annotate Add_chr_to_first_column_of_a_6_columns_BED_file.ga @ 0:16fc7f46ee23 draft default tip

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author bgruening
date Thu, 03 Apr 2014 11:11:15 -0400
parents
children
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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": "Add 'chr' to first column of a BED file (must have 6 columns)",
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6 "steps": {
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7 "0": {
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8 "annotation": "",
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11 "inputs": [
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12 {
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13 "description": "",
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14 "name": "BED file"
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15 }
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16 ],
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17 "name": "Input dataset",
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18 "outputs": [],
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19 "position": {
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20 "left": 200,
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21 "top": 193
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22 },
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25 "tool_state": "{\"name\": \"BED file\"}",
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26 "tool_version": null,
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27 "type": "data_input",
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28 "user_outputs": []
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29 },
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30 "1": {
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31 "annotation": "",
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32 "id": 1,
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33 "input_connections": {
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34 "input": {
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35 "id": 0,
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36 "output_name": "output"
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37 }
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38 },
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39 "inputs": [],
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40 "name": "Add column",
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41 "outputs": [
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42 {
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43 "name": "out_file1",
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44 "type": "input"
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45 }
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46 ],
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47 "position": {
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49 "top": 200
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50 },
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53 "action_arguments": {},
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54 "action_type": "HideDatasetAction",
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55 "output_name": "out_file1"
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56 }
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57 },
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58 "tool_errors": null,
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60 "tool_state": "{\"__page__\": 0, \"__rerun_remap_job_id__\": null, \"exp\": \"\\\"chr\\\"\", \"iterate\": \"\\\"no\\\"\", \"input\": \"null\", \"chromInfo\": \"\\\"/data2/galaxy/galaxy-dist/tool-data/shared/ucsc/chrom/mm9.len\\\"\"}",
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61 "tool_version": "1.0.0",
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62 "type": "tool",
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63 "user_outputs": []
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64 },
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65 "2": {
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66 "annotation": "",
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67 "id": 2,
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68 "input_connections": {
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69 "input1": {
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70 "id": 1,
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71 "output_name": "out_file1"
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72 }
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73 },
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74 "inputs": [],
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75 "name": "Merge Columns",
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76 "outputs": [
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77 {
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78 "name": "out_file1",
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79 "type": "tabular"
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80 }
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81 ],
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82 "position": {
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85 },
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88 "action_arguments": {},
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89 "action_type": "HideDatasetAction",
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91 }
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92 },
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95 "tool_state": "{\"__page__\": 0, \"input1\": \"null\", \"__rerun_remap_job_id__\": null, \"col2\": \"{\\\"__class__\\\": \\\"UnvalidatedValue\\\", \\\"value\\\": \\\"1\\\"}\", \"col1\": \"{\\\"__class__\\\": \\\"UnvalidatedValue\\\", \\\"value\\\": \\\"7\\\"}\", \"chromInfo\": \"\\\"/data2/galaxy/galaxy-dist/tool-data/shared/ucsc/chrom/mm9.len\\\"\", \"columns\": \"[]\"}",
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96 "tool_version": "1.0.1",
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97 "type": "tool",
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98 "user_outputs": []
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99 },
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100 "3": {
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101 "annotation": "",
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103 "input_connections": {
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104 "input": {
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106 "output_name": "out_file1"
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107 }
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108 },
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109 "inputs": [],
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110 "name": "Cut",
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111 "outputs": [
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112 {
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113 "name": "out_file1",
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114 "type": "tabular"
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115 }
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116 ],
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117 "position": {
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118 "left": 872,
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119 "top": 205
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120 },
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123 "action_arguments": {
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125 },
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126 "action_type": "ChangeDatatypeAction",
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127 "output_name": "out_file1"
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128 },
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130 "action_arguments": {
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131 "newname": "added \"chr\" to chromosome name"
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132 },
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133 "action_type": "RenameDatasetAction",
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134 "output_name": "out_file1"
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135 }
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138 "tool_id": "Cut1",
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139 "tool_state": "{\"__page__\": 0, \"__rerun_remap_job_id__\": null, \"delimiter\": \"\\\"T\\\"\", \"columnList\": \"\\\"c8,c2,c3,c4,c5,c6\\\"\", \"input\": \"null\", \"chromInfo\": \"\\\"/data2/galaxy/galaxy-dist/tool-data/shared/ucsc/chrom/mm9.len\\\"\"}",
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140 "tool_version": "1.0.2",
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141 "type": "tool",
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142 "user_outputs": []
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143 }
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144 }
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145 }