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0
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1 {
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2 "a_galaxy_workflow": "true",
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3 "annotation": "",
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4 "format-version": "0.1",
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5 "name": "mt analysis 0.01 strand-specific (fastq double)",
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6 "steps": {
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7 "0": {
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8 "annotation": "The second input dataset. Usually the second PCR replicate for a given sample.",
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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 "name": "Map with BWA",
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13 "outputs": [
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14 {
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15 "name": "output",
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16 "type": "sam"
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17 }
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18 ],
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19 "position": {
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20 "left": 229,
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21 "top": 388
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22 },
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23 "tool_errors": null,
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24 "tool_id": "bwa_wrapper",
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25 "tool_state": "{\"genomeSource\": \"{\\\"indices\\\": \\\"/mnt/galaxyIndices/hg19/bwa/base/hg19\\\", \\\"refGenomeSource\\\": \\\"indexed\\\", \\\"__current_case__\\\": 0}\", \"paired\": \"{\\\"sPaired\\\": \\\"single\\\", \\\"input1\\\": null, \\\"__current_case__\\\": 0}\", \"params\": \"{\\\"__current_case__\\\": 0, \\\"source_select\\\": \\\"pre_set\\\"}\", \"suppressHeader\": \"\\\"True\\\"\", \"__page__\": 0}",
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26 "tool_version": "1.0.3",
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27 "type": "tool",
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28 "user_outputs": []
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29 },
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30 "1": {
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31 "annotation": "The first input dataset. Usually the first PCR replicate for a given sample.",
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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 "name": "Map with BWA",
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36 "outputs": [
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37 {
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38 "name": "output",
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39 "type": "sam"
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40 }
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41 ],
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42 "position": {
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43 "left": 229,
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44 "top": 154
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45 },
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46 "tool_errors": null,
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47 "tool_id": "bwa_wrapper",
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48 "tool_state": "{\"genomeSource\": \"{\\\"indices\\\": \\\"/mnt/galaxyIndices/hg19/bwa/base/hg19\\\", \\\"refGenomeSource\\\": \\\"indexed\\\", \\\"__current_case__\\\": 0}\", \"paired\": \"{\\\"sPaired\\\": \\\"single\\\", \\\"input1\\\": null, \\\"__current_case__\\\": 0}\", \"params\": \"{\\\"__current_case__\\\": 0, \\\"source_select\\\": \\\"pre_set\\\"}\", \"suppressHeader\": \"\\\"True\\\"\", \"__page__\": 0}",
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49 "tool_version": "1.0.3",
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50 "type": "tool",
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51 "user_outputs": []
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52 },
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53 "2": {
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54 "annotation": "Here SAM datasets generated by BWA are merged together",
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55 "id": 2,
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56 "input_connections": {
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57 "input1": {
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58 "id": 1,
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59 "output_name": "output"
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60 },
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61 "queries_0|input2": {
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62 "id": 0,
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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 "name": "Concatenate queries",
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68 "outputs": [
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69 {
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70 "name": "out_file1",
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71 "type": "input"
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72 }
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73 ],
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74 "position": {
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75 "left": 410,
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76 "top": 257
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77 },
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78 "tool_errors": null,
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79 "tool_id": "cat1",
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80 "tool_state": "{\"__page__\": 0, \"input1\": \"null\", \"queries\": \"[{\\\"input2\\\": null, \\\"__index__\\\": 0}]\"}",
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81 "tool_version": "1.0.0",
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82 "type": "tool",
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83 "user_outputs": []
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84 },
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85 "3": {
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86 "annotation": "By selecting only lines containing the X0:i:1 tag we eliminate reads that map multiple times. Thus this step removes reads that map more than once.",
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87 "id": 3,
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88 "input_connections": {
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89 "input": {
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90 "id": 2,
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91 "output_name": "out_file1"
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92 }
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93 },
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94 "inputs": [],
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95 "name": "Select",
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96 "outputs": [
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97 {
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98 "name": "out_file1",
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99 "type": "input"
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100 }
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101 ],
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102 "position": {
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103 "left": 492,
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104 "top": 468
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105 },
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106 "tool_errors": null,
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107 "tool_id": "Grep1",
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108 "tool_state": "{\"__page__\": 0, \"input\": \"null\", \"invert\": \"\\\"false\\\"\", \"pattern\": \"\\\"X0:i:1\\\"\"}",
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109 "tool_version": "1.0.1",
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110 "type": "tool",
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111 "user_outputs": []
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112 },
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113 "4": {
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114 "annotation": "Selecting reads mapping to the PLUS strand",
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115 "id": 4,
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116 "input_connections": {
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117 "input1": {
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118 "id": 3,
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119 "output_name": "out_file1"
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120 }
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121 },
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122 "inputs": [],
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123 "name": "Filter SAM",
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124 "outputs": [
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125 {
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126 "name": "out_file1",
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127 "type": "sam"
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128 }
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129 ],
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130 "position": {
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131 "left": 333,
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132 "top": 610
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133 },
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134 "tool_errors": null,
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135 "tool_id": "sam_bw_filter",
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136 "tool_state": "{\"chromInfo\": \"\\\"/galaxy/home/g2main/galaxy_main/tool-data/shared/ucsc/chrom/hg19.len\\\"\", \"input1\": \"null\", \"bits\": \"[{\\\"states\\\": \\\"0\\\", \\\"__index__\\\": 0, \\\"flags\\\": \\\"--0x0004\\\"}, {\\\"states\\\": \\\"0\\\", \\\"__index__\\\": 1, \\\"flags\\\": \\\"--0x0010\\\"}]\", \"__page__\": 0}",
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137 "tool_version": "1.0.0",
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138 "type": "tool",
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139 "user_outputs": []
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140 },
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141 "5": {
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142 "annotation": "Selecting reads mapping to the MINUS strand",
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143 "id": 5,
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144 "input_connections": {
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145 "input1": {
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146 "id": 3,
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147 "output_name": "out_file1"
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148 }
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149 },
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150 "inputs": [],
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151 "name": "Filter SAM",
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152 "outputs": [
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153 {
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154 "name": "out_file1",
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155 "type": "sam"
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156 }
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157 ],
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158 "position": {
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159 "left": 271,
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160 "top": 879
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161 },
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162 "tool_errors": null,
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163 "tool_id": "sam_bw_filter",
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164 "tool_state": "{\"__page__\": 0, \"input1\": \"null\", \"bits\": \"[{\\\"states\\\": \\\"0\\\", \\\"__index__\\\": 0, \\\"flags\\\": \\\"--0x0004\\\"}, {\\\"states\\\": \\\"1\\\", \\\"__index__\\\": 1, \\\"flags\\\": \\\"--0x0010\\\"}]\"}",
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165 "tool_version": "1.0.0",
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166 "type": "tool",
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167 "user_outputs": []
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168 },
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169 "6": {
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170 "annotation": "Converting SAM to its binary representation (BAM) to allow pileup generation",
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171 "id": 6,
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172 "input_connections": {
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173 "source|input1": {
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174 "id": 4,
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175 "output_name": "out_file1"
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176 }
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177 },
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178 "inputs": [],
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179 "name": "SAM-to-BAM",
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180 "outputs": [
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181 {
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182 "name": "output1",
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183 "type": "bam"
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184 }
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185 ],
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186 "position": {
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187 "left": 438,
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188 "top": 785
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189 },
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190 "tool_errors": null,
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191 "tool_id": "sam_to_bam",
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192 "tool_state": "{\"source\": \"{\\\"index_source\\\": \\\"cached\\\", \\\"input1\\\": null, \\\"__current_case__\\\": 0}\", \"chromInfo\": \"\\\"/galaxy/home/g2main/galaxy_main/tool-data/shared/ucsc/chrom/hg19.len\\\"\", \"__page__\": 0}",
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193 "tool_version": "1.1.0",
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194 "type": "tool",
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195 "user_outputs": []
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196 },
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197 "7": {
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198 "annotation": "Converting SAM to its binary representation (BAM) to allow pileup generation",
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199 "id": 7,
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200 "input_connections": {
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201 "source|input1": {
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202 "id": 5,
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203 "output_name": "out_file1"
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204 }
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205 },
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206 "inputs": [],
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207 "name": "SAM-to-BAM",
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208 "outputs": [
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209 {
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210 "name": "output1",
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211 "type": "bam"
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212 }
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213 ],
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214 "position": {
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215 "left": 404,
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216 "top": 1043
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217 },
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218 "tool_errors": null,
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219 "tool_id": "sam_to_bam",
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220 "tool_state": "{\"source\": \"{\\\"index_source\\\": \\\"cached\\\", \\\"input1\\\": null, \\\"__current_case__\\\": 0}\", \"__page__\": 0}",
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221 "tool_version": "1.1.0",
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222 "type": "tool",
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223 "user_outputs": []
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224 },
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225 "8": {
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226 "annotation": "Generating standard 6 column pileup without MAQ consensus option for PLUS strand",
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227 "id": 8,
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228 "input_connections": {
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229 "refOrHistory|input1": {
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230 "id": 6,
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231 "output_name": "output1"
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232 }
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233 },
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234 "inputs": [],
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235 "name": "Generate pileup",
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236 "outputs": [
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237 {
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238 "name": "output1",
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239 "type": "tabular"
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240 }
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241 ],
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242 "position": {
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243 "left": 643,
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244 "top": 756
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245 },
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246 "tool_errors": null,
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247 "tool_id": "sam_pileup",
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248 "tool_state": "{\"__page__\": 0, \"c\": \"{\\\"consensus\\\": \\\"no\\\", \\\"__current_case__\\\": 0}\", \"indels\": \"\\\"no\\\"\", \"refOrHistory\": \"{\\\"input1\\\": null, \\\"reference\\\": \\\"indexed\\\", \\\"__current_case__\\\": 0}\", \"chromInfo\": \"\\\"/galaxy/home/g2main/galaxy_main/tool-data/shared/ucsc/chrom/hg19.len\\\"\", \"lastCol\": \"\\\"no\\\"\", \"mapCap\": \"\\\"60\\\"\"}",
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249 "tool_version": "1.1.0",
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250 "type": "tool",
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251 "user_outputs": []
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252 },
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253 "9": {
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254 "annotation": "Generating standard 6 column pileup without MAQ consensus option for MINUS strand",
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255 "id": 9,
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256 "input_connections": {
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257 "refOrHistory|input1": {
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258 "id": 7,
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259 "output_name": "output1"
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260 }
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261 },
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262 "inputs": [],
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263 "name": "Generate pileup",
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264 "outputs": [
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265 {
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266 "name": "output1",
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267 "type": "tabular"
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268 }
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269 ],
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270 "position": {
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271 "left": 630,
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272 "top": 1039
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273 },
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274 "tool_errors": null,
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275 "tool_id": "sam_pileup",
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276 "tool_state": "{\"__page__\": 0, \"c\": \"{\\\"consensus\\\": \\\"no\\\", \\\"__current_case__\\\": 0}\", \"indels\": \"\\\"no\\\"\", \"refOrHistory\": \"{\\\"input1\\\": null, \\\"reference\\\": \\\"indexed\\\", \\\"__current_case__\\\": 0}\", \"lastCol\": \"\\\"no\\\"\", \"mapCap\": \"\\\"60\\\"\"}",
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277 "tool_version": "1.1.0",
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278 "type": "tool",
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279 "user_outputs": []
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280 },
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281 "10": {
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282 "annotation": "PLUS strand. Here pileup is filtered to restrict the dataset to positions covered by al least 100 reads containing high quality bases (phred 30 or above).",
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283 "id": 10,
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284 "input_connections": {
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285 "input": {
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286 "id": 8,
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287 "output_name": "output1"
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288 }
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289 },
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290 "inputs": [],
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291 "name": "Filter pileup",
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292 "outputs": [
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293 {
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294 "name": "out_file1",
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295 "type": "tabular"
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296 }
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297 ],
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298 "position": {
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299 "left": 774,
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300 "top": 532
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301 },
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302 "tool_errors": null,
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303 "tool_id": "pileup_parser",
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304 "tool_state": "{\"snps_only\": \"\\\"No\\\"\", \"__page__\": 0, \"qc_base\": \"\\\"No\\\"\", \"cvrg_cutoff\": \"\\\"100\\\"\", \"interval\": \"\\\"Yes\\\"\", \"pileup_type\": \"{\\\"type_select\\\": \\\"six\\\", \\\"__current_case__\\\": 1}\", \"input\": \"null\", \"diff\": \"\\\"Yes\\\"\", \"qv_cutoff\": \"\\\"30\\\"\", \"chromInfo\": \"\\\"/galaxy/home/g2main/galaxy_main/tool-data/shared/ucsc/chrom/hg19.len\\\"\"}",
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305 "tool_version": "1.0.2",
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306 "type": "tool",
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307 "user_outputs": []
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308 },
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309 "11": {
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310 "annotation": "MINUS strand. Here pileup is filtered to restrict the dataset to positions covered by al least 100 reads containing high quality bases (phred 30 or above).",
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311 "id": 11,
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312 "input_connections": {
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313 "input": {
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314 "id": 9,
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315 "output_name": "output1"
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316 }
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317 },
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318 "inputs": [],
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319 "name": "Filter pileup",
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320 "outputs": [
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321 {
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322 "name": "out_file1",
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323 "type": "tabular"
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324 }
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325 ],
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326 "position": {
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327 "left": 737,
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328 "top": 1228
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329 },
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330 "tool_errors": null,
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331 "tool_id": "pileup_parser",
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332 "tool_state": "{\"snps_only\": \"\\\"No\\\"\", \"__page__\": 0, \"qc_base\": \"\\\"No\\\"\", \"cvrg_cutoff\": \"\\\"100\\\"\", \"interval\": \"\\\"Yes\\\"\", \"pileup_type\": \"{\\\"type_select\\\": \\\"six\\\", \\\"__current_case__\\\": 1}\", \"input\": \"null\", \"diff\": \"\\\"Yes\\\"\", \"qv_cutoff\": \"\\\"30\\\"\"}",
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333 "tool_version": "1.0.2",
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334 "type": "tool",
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335 "user_outputs": []
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336 },
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337 "12": {
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338 "annotation": "PLUS strand. Removing all non mtDNA positions from the dataset (as mtDNA was enriched by PCR there is some genomic DNA contamination which is being removed here)",
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339 "id": 12,
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340 "input_connections": {
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341 "input": {
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342 "id": 10,
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343 "output_name": "out_file1"
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344 }
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345 },
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346 "inputs": [],
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347 "name": "Filter",
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348 "outputs": [
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349 {
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350 "name": "out_file1",
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351 "type": "input"
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352 }
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353 ],
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354 "position": {
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355 "left": 885,
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356 "top": 233
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357 },
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358 "tool_errors": null,
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359 "tool_id": "Filter1",
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360 "tool_state": "{\"__page__\": 0, \"cond\": \"\\\"c1=='chrM' and c10 >= 100\\\"\", \"chromInfo\": \"\\\"/galaxy/home/g2main/galaxy_main/tool-data/shared/ucsc/chrom/hg19.len\\\"\", \"input\": \"null\"}",
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361 "tool_version": "1.0.1",
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362 "type": "tool",
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363 "user_outputs": []
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364 },
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365 "13": {
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366 "annotation": "MINUS strand. Removing all non mtDNA positions from the dataset (as mtDNA was enriched by PCR there is some genomic DNA contamination which is being removed here)",
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367 "id": 13,
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368 "input_connections": {
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369 "input": {
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370 "id": 11,
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371 "output_name": "out_file1"
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372 }
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373 },
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374 "inputs": [],
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375 "name": "Filter",
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376 "outputs": [
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377 {
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378 "name": "out_file1",
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379 "type": "input"
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380 }
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381 ],
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382 "position": {
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383 "left": 889,
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384 "top": 1445
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385 },
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386 "tool_errors": null,
|
|
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387 "tool_id": "Filter1",
|
|
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388 "tool_state": "{\"input\": \"null\", \"cond\": \"\\\"c1=='chrM' and c10 >= 100\\\"\", \"__page__\": 0}",
|
|
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389 "tool_version": "1.0.1",
|
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390 "type": "tool",
|
|
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391 "user_outputs": []
|
|
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392 },
|
|
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393 "14": {
|
|
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394 "annotation": "PLUS strand. Filtering all positions where frequency of G allele (c8 is the number of Gs, c10 is the coverage, c6/c10 = frequency of Gs) is higher than 1%. The second expression (c11/c10) verifies that the position contains a variant (c11 contains the total number of variants computed by \"Filter Pileup\" tool).",
|
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395 "id": 14,
|
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396 "input_connections": {
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397 "input": {
|
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398 "id": 12,
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399 "output_name": "out_file1"
|
|
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400 }
|
|
|
401 },
|
|
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402 "inputs": [],
|
|
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403 "name": "Filter",
|
|
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404 "outputs": [
|
|
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405 {
|
|
|
406 "name": "out_file1",
|
|
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407 "type": "input"
|
|
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408 }
|
|
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409 ],
|
|
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410 "position": {
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411 "left": 1130,
|
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412 "top": 434
|
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413 },
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414 "tool_errors": null,
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415 "tool_id": "Filter1",
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|
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416 "tool_state": "{\"input\": \"null\", \"cond\": \"\\\"c8/c10 >= 0.01 and c11/c10 >= 0.01\\\"\", \"__page__\": 0}",
|
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417 "tool_version": "1.0.1",
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418 "type": "tool",
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419 "user_outputs": []
|
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420 },
|
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421 "15": {
|
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422 "annotation": "PLUS strand. Filtering all positions where frequency of C allele (c7 is the number of Cs, c10 is the coverage, c6/c10 = frequency of Cs) is higher than 1%. The second expression (c11/c10) verifies that the position contains a variant (c11 contains the total number of variants computed by \"Filter Pileup\" tool).",
|
|
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423 "id": 15,
|
|
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424 "input_connections": {
|
|
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425 "input": {
|
|
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426 "id": 12,
|
|
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427 "output_name": "out_file1"
|
|
|
428 }
|
|
|
429 },
|
|
|
430 "inputs": [],
|
|
|
431 "name": "Filter",
|
|
|
432 "outputs": [
|
|
|
433 {
|
|
|
434 "name": "out_file1",
|
|
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435 "type": "input"
|
|
|
436 }
|
|
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437 ],
|
|
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438 "position": {
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439 "left": 1134,
|
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440 "top": 303
|
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441 },
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442 "tool_errors": null,
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443 "tool_id": "Filter1",
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444 "tool_state": "{\"input\": \"null\", \"cond\": \"\\\"c7/c10 >= 0.01 and c11/c10 >= 0.01\\\"\", \"__page__\": 0}",
|
|
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445 "tool_version": "1.0.1",
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446 "type": "tool",
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447 "user_outputs": []
|
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448 },
|
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449 "16": {
|
|
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450 "annotation": "PLUS strand. Filtering all positions where frequency of T allele (c9 is the number of Ts, c10 is the coverage, c6/c10 = frequency of Ts) is higher than 1%. The second expression (c11/c10) verifies that the position contains a variant (c11 contains the total number of variants computed by \"Filter Pileup\" tool).",
|
|
|
451 "id": 16,
|
|
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452 "input_connections": {
|
|
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453 "input": {
|
|
|
454 "id": 12,
|
|
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455 "output_name": "out_file1"
|
|
|
456 }
|
|
|
457 },
|
|
|
458 "inputs": [],
|
|
|
459 "name": "Filter",
|
|
|
460 "outputs": [
|
|
|
461 {
|
|
|
462 "name": "out_file1",
|
|
|
463 "type": "input"
|
|
|
464 }
|
|
|
465 ],
|
|
|
466 "position": {
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467 "left": 1134,
|
|
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468 "top": 566
|
|
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469 },
|
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470 "tool_errors": null,
|
|
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471 "tool_id": "Filter1",
|
|
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472 "tool_state": "{\"input\": \"null\", \"cond\": \"\\\"c9/c10 >= 0.01 and c11/c10 >= 0.01\\\"\", \"__page__\": 0}",
|
|
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473 "tool_version": "1.0.1",
|
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474 "type": "tool",
|
|
|
475 "user_outputs": []
|
|
|
476 },
|
|
|
477 "17": {
|
|
|
478 "annotation": "PLUS strand. Filtering all positions where frequency of A allele (c6 is the number of As, c10 is the coverage, c6/c10 = frequency of As) is higher than 1%. The second expression (c11/c10) verifies that the position contains a variant (c11 contains the total number of variants computed by \"Filter Pileup\" tool).",
|
|
|
479 "id": 17,
|
|
|
480 "input_connections": {
|
|
|
481 "input": {
|
|
|
482 "id": 12,
|
|
|
483 "output_name": "out_file1"
|
|
|
484 }
|
|
|
485 },
|
|
|
486 "inputs": [],
|
|
|
487 "name": "Filter",
|
|
|
488 "outputs": [
|
|
|
489 {
|
|
|
490 "name": "out_file1",
|
|
|
491 "type": "input"
|
|
|
492 }
|
|
|
493 ],
|
|
|
494 "position": {
|
|
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495 "left": 1129,
|
|
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496 "top": 175
|
|
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497 },
|
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498 "tool_errors": null,
|
|
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499 "tool_id": "Filter1",
|
|
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500 "tool_state": "{\"input\": \"null\", \"cond\": \"\\\"c6/c10 >= 0.01 and c11/c10 >= 0.01\\\"\", \"__page__\": 0}",
|
|
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501 "tool_version": "1.0.1",
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502 "type": "tool",
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503 "user_outputs": []
|
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504 },
|
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505 "18": {
|
|
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506 "annotation": "",
|
|
|
507 "id": 18,
|
|
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508 "input_connections": {
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509 "input": {
|
|
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510 "id": 13,
|
|
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511 "output_name": "out_file1"
|
|
|
512 }
|
|
|
513 },
|
|
|
514 "inputs": [],
|
|
|
515 "name": "Filter",
|
|
|
516 "outputs": [
|
|
|
517 {
|
|
|
518 "name": "out_file1",
|
|
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519 "type": "input"
|
|
|
520 }
|
|
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521 ],
|
|
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522 "position": {
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523 "left": 1135,
|
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524 "top": 1354
|
|
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525 },
|
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526 "tool_errors": null,
|
|
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527 "tool_id": "Filter1",
|
|
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528 "tool_state": "{\"input\": \"null\", \"cond\": \"\\\"c8/c10 >= 0.01 and c11/c10 >= 0.01\\\"\", \"__page__\": 0}",
|
|
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529 "tool_version": "1.0.1",
|
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530 "type": "tool",
|
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531 "user_outputs": []
|
|
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532 },
|
|
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533 "19": {
|
|
|
534 "annotation": "MINUS strand. Filtering all positions where frequency of A allele (c6 is the number of As, c10 is the coverage, c6/c10 = frequency of As) is higher than 1%. The second expression (c11/c10) verifies that the position contains a variant (c11 contains the total number of variants computed by \"Filter Pileup\" tool).",
|
|
|
535 "id": 19,
|
|
|
536 "input_connections": {
|
|
|
537 "input": {
|
|
|
538 "id": 13,
|
|
|
539 "output_name": "out_file1"
|
|
|
540 }
|
|
|
541 },
|
|
|
542 "inputs": [],
|
|
|
543 "name": "Filter",
|
|
|
544 "outputs": [
|
|
|
545 {
|
|
|
546 "name": "out_file1",
|
|
|
547 "type": "input"
|
|
|
548 }
|
|
|
549 ],
|
|
|
550 "position": {
|
|
|
551 "left": 1136,
|
|
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552 "top": 1105
|
|
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553 },
|
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554 "tool_errors": null,
|
|
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555 "tool_id": "Filter1",
|
|
|
556 "tool_state": "{\"input\": \"null\", \"cond\": \"\\\"c6/c10 >= 0.01 and c11/c10 >= 0.01\\\"\", \"__page__\": 0}",
|
|
|
557 "tool_version": "1.0.1",
|
|
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558 "type": "tool",
|
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559 "user_outputs": []
|
|
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560 },
|
|
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561 "20": {
|
|
|
562 "annotation": "",
|
|
|
563 "id": 20,
|
|
|
564 "input_connections": {
|
|
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565 "input": {
|
|
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566 "id": 13,
|
|
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567 "output_name": "out_file1"
|
|
|
568 }
|
|
|
569 },
|
|
|
570 "inputs": [],
|
|
|
571 "name": "Filter",
|
|
|
572 "outputs": [
|
|
|
573 {
|
|
|
574 "name": "out_file1",
|
|
|
575 "type": "input"
|
|
|
576 }
|
|
|
577 ],
|
|
|
578 "position": {
|
|
|
579 "left": 1128,
|
|
|
580 "top": 1449
|
|
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581 },
|
|
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582 "tool_errors": null,
|
|
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583 "tool_id": "Filter1",
|
|
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584 "tool_state": "{\"input\": \"null\", \"cond\": \"\\\"c9/c10 >= 0.01 and c11/c10 >= 0.01\\\"\", \"__page__\": 0}",
|
|
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585 "tool_version": "1.0.1",
|
|
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586 "type": "tool",
|
|
|
587 "user_outputs": []
|
|
|
588 },
|
|
|
589 "21": {
|
|
|
590 "annotation": "MINUS strand. Filtering all positions where frequency of C allele (c7 is the number of Cs, c10 is the coverage, c6/c10 = frequency of Cs) is higher than 1%. The second expression (c11/c10) verifies that the position contains a variant (c11 contains the total number of variants computed by \"Filter Pileup\" tool).",
|
|
|
591 "id": 21,
|
|
|
592 "input_connections": {
|
|
|
593 "input": {
|
|
|
594 "id": 13,
|
|
|
595 "output_name": "out_file1"
|
|
|
596 }
|
|
|
597 },
|
|
|
598 "inputs": [],
|
|
|
599 "name": "Filter",
|
|
|
600 "outputs": [
|
|
|
601 {
|
|
|
602 "name": "out_file1",
|
|
|
603 "type": "input"
|
|
|
604 }
|
|
|
605 ],
|
|
|
606 "position": {
|
|
|
607 "left": 1128,
|
|
|
608 "top": 1233
|
|
|
609 },
|
|
|
610 "tool_errors": null,
|
|
|
611 "tool_id": "Filter1",
|
|
|
612 "tool_state": "{\"input\": \"null\", \"cond\": \"\\\"c7/c10 >= 0.01 and c11/c10 >= 0.01\\\"\", \"__page__\": 0}",
|
|
|
613 "tool_version": "1.0.1",
|
|
|
614 "type": "tool",
|
|
|
615 "user_outputs": []
|
|
|
616 },
|
|
|
617 "22": {
|
|
|
618 "annotation": "PLUS strand. Results of the fout filtering steps are concatenated. If a position has two alleles with frequency above 1% it will be listed twice in this dataset. The next tool (\"Group\") takes advantage of this.",
|
|
|
619 "id": 22,
|
|
|
620 "input_connections": {
|
|
|
621 "input1": {
|
|
|
622 "id": 17,
|
|
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623 "output_name": "out_file1"
|
|
|
624 },
|
|
|
625 "queries_0|input2": {
|
|
|
626 "id": 15,
|
|
|
627 "output_name": "out_file1"
|
|
|
628 },
|
|
|
629 "queries_1|input2": {
|
|
|
630 "id": 14,
|
|
|
631 "output_name": "out_file1"
|
|
|
632 },
|
|
|
633 "queries_2|input2": {
|
|
|
634 "id": 16,
|
|
|
635 "output_name": "out_file1"
|
|
|
636 }
|
|
|
637 },
|
|
|
638 "inputs": [],
|
|
|
639 "name": "Concatenate queries",
|
|
|
640 "outputs": [
|
|
|
641 {
|
|
|
642 "name": "out_file1",
|
|
|
643 "type": "input"
|
|
|
644 }
|
|
|
645 ],
|
|
|
646 "position": {
|
|
|
647 "left": 1394,
|
|
|
648 "top": 636
|
|
|
649 },
|
|
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650 "tool_errors": null,
|
|
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651 "tool_id": "cat1",
|
|
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652 "tool_state": "{\"__page__\": 0, \"input1\": \"null\", \"queries\": \"[{\\\"input2\\\": null, \\\"__index__\\\": 0}, {\\\"input2\\\": null, \\\"__index__\\\": 1}, {\\\"input2\\\": null, \\\"__index__\\\": 2}]\"}",
|
|
|
653 "tool_version": "1.0.0",
|
|
|
654 "type": "tool",
|
|
|
655 "user_outputs": []
|
|
|
656 },
|
|
|
657 "23": {
|
|
|
658 "annotation": "MINUS strand. Results of the fout filtering steps are concatenated. If a position has two alleles with frequency above 1% it will be listed twice in this dataset. The next tool (\"Group\") takes advantage of this.",
|
|
|
659 "id": 23,
|
|
|
660 "input_connections": {
|
|
|
661 "input1": {
|
|
|
662 "id": 19,
|
|
|
663 "output_name": "out_file1"
|
|
|
664 },
|
|
|
665 "queries_0|input2": {
|
|
|
666 "id": 21,
|
|
|
667 "output_name": "out_file1"
|
|
|
668 },
|
|
|
669 "queries_1|input2": {
|
|
|
670 "id": 18,
|
|
|
671 "output_name": "out_file1"
|
|
|
672 },
|
|
|
673 "queries_2|input2": {
|
|
|
674 "id": 20,
|
|
|
675 "output_name": "out_file1"
|
|
|
676 }
|
|
|
677 },
|
|
|
678 "inputs": [],
|
|
|
679 "name": "Concatenate queries",
|
|
|
680 "outputs": [
|
|
|
681 {
|
|
|
682 "name": "out_file1",
|
|
|
683 "type": "input"
|
|
|
684 }
|
|
|
685 ],
|
|
|
686 "position": {
|
|
|
687 "left": 1397,
|
|
|
688 "top": 862
|
|
|
689 },
|
|
|
690 "tool_errors": null,
|
|
|
691 "tool_id": "cat1",
|
|
|
692 "tool_state": "{\"__page__\": 0, \"input1\": \"null\", \"queries\": \"[{\\\"input2\\\": null, \\\"__index__\\\": 0}, {\\\"input2\\\": null, \\\"__index__\\\": 1}, {\\\"input2\\\": null, \\\"__index__\\\": 2}]\"}",
|
|
|
693 "tool_version": "1.0.0",
|
|
|
694 "type": "tool",
|
|
|
695 "user_outputs": []
|
|
|
696 },
|
|
|
697 "24": {
|
|
|
698 "annotation": "PLUS strand. The previous tool outputs alleles with frequency above 1%. If a position has two alleles (i.e., a heteroplasmy), it will be listed twice. Group tool counts the individual positions and outputs them in the form \"position[tab]count\"",
|
|
|
699 "id": 24,
|
|
|
700 "input_connections": {
|
|
|
701 "input1": {
|
|
|
702 "id": 22,
|
|
|
703 "output_name": "out_file1"
|
|
|
704 }
|
|
|
705 },
|
|
|
706 "inputs": [],
|
|
|
707 "name": "Group",
|
|
|
708 "outputs": [
|
|
|
709 {
|
|
|
710 "name": "out_file1",
|
|
|
711 "type": "tabular"
|
|
|
712 }
|
|
|
713 ],
|
|
|
714 "position": {
|
|
|
715 "left": 1448,
|
|
|
716 "top": 464
|
|
|
717 },
|
|
|
718 "tool_errors": null,
|
|
|
719 "tool_id": "Grouping1",
|
|
|
720 "tool_state": "{\"ignorecase\": \"\\\"False\\\"\", \"groupcol\": \"{\\\"__class__\\\": \\\"UnvalidatedValue\\\", \\\"value\\\": \\\"2\\\"}\", \"input1\": \"null\", \"operations\": \"[{\\\"opcol\\\": {\\\"__class__\\\": \\\"UnvalidatedValue\\\", \\\"value\\\": \\\"2\\\"}, \\\"__index__\\\": 0, \\\"optype\\\": \\\"length\\\", \\\"opround\\\": \\\"yes\\\"}]\", \"__page__\": 0}",
|
|
|
721 "tool_version": "1.9.1",
|
|
|
722 "type": "tool",
|
|
|
723 "user_outputs": []
|
|
|
724 },
|
|
|
725 "25": {
|
|
|
726 "annotation": "MINUS strand. The previous tool outputs alleles with frequency above 1%. If a position has two alleles (i.e., a heteroplasmy), it will be listed twice. Group tool counts the individual positions and outputs them in the form \"position[tab]count\"",
|
|
|
727 "id": 25,
|
|
|
728 "input_connections": {
|
|
|
729 "input1": {
|
|
|
730 "id": 23,
|
|
|
731 "output_name": "out_file1"
|
|
|
732 }
|
|
|
733 },
|
|
|
734 "inputs": [],
|
|
|
735 "name": "Group",
|
|
|
736 "outputs": [
|
|
|
737 {
|
|
|
738 "name": "out_file1",
|
|
|
739 "type": "tabular"
|
|
|
740 }
|
|
|
741 ],
|
|
|
742 "position": {
|
|
|
743 "left": 1490,
|
|
|
744 "top": 1104
|
|
|
745 },
|
|
|
746 "tool_errors": null,
|
|
|
747 "tool_id": "Grouping1",
|
|
|
748 "tool_state": "{\"ignorecase\": \"\\\"False\\\"\", \"groupcol\": \"{\\\"__class__\\\": \\\"UnvalidatedValue\\\", \\\"value\\\": \\\"2\\\"}\", \"input1\": \"null\", \"operations\": \"[{\\\"opcol\\\": {\\\"__class__\\\": \\\"UnvalidatedValue\\\", \\\"value\\\": \\\"2\\\"}, \\\"__index__\\\": 0, \\\"optype\\\": \\\"length\\\", \\\"opround\\\": \\\"yes\\\"}]\", \"__page__\": 0}",
|
|
|
749 "tool_version": "1.9.1",
|
|
|
750 "type": "tool",
|
|
|
751 "user_outputs": []
|
|
|
752 },
|
|
|
753 "26": {
|
|
|
754 "annotation": "PLUS strand. Here the workflow joins the original dataset with the output of the group tools. As a result the output contains the original data plus the count of allelic variants at that site, If there are no allelic variants at a site, the missing column is filled with \"0\" as specified by \"Fill columns by\" option of the Join tool.",
|
|
|
755 "id": 26,
|
|
|
756 "input_connections": {
|
|
|
757 "input1": {
|
|
|
758 "id": 12,
|
|
|
759 "output_name": "out_file1"
|
|
|
760 },
|
|
|
761 "input2": {
|
|
|
762 "id": 24,
|
|
|
763 "output_name": "out_file1"
|
|
|
764 }
|
|
|
765 },
|
|
|
766 "inputs": [],
|
|
|
767 "name": "Join two Queries",
|
|
|
768 "outputs": [
|
|
|
769 {
|
|
|
770 "name": "out_file1",
|
|
|
771 "type": "input"
|
|
|
772 }
|
|
|
773 ],
|
|
|
774 "position": {
|
|
|
775 "left": 1505,
|
|
|
776 "top": 282
|
|
|
777 },
|
|
|
778 "tool_errors": null,
|
|
|
779 "tool_id": "join1",
|
|
|
780 "tool_state": "{\"input2\": \"null\", \"__page__\": 0, \"field1\": \"{\\\"__class__\\\": \\\"UnvalidatedValue\\\", \\\"value\\\": \\\"2\\\"}\", \"partial\": \"\\\"\\\"\", \"field2\": \"{\\\"__class__\\\": \\\"UnvalidatedValue\\\", \\\"value\\\": \\\"1\\\"}\", \"fill_empty_columns\": \"{\\\"fill_empty_columns_switch\\\": \\\"fill_empty\\\", \\\"do_fill_empty_columns\\\": {\\\"column_fill_type\\\": \\\"single_fill_value\\\", \\\"fill_value\\\": \\\"0\\\", \\\"__current_case__\\\": 0}, \\\"fill_columns_by\\\": \\\"fill_unjoined_only\\\", \\\"__current_case__\\\": 1}\", \"unmatched\": \"\\\"-u\\\"\", \"input1\": \"null\"}",
|
|
|
781 "tool_version": "2.0.2",
|
|
|
782 "type": "tool",
|
|
|
783 "user_outputs": []
|
|
|
784 },
|
|
|
785 "27": {
|
|
|
786 "annotation": "MINUS strand. Here the workflow joins the original dataset with the output of the group tools. As a result the output contains the original data plus the count of allelic variants at that site, If there are no allelic variants at a site, the missing column is filled with \"0\" as specified by \"Fill columns by\" option of the Join tool.",
|
|
|
787 "id": 27,
|
|
|
788 "input_connections": {
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789 "input1": {
|
|
|
790 "id": 13,
|
|
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791 "output_name": "out_file1"
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|
|
792 },
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793 "input2": {
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|
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794 "id": 25,
|
|
|
795 "output_name": "out_file1"
|
|
|
796 }
|
|
|
797 },
|
|
|
798 "inputs": [],
|
|
|
799 "name": "Join two Queries",
|
|
|
800 "outputs": [
|
|
|
801 {
|
|
|
802 "name": "out_file1",
|
|
|
803 "type": "input"
|
|
|
804 }
|
|
|
805 ],
|
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806 "position": {
|
|
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807 "left": 1538,
|
|
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808 "top": 1223
|
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809 },
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810 "tool_errors": null,
|
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811 "tool_id": "join1",
|
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812 "tool_state": "{\"input2\": \"null\", \"__page__\": 0, \"field1\": \"{\\\"__class__\\\": \\\"UnvalidatedValue\\\", \\\"value\\\": \\\"2\\\"}\", \"partial\": \"\\\"\\\"\", \"field2\": \"{\\\"__class__\\\": \\\"UnvalidatedValue\\\", \\\"value\\\": \\\"1\\\"}\", \"fill_empty_columns\": \"{\\\"fill_empty_columns_switch\\\": \\\"fill_empty\\\", \\\"do_fill_empty_columns\\\": {\\\"column_fill_type\\\": \\\"single_fill_value\\\", \\\"fill_value\\\": \\\"0\\\", \\\"__current_case__\\\": 0}, \\\"fill_columns_by\\\": \\\"fill_unjoined_only\\\", \\\"__current_case__\\\": 1}\", \"unmatched\": \"\\\"-u\\\"\", \"input1\": \"null\"}",
|
|
|
813 "tool_version": "2.0.2",
|
|
|
814 "type": "tool",
|
|
|
815 "user_outputs": []
|
|
|
816 },
|
|
|
817 "28": {
|
|
|
818 "annotation": "PLUS strand. Removing unnecessary columns from the data.",
|
|
|
819 "id": 28,
|
|
|
820 "input_connections": {
|
|
|
821 "input": {
|
|
|
822 "id": 26,
|
|
|
823 "output_name": "out_file1"
|
|
|
824 }
|
|
|
825 },
|
|
|
826 "inputs": [],
|
|
|
827 "name": "Cut",
|
|
|
828 "outputs": [
|
|
|
829 {
|
|
|
830 "name": "out_file1",
|
|
|
831 "type": "tabular"
|
|
|
832 }
|
|
|
833 ],
|
|
|
834 "position": {
|
|
|
835 "left": 1690,
|
|
|
836 "top": 706
|
|
|
837 },
|
|
|
838 "tool_errors": null,
|
|
|
839 "tool_id": "Cut1",
|
|
|
840 "tool_state": "{\"columnList\": \"\\\"c1,c2,c3,c4,c6,c7,c8,c9,c10,c11,c13\\\"\", \"input\": \"null\", \"delimiter\": \"\\\"T\\\"\", \"__page__\": 0}",
|
|
|
841 "tool_version": "1.0.1",
|
|
|
842 "type": "tool",
|
|
|
843 "user_outputs": []
|
|
|
844 },
|
|
|
845 "29": {
|
|
|
846 "annotation": "MINUS strand. Removing unnecessary columns from the data.",
|
|
|
847 "id": 29,
|
|
|
848 "input_connections": {
|
|
|
849 "input": {
|
|
|
850 "id": 27,
|
|
|
851 "output_name": "out_file1"
|
|
|
852 }
|
|
|
853 },
|
|
|
854 "inputs": [],
|
|
|
855 "name": "Cut",
|
|
|
856 "outputs": [
|
|
|
857 {
|
|
|
858 "name": "out_file1",
|
|
|
859 "type": "tabular"
|
|
|
860 }
|
|
|
861 ],
|
|
|
862 "position": {
|
|
|
863 "left": 1677,
|
|
|
864 "top": 823
|
|
|
865 },
|
|
|
866 "tool_errors": null,
|
|
|
867 "tool_id": "Cut1",
|
|
|
868 "tool_state": "{\"columnList\": \"\\\"c1,c2,c3,c4,c6,c7,c8,c9,c10,c11,c13\\\"\", \"input\": \"null\", \"delimiter\": \"\\\"T\\\"\", \"__page__\": 0}",
|
|
|
869 "tool_version": "1.0.1",
|
|
|
870 "type": "tool",
|
|
|
871 "user_outputs": []
|
|
|
872 },
|
|
|
873 "30": {
|
|
|
874 "annotation": "Joining PLUS and MINUS strands side by side.",
|
|
|
875 "id": 30,
|
|
|
876 "input_connections": {
|
|
|
877 "input1": {
|
|
|
878 "id": 28,
|
|
|
879 "output_name": "out_file1"
|
|
|
880 },
|
|
|
881 "input2": {
|
|
|
882 "id": 29,
|
|
|
883 "output_name": "out_file1"
|
|
|
884 }
|
|
|
885 },
|
|
|
886 "inputs": [],
|
|
|
887 "name": "Join two Queries",
|
|
|
888 "outputs": [
|
|
|
889 {
|
|
|
890 "name": "out_file1",
|
|
|
891 "type": "input"
|
|
|
892 }
|
|
|
893 ],
|
|
|
894 "position": {
|
|
|
895 "left": 1786,
|
|
|
896 "top": 195
|
|
|
897 },
|
|
|
898 "tool_errors": null,
|
|
|
899 "tool_id": "join1",
|
|
|
900 "tool_state": "{\"input2\": \"null\", \"__page__\": 0, \"field1\": \"{\\\"__class__\\\": \\\"UnvalidatedValue\\\", \\\"value\\\": \\\"2\\\"}\", \"partial\": \"\\\"\\\"\", \"field2\": \"{\\\"__class__\\\": \\\"UnvalidatedValue\\\", \\\"value\\\": \\\"2\\\"}\", \"fill_empty_columns\": \"{\\\"fill_empty_columns_switch\\\": \\\"no_fill\\\", \\\"__current_case__\\\": 0}\", \"unmatched\": \"\\\"\\\"\", \"input1\": \"null\"}",
|
|
|
901 "tool_version": "2.0.2",
|
|
|
902 "type": "tool",
|
|
|
903 "user_outputs": []
|
|
|
904 },
|
|
|
905 "31": {
|
|
|
906 "annotation": "Validating strandedness of variants. We require true variants to be validated on both strands. Columns 11 and 22 in the input dataset contain counts of variants computed with the Group tool three steps earlier (\"Group\" step for PLUS and MINUS strand). If the counts are identical (c11== c22) the tool will return \"True\". Otherwise it will return \"Fasle\".",
|
|
|
907 "id": 31,
|
|
|
908 "input_connections": {
|
|
|
909 "input": {
|
|
|
910 "id": 30,
|
|
|
911 "output_name": "out_file1"
|
|
|
912 }
|
|
|
913 },
|
|
|
914 "inputs": [],
|
|
|
915 "name": "Compute",
|
|
|
916 "outputs": [
|
|
|
917 {
|
|
|
918 "name": "out_file1",
|
|
|
919 "type": "input"
|
|
|
920 }
|
|
|
921 ],
|
|
|
922 "position": {
|
|
|
923 "left": 1896,
|
|
|
924 "top": 369
|
|
|
925 },
|
|
|
926 "tool_errors": null,
|
|
|
927 "tool_id": "Add_a_column1",
|
|
|
928 "tool_state": "{\"input\": \"null\", \"cond\": \"\\\"c11 == c22\\\"\", \"round\": \"\\\"no\\\"\", \"__page__\": 0}",
|
|
|
929 "tool_version": "1.1.0",
|
|
|
930 "type": "tool",
|
|
|
931 "user_outputs": []
|
|
|
932 },
|
|
|
933 "32": {
|
|
|
934 "annotation": "Filtering sites where variants did not validate",
|
|
|
935 "id": 32,
|
|
|
936 "input_connections": {
|
|
|
937 "input": {
|
|
|
938 "id": 31,
|
|
|
939 "output_name": "out_file1"
|
|
|
940 }
|
|
|
941 },
|
|
|
942 "inputs": [],
|
|
|
943 "name": "Filter",
|
|
|
944 "outputs": [
|
|
|
945 {
|
|
|
946 "name": "out_file1",
|
|
|
947 "type": "input"
|
|
|
948 }
|
|
|
949 ],
|
|
|
950 "position": {
|
|
|
951 "left": 2105,
|
|
|
952 "top": 404
|
|
|
953 },
|
|
|
954 "tool_errors": null,
|
|
|
955 "tool_id": "Filter1",
|
|
|
956 "tool_state": "{\"input\": \"null\", \"cond\": \"\\\"c23=='False'\\\"\", \"__page__\": 0}",
|
|
|
957 "tool_version": "1.0.1",
|
|
|
958 "type": "tool",
|
|
|
959 "user_outputs": []
|
|
|
960 },
|
|
|
961 "33": {
|
|
|
962 "annotation": "Filtering all True variants",
|
|
|
963 "id": 33,
|
|
|
964 "input_connections": {
|
|
|
965 "input": {
|
|
|
966 "id": 31,
|
|
|
967 "output_name": "out_file1"
|
|
|
968 }
|
|
|
969 },
|
|
|
970 "inputs": [],
|
|
|
971 "name": "Filter",
|
|
|
972 "outputs": [
|
|
|
973 {
|
|
|
974 "name": "out_file1",
|
|
|
975 "type": "input"
|
|
|
976 }
|
|
|
977 ],
|
|
|
978 "position": {
|
|
|
979 "left": 2108,
|
|
|
980 "top": 168
|
|
|
981 },
|
|
|
982 "tool_errors": null,
|
|
|
983 "tool_id": "Filter1",
|
|
|
984 "tool_state": "{\"input\": \"null\", \"cond\": \"\\\"c23=='True'\\\"\", \"__page__\": 0}",
|
|
|
985 "tool_version": "1.0.1",
|
|
|
986 "type": "tool",
|
|
|
987 "user_outputs": []
|
|
|
988 },
|
|
|
989 "34": {
|
|
|
990 "annotation": "For sites that do not contain true variants we force the value of new column to \"0\".",
|
|
|
991 "id": 34,
|
|
|
992 "input_connections": {
|
|
|
993 "input": {
|
|
|
994 "id": 32,
|
|
|
995 "output_name": "out_file1"
|
|
|
996 }
|
|
|
997 },
|
|
|
998 "inputs": [],
|
|
|
999 "name": "Add column",
|
|
|
1000 "outputs": [
|
|
|
1001 {
|
|
|
1002 "name": "out_file1",
|
|
|
1003 "type": "input"
|
|
|
1004 }
|
|
|
1005 ],
|
|
|
1006 "position": {
|
|
|
1007 "left": 1864,
|
|
|
1008 "top": 1247
|
|
|
1009 },
|
|
|
1010 "tool_errors": null,
|
|
|
1011 "tool_id": "addValue",
|
|
|
1012 "tool_state": "{\"__page__\": 0, \"input\": \"null\", \"exp\": \"\\\"0\\\"\", \"iterate\": \"\\\"no\\\"\"}",
|
|
|
1013 "tool_version": "1.0.0",
|
|
|
1014 "type": "tool",
|
|
|
1015 "user_outputs": []
|
|
|
1016 },
|
|
|
1017 "35": {
|
|
|
1018 "annotation": "For True variants we add additional column duplicating column c22, which contains the number of true variants at a site.",
|
|
|
1019 "id": 35,
|
|
|
1020 "input_connections": {
|
|
|
1021 "input": {
|
|
|
1022 "id": 33,
|
|
|
1023 "output_name": "out_file1"
|
|
|
1024 }
|
|
|
1025 },
|
|
|
1026 "inputs": [],
|
|
|
1027 "name": "Compute",
|
|
|
1028 "outputs": [
|
|
|
1029 {
|
|
|
1030 "name": "out_file1",
|
|
|
1031 "type": "input"
|
|
|
1032 }
|
|
|
1033 ],
|
|
|
1034 "position": {
|
|
|
1035 "left": 1861,
|
|
|
1036 "top": 1082
|
|
|
1037 },
|
|
|
1038 "tool_errors": null,
|
|
|
1039 "tool_id": "Add_a_column1",
|
|
|
1040 "tool_state": "{\"input\": \"null\", \"cond\": \"\\\"c22\\\"\", \"round\": \"\\\"yes\\\"\", \"__page__\": 0}",
|
|
|
1041 "tool_version": "1.1.0",
|
|
|
1042 "type": "tool",
|
|
|
1043 "user_outputs": []
|
|
|
1044 },
|
|
|
1045 "36": {
|
|
|
1046 "annotation": "Concatenating true variants and other sites tail-to-head.",
|
|
|
1047 "id": 36,
|
|
|
1048 "input_connections": {
|
|
|
1049 "input1": {
|
|
|
1050 "id": 35,
|
|
|
1051 "output_name": "out_file1"
|
|
|
1052 },
|
|
|
1053 "queries_0|input2": {
|
|
|
1054 "id": 34,
|
|
|
1055 "output_name": "out_file1"
|
|
|
1056 }
|
|
|
1057 },
|
|
|
1058 "inputs": [],
|
|
|
1059 "name": "Concatenate queries",
|
|
|
1060 "outputs": [
|
|
|
1061 {
|
|
|
1062 "name": "out_file1",
|
|
|
1063 "type": "input"
|
|
|
1064 }
|
|
|
1065 ],
|
|
|
1066 "position": {
|
|
|
1067 "left": 2073,
|
|
|
1068 "top": 1156
|
|
|
1069 },
|
|
|
1070 "tool_errors": null,
|
|
|
1071 "tool_id": "cat1",
|
|
|
1072 "tool_state": "{\"__page__\": 0, \"input1\": \"null\", \"queries\": \"[{\\\"input2\\\": null, \\\"__index__\\\": 0}]\"}",
|
|
|
1073 "tool_version": "1.0.0",
|
|
|
1074 "type": "tool",
|
|
|
1075 "user_outputs": []
|
|
|
1076 },
|
|
|
1077 "37": {
|
|
|
1078 "annotation": "Because the input dataset contains plus and minus strand data side by side (remember we joined PLUS and MINUS five steps ago using \"Join two Queries\" tool), we need to combine allelic counts by summing up all As (column 5 in PLUS and column 16 in MINUS)",
|
|
|
1079 "id": 37,
|
|
|
1080 "input_connections": {
|
|
|
1081 "input": {
|
|
|
1082 "id": 36,
|
|
|
1083 "output_name": "out_file1"
|
|
|
1084 }
|
|
|
1085 },
|
|
|
1086 "inputs": [],
|
|
|
1087 "name": "Compute",
|
|
|
1088 "outputs": [
|
|
|
1089 {
|
|
|
1090 "name": "out_file1",
|
|
|
1091 "type": "input"
|
|
|
1092 }
|
|
|
1093 ],
|
|
|
1094 "position": {
|
|
|
1095 "left": 2137,
|
|
|
1096 "top": 1030
|
|
|
1097 },
|
|
|
1098 "tool_errors": null,
|
|
|
1099 "tool_id": "Add_a_column1",
|
|
|
1100 "tool_state": "{\"input\": \"null\", \"cond\": \"\\\"c5+c16\\\"\", \"round\": \"\\\"yes\\\"\", \"__page__\": 0}",
|
|
|
1101 "tool_version": "1.1.0",
|
|
|
1102 "type": "tool",
|
|
|
1103 "user_outputs": []
|
|
|
1104 },
|
|
|
1105 "38": {
|
|
|
1106 "annotation": "... summing up all Cs (column 6 in PLUS and column 17 in MINUS)",
|
|
|
1107 "id": 38,
|
|
|
1108 "input_connections": {
|
|
|
1109 "input": {
|
|
|
1110 "id": 37,
|
|
|
1111 "output_name": "out_file1"
|
|
|
1112 }
|
|
|
1113 },
|
|
|
1114 "inputs": [],
|
|
|
1115 "name": "Compute",
|
|
|
1116 "outputs": [
|
|
|
1117 {
|
|
|
1118 "name": "out_file1",
|
|
|
1119 "type": "input"
|
|
|
1120 }
|
|
|
1121 ],
|
|
|
1122 "position": {
|
|
|
1123 "left": 2185,
|
|
|
1124 "top": 936
|
|
|
1125 },
|
|
|
1126 "tool_errors": null,
|
|
|
1127 "tool_id": "Add_a_column1",
|
|
|
1128 "tool_state": "{\"input\": \"null\", \"cond\": \"\\\"c6+c17\\\"\", \"round\": \"\\\"yes\\\"\", \"__page__\": 0}",
|
|
|
1129 "tool_version": "1.1.0",
|
|
|
1130 "type": "tool",
|
|
|
1131 "user_outputs": []
|
|
|
1132 },
|
|
|
1133 "39": {
|
|
|
1134 "annotation": "... summing up all Gs (column 7 in PLUS and column 18 in MINUS)",
|
|
|
1135 "id": 39,
|
|
|
1136 "input_connections": {
|
|
|
1137 "input": {
|
|
|
1138 "id": 38,
|
|
|
1139 "output_name": "out_file1"
|
|
|
1140 }
|
|
|
1141 },
|
|
|
1142 "inputs": [],
|
|
|
1143 "name": "Compute",
|
|
|
1144 "outputs": [
|
|
|
1145 {
|
|
|
1146 "name": "out_file1",
|
|
|
1147 "type": "input"
|
|
|
1148 }
|
|
|
1149 ],
|
|
|
1150 "position": {
|
|
|
1151 "left": 2221,
|
|
|
1152 "top": 831
|
|
|
1153 },
|
|
|
1154 "tool_errors": null,
|
|
|
1155 "tool_id": "Add_a_column1",
|
|
|
1156 "tool_state": "{\"input\": \"null\", \"cond\": \"\\\"c7+c18\\\"\", \"round\": \"\\\"yes\\\"\", \"__page__\": 0}",
|
|
|
1157 "tool_version": "1.1.0",
|
|
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1158 "type": "tool",
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1159 "user_outputs": []
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1160 },
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1161 "40": {
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1162 "annotation": "... summing up all Ts (column 8 in PLUS and column 19 in MINUS)",
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1163 "id": 40,
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1164 "input_connections": {
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1165 "input": {
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1166 "id": 39,
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1167 "output_name": "out_file1"
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1168 }
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1169 },
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1170 "inputs": [],
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1171 "name": "Compute",
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1172 "outputs": [
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1173 {
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1174 "name": "out_file1",
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1175 "type": "input"
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1176 }
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1177 ],
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1180 "top": 716
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1181 },
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1185 "tool_version": "1.1.0",
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1186 "type": "tool",
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1187 "user_outputs": []
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1188 },
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1189 "41": {
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1190 "annotation": "... summing up coverage (column 9 in PLUS and column 20 in MINUS)",
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1191 "id": 41,
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1192 "input_connections": {
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1196 }
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1197 },
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1198 "inputs": [],
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1199 "name": "Compute",
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1200 "outputs": [
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1201 {
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1202 "name": "out_file1",
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1203 "type": "input"
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1204 }
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1208 "top": 598
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1209 },
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1215 "user_outputs": []
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1216 },
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1217 "42": {
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1218 "annotation": "Finally, we clean up all unnecessary columns and generate a combined dataset that will contain 10 columns:\n[1] Chromosome\n[2] Start\n[3] End\n[4] Base in the reference genome\n[5] Number of As\n[6] Number of Cs\n[7] Number of Gs\n[8] Number of Ts\n[9] Coverage at that position\n[10] Number of variants (differences from reference abve 1% level).",
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1219 "id": 42,
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1220 "input_connections": {
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1221 "input": {
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1222 "id": 41,
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1223 "output_name": "out_file1"
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1224 }
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1225 },
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1226 "inputs": [],
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1227 "name": "Cut",
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1228 "outputs": [
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1229 {
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1230 "name": "out_file1",
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1231 "type": "tabular"
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1232 }
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1233 ],
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1234 "position": {
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1235 "left": 2439,
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1236 "top": 1185
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1237 },
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1239 "tool_id": "Cut1",
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1240 "tool_state": "{\"columnList\": \"\\\"c1,c2,c3,c4,c25,c26,c27,c28,c29,c24\\\"\", \"input\": \"null\", \"delimiter\": \"\\\"T\\\"\", \"__page__\": 0}",
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1241 "tool_version": "1.0.1",
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1242 "type": "tool",
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1243 "user_outputs": []
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1244 }
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1245 }
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1246 } |
