25
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1 {
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2 "a_galaxy_workflow": "true",
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3 "annotation": "Normalizes 2 BAM files to each other (log2ratio of BAM-file 1 / BAM file 2). Then generates a heatmap for regions supplied in 1 BED file (clustering possible). Output: bigWig file, computeMatrix table, heatmapper image",
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4 "format-version": "0.1",
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5 "name": "2 BAM files -->(clustered) Heatmap of read coverages",
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6 "steps": {
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7 "0": {
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8 "annotation": "sorted BAM file",
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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": "sorted BAM file",
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14 "name": "file 1 of mapped reads, e.g. treated sample"
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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": 257.5,
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21 "top": 480
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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\": \"file 1 of mapped reads, e.g. treated sample\"}",
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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": "BED or INTERVAL file of genome regions to plot the read coverage for",
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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": "BED or INTERVAL file of genome regions to plot the read coverage for",
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37 "name": "regions"
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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": 590.5,
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44 "top": 239
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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\": \"regions\"}",
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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": "sorted BAM file",
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55 "id": 2,
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56 "input_connections": {},
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57 "inputs": [
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58 {
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59 "description": "sorted BAM file",
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60 "name": "file 2 of mapped reads, e.g. control sample"
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61 }
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62 ],
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63 "name": "Input dataset",
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64 "outputs": [],
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65 "position": {
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66 "left": 276.5,
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67 "top": 594.5
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68 },
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69 "tool_errors": null,
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70 "tool_id": null,
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71 "tool_state": "{\"name\": \"file 2 of mapped reads, e.g. control sample\"}",
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72 "tool_version": null,
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73 "type": "data_input",
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74 "user_outputs": []
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75 },
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76 "3": {
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77 "annotation": "generates a normalized coverage file (bigWig format)",
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78 "id": 3,
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79 "input_connections": {
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80 "bamFile1": {
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81 "id": 0,
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82 "output_name": "output"
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83 },
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84 "bamFile2": {
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85 "id": 2,
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86 "output_name": "output"
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87 }
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88 },
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89 "inputs": [
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90 {
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91 "description": "runtime parameter for tool bamCompare",
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92 "name": "region"
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93 },
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94 {
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95 "description": "runtime parameter for tool bamCompare",
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96 "name": "advancedOpt"
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97 },
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98 {
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99 "description": "runtime parameter for tool bamCompare",
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100 "name": "fragmentLength"
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101 }
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102 ],
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103 "name": "bamCompare",
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104 "outputs": [
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105 {
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106 "name": "outFileName",
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107 "type": "bigwig"
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108 }
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109 ],
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110 "position": {
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111 "left": 476.5,
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112 "top": 486.5
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113 },
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114 "post_job_actions": {
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115 "HideDatasetActionoutFileName": {
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116 "action_arguments": {},
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117 "action_type": "HideDatasetAction",
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118 "output_name": "outFileName"
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119 },
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120 "RenameDatasetActionoutFileName": {
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121 "action_arguments": {
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122 "newname": "BAM1_vs_BAM2_log2ratio.bigwig"
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123 },
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124 "action_type": "RenameDatasetAction",
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125 "output_name": "outFileName"
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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": "toolshed.g2.bx.psu.edu/repos/bgruening/deeptools/deeptools_bamCompare/1.0.4",
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130 "tool_state": "{\"comparison\": \"{\\\"type\\\": \\\"log2\\\", \\\"__current_case__\\\": 0}\", \"bamFile2\": \"null\", \"outFileFormat\": \"\\\"bigwig\\\"\", \"bamFile1\": \"null\", \"__page__\": 0, \"region\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"binSize\": \"\\\"50\\\"\", \"scaling\": \"{\\\"method\\\": \\\"readCount\\\", \\\"__current_case__\\\": 1}\", \"__rerun_remap_job_id__\": null, \"advancedOpt\": \"{\\\"ignoreDuplicates\\\": \\\"True\\\", \\\"ignoreForNormalization\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"doNotExtendPairedEnds\\\": \\\"False\\\", \\\"missingDataAsZero\\\": \\\"True\\\", \\\"smoothLength\\\": \\\"150\\\", \\\"showAdvancedOpt\\\": \\\"yes\\\", \\\"__current_case__\\\": 1, \\\"minMappingQuality\\\": \\\"10\\\"}\", \"fragmentLength\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\"}",
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131 "tool_version": "1.0.4",
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132 "type": "tool",
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133 "user_outputs": []
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134 },
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135 "4": {
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136 "annotation": "",
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137 "id": 4,
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138 "input_connections": {
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139 "regionsFiles_0|regionsFile": {
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140 "id": 1,
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141 "output_name": "output"
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142 },
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143 "scoreFile": {
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144 "id": 3,
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145 "output_name": "outFileName"
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146 }
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147 },
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148 "inputs": [],
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149 "name": "computeMatrix",
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150 "outputs": [
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151 {
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152 "name": "outFileName",
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153 "type": "bgzip"
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154 },
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155 {
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156 "name": "outFileNameData",
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157 "type": "tabular"
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158 },
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159 {
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160 "name": "outFileSortedRegions",
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161 "type": "bed"
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162 },
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163 {
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164 "name": "outFileNameMatrix",
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165 "type": "tabular"
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166 }
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167 ],
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168 "position": {
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169 "left": 835.61669921875,
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170 "top": 364.1166687011719
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171 },
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172 "post_job_actions": {
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173 "HideDatasetActionoutFileNameData": {
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174 "action_arguments": {},
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175 "action_type": "HideDatasetAction",
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176 "output_name": "outFileNameData"
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177 },
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178 "HideDatasetActionoutFileNameMatrix": {
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179 "action_arguments": {},
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180 "action_type": "HideDatasetAction",
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181 "output_name": "outFileNameMatrix"
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182 },
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183 "HideDatasetActionoutFileSortedRegions": {
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184 "action_arguments": {},
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185 "action_type": "HideDatasetAction",
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186 "output_name": "outFileSortedRegions"
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187 },
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188 "RenameDatasetActionoutFileName": {
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189 "action_arguments": {
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190 "newname": "computeMatrix: matrix of coverage values for BED file"
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191 },
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192 "action_type": "RenameDatasetAction",
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193 "output_name": "outFileName"
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196 "tool_errors": null,
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197 "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/deeptools/deeptools_computeMatrix/1.0.4",
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198 "tool_state": "{\"__page__\": 0, \"scoreFile\": \"null\", \"__rerun_remap_job_id__\": null, \"mode\": \"{\\\"startLabel\\\": \\\"TSS\\\", \\\"regionStartLength\\\": {\\\"afterRegionStartLength\\\": \\\"1000\\\", \\\"regionStartLength_select\\\": \\\"yes\\\", \\\"beforeRegionStartLength\\\": \\\"1000\\\", \\\"__current_case__\\\": 1}, \\\"__current_case__\\\": 0, \\\"endLabel\\\": \\\"TES\\\", \\\"regionBodyLength\\\": \\\"2000\\\", \\\"mode_select\\\": \\\"scale-regions\\\"}\", \"output\": \"{\\\"showOutputSettings\\\": \\\"no\\\", \\\"__current_case__\\\": 0}\", \"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\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}}]\"}",
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199 "tool_version": "1.0.4",
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200 "type": "tool",
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201 "user_outputs": []
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202 },
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203 "5": {
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204 "annotation": "create a heatmap, if wanted, kmeans clustering can be performed",
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205 "id": 5,
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206 "input_connections": {
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207 "matrixFile": {
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208 "id": 4,
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209 "output_name": "outFileName"
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210 }
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211 },
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212 "inputs": [
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213 {
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214 "description": "runtime parameter for tool heatmapper",
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215 "name": "output"
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216 },
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217 {
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218 "description": "runtime parameter for tool heatmapper",
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219 "name": "advancedOpt"
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220 },
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221 {
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222 "description": "runtime parameter for tool heatmapper",
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223 "name": "advancedOpt"
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224 },
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225 {
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226 "description": "runtime parameter for tool heatmapper",
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227 "name": "advancedOpt"
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228 },
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229 {
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230 "description": "runtime parameter for tool heatmapper",
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231 "name": "advancedOpt"
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232 },
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233 {
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234 "description": "runtime parameter for tool heatmapper",
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235 "name": "advancedOpt"
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236 }
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237 ],
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238 "name": "heatmapper",
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239 "outputs": [
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240 {
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241 "name": "outFileName",
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242 "type": "png"
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243 },
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244 {
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245 "name": "outFileNameData",
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246 "type": "tabular"
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249 "name": "outFileSortedRegions",
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250 "type": "bed"
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251 },
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252 {
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253 "name": "outFileNameMatrix",
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254 "type": "tabular"
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255 }
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256 ],
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261 "post_job_actions": {
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263 "action_arguments": {},
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265 "output_name": "outFileNameData"
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266 },
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267 "HideDatasetActionoutFileNameMatrix": {
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276 },
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277 "RenameDatasetActionoutFileName": {
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278 "action_arguments": {
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279 "newname": "Heatmap of treatment_control_log2ratios"
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280 },
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281 "action_type": "RenameDatasetAction",
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282 "output_name": "outFileName"
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285 "tool_errors": null,
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286 "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/deeptools/deeptools_heatmapper/1.0.4",
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287 "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\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"xAxisLabel\\\": \\\"\\\", \\\"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\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"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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288 "tool_version": "1.0.4",
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289 "type": "tool",
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290 "user_outputs": []
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291 }
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292 }
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293 } |