{\\\"afterRegionStartLength\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"beforeRegionStartLength\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"nanAfterEnd\\\": \\\"False\\\", \\\"__current_case__\\\": 1, \\\"referencePoint\\\": \\\"TSS\\\", \\\"mode_select\\\": \\\"reference-point\\\"}\", \"output\": \"{\\\"saveMatrix\\\": \\\"False\\\", \\\"saveSortedRegions\\\": \\\"True\\\", \\\"showOutputSettings\\\": \\\"yes\\\", \\\"__current_case__\\\": 1, \\\"saveData\\\": \\\"False\\\"}\", \"advancedOpt\": \"{\\\"averageTypeBins\\\": \\\"mean\\\", \\\"maxThreshold\\\": \\\"\\\", \\\"sortUsing\\\": \\\"mean\\\", \\\"skipZeros\\\": \\\"True\\\", \\\"binSize\\\": \\\"50\\\", \\\"showAdvancedOpt\\\": \\\"yes\\\", \\\"scale\\\": \\\"\\\", \\\"__current_case__\\\": 1, \\\"minThreshold\\\": \\\"\\\", \\\"sortRegions\\\": \\\"no\\\", \\\"missingDataAsZero\\\": \\\"True\\\"}\", \"regionsFiles\": \"[{\\\"__index__\\\": 0, \\\"regionsFile\\\": null, \\\"label\\\": \\\"Genes\\\"}]\"}",
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119 "tool_version": "1.0.3",
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120 "type": "tool",
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121 "user_outputs": []
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122 },
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123 "3": {
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124 "annotation": "",
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125 "id": 3,
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126 "input_connections": {
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127 "matrixFile": {
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128 "id": 2,
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129 "output_name": "outFileName"
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130 }
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131 },
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132 "inputs": [
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133 {
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134 "description": "runtime parameter for tool heatmapper",
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135 "name": "output"
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136 },
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137 {
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138 "description": "runtime parameter for tool heatmapper",
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139 "name": "advancedOpt"
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140 },
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141 {
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142 "description": "runtime parameter for tool heatmapper",
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143 "name": "advancedOpt"
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144 },
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145 {
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146 "description": "runtime parameter for tool heatmapper",
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147 "name": "advancedOpt"
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148 }
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149 ],
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150 "name": "heatmapper",
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151 "outputs": [
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152 {
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153 "name": "outFileName",
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154 "type": "png"
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155 },
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156 {
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157 "name": "outFileNameData",
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158 "type": "tabular"
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159 },
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160 {
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161 "name": "outFileSortedRegions",
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162 "type": "bed"
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163 },
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164 {
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165 "name": "outFileNameMatrix",
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166 "type": "tabular"
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167 }
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168 ],
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169 "position": {
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170 "left": 834,
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171 "top": 487.5
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172 },
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173 "post_job_actions": {
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174 "HideDatasetActionoutFileNameData": {
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175 "action_arguments": {},
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176 "action_type": "HideDatasetAction",
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177 "output_name": "outFileNameData"
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178 },
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179 "HideDatasetActionoutFileNameMatrix": {
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180 "action_arguments": {},
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181 "action_type": "HideDatasetAction",
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182 "output_name": "outFileNameMatrix"
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183 },
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184 "HideDatasetActionoutFileSortedRegions": {
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185 "action_arguments": {},
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186 "action_type": "HideDatasetAction",
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187 "output_name": "outFileSortedRegions"
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188 },
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189 "RenameDatasetActionoutFileName": {
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190 "action_arguments": {
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191 "newname": "Heatmap of scores around the TSS"
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192 },
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193 "action_type": "RenameDatasetAction",
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194 "output_name": "outFileName"
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195 }
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196 },
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197 "tool_errors": null,
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198 "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/deeptools/deeptools_heatmapper/1.0.3",
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199 "tool_state": "{\"__page__\": 0, \"output\": \"{\\\"outFileFormat\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"saveMatrix\\\": \\\"False\\\", \\\"showOutputSettings\\\": \\\"yes\\\", \\\"saveSortedRegions\\\": \\\"False\\\", \\\"__current_case__\\\": 1, \\\"saveData\\\": \\\"False\\\"}\", \"advancedOpt\": \"{\\\"used_multiple_regions\\\": {\\\"clustering\\\": {\\\"k_kmeans\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"__current_case__\\\": 0, \\\"clustering_options\\\": \\\"kmeans\\\"}, \\\"used_multiple_regions_options\\\": \\\"no\\\", \\\"__current_case__\\\": 0}, \\\"yAxisLabel\\\": \\\"genes\\\", \\\"xAxisLabel\\\": \\\"distance from TSS (bp)\\\", \\\"zMax\\\": \\\"\\\", \\\"heatmapWidth\\\": \\\"7.5\\\", \\\"sortUsing\\\": \\\"mean\\\", \\\"zMin\\\": \\\"\\\", \\\"plotTitle\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"averageTypeSummaryPlot\\\": \\\"mean\\\", \\\"whatToShow\\\": \\\"plot, heatmap and colorbar\\\", \\\"missingDataColor\\\": \\\"black\\\", \\\"referencePointLabel\\\": \\\"TSS\\\", \\\"yMin\\\": \\\"\\\", \\\"onePlotPerGroup\\\": \\\"False\\\", \\\"regionsLabel\\\": \\\"genes\\\", \\\"yMax\\\": \\\"\\\", \\\"endLabel\\\": \\\"TES\\\", \\\"sortRegions\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"startLabel\\\": \\\"TSS\\\", \\\"colorMap\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"showAdvancedOpt\\\": \\\"yes\\\", \\\"__current_case__\\\": 1, \\\"heatmapHeight\\\": \\\"15.0\\\"}\", \"__rerun_remap_job_id__\": null, \"matrixFile\": \"null\"}",
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200 "tool_version": "1.0.3",
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201 "type": "tool",
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202 "user_outputs": []
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203 }
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204 }
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205 } |
