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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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1
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5 "name": "Detrprok_wf",
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0
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6 "steps": {
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7 "0": {
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1
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8 "annotation": "Select here annotation file containing coding genes, tRNAs, rRNAs and known ncRNAs. You can download it from GJI (http://genome.jgi.doe.gov) or NCBI (http://ftp.ncbi.nih.gov/genomes/Bacteria). Caution: 1srt column should have exactly the same identifier as the genome sequence used for mapping.",
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0
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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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1
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13 "description": "Select here annotation file containing coding genes, tRNAs, rRNAs and known ncRNAs. You can download it from GJI (http://genome.jgi.doe.gov) or NCBI (http://ftp.ncbi.nih.gov/genomes/Bacteria). Caution: 1srt column should have exactly the same identifier as the genome sequence used for mapping.",
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14 "name": "genome annotations"
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0
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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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1
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20 "left": 200,
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21 "top": 231.00001525878906
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0
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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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1
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25 "tool_state": "{\"name\": \"genome annotations\"}",
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0
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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": "Select here the bam file resulting from the mapping of RNA-seq reads on the genome sequence. You may use Bowtie or another mapper (use appropriate mapping option to retain only uniquely mapping reads).",
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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": "Select here the bam file resulting from the mapping of RNA-seq reads on the genome sequence. You may use Bowtie or another mapper (use appropriate mapping option to retain only uniquely mapping reads).",
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37 "name": "read alignments on genome"
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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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1
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43 "left": 205,
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44 "top": 403.00001525878906
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0
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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\": \"read alignments on genome\"}",
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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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1
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54 "annotation": "Select here the GFF file features that will be considered as initial annotations. Any term added here will cause pre-existing features with this term not to be predicted again by the workflow. Please use a comma separated list and use \"CDS\" rather than \"gene\" for protein coding genes. Suggested value: rRNA,tRNA,ncRNA,CDS",
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0
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55 "id": 2,
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56 "input_connections": {
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1
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57 "formatType|inputFileName": {
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0
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58 "id": 0,
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59 "output_name": "output"
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60 }
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61 },
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1
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62 "inputs": [
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63 {
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64 "description": "runtime parameter for tool clean transcript file",
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65 "name": "optionType"
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66 }
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67 ],
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68 "name": "clean transcript file",
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0
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69 "outputs": [
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70 {
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71 "name": "outputFile",
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1
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72 "type": "gtf"
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0
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73 }
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74 ],
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75 "position": {
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1
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76 "left": 457,
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77 "top": 218.00001525878906
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0
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78 },
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1
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79 "post_job_actions": {
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80 "RenameDatasetActionoutputFile": {
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81 "action_arguments": {
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82 "newname": "annotation selection"
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83 },
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84 "action_type": "RenameDatasetAction",
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85 "output_name": "outputFile"
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86 }
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87 },
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0
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88 "tool_errors": null,
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1
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89 "tool_id": "toolshed.g2.bx.psu.edu/repos/yufei-luo/s_mart/CleanTranscriptFile/1.0.0",
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90 "tool_state": "{\"optionType\": \"{\\\"type\\\": \\\"Yes\\\", \\\"value\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"__current_case__\\\": 0}\", \"formatType\": \"{\\\"inputFileName\\\": null, \\\"__current_case__\\\": 0, \\\"FormatInputFileName\\\": \\\"gff\\\"}\", \"chromInfo\": \"\\\"/srv/galaxy/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\", \"__page__\": 0}",
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0
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91 "tool_version": "1.0.0",
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92 "type": "tool",
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93 "user_outputs": []
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94 },
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95 "3": {
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96 "annotation": "Technical step (format change).",
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97 "id": 3,
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98 "input_connections": {
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99 "input1": {
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100 "id": 1,
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101 "output_name": "output"
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102 }
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103 },
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104 "inputs": [],
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105 "name": "BAM-to-SAM",
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106 "outputs": [
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107 {
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108 "name": "output1",
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109 "type": "sam"
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110 }
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111 ],
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112 "position": {
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1
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113 "left": 428,
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114 "top": 400.00001525878906
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0
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115 },
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116 "post_job_actions": {
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117 "RenameDatasetActionoutput1": {
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118 "action_arguments": {
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1
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119 "newname": "Read alignments (SAM format)"
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0
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120 },
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121 "action_type": "RenameDatasetAction",
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122 "output_name": "output1"
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123 }
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124 },
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125 "tool_errors": null,
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126 "tool_id": "bam_to_sam",
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1
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127 "tool_state": "{\"header\": \"\\\"True\\\"\", \"input1\": \"null\", \"chromInfo\": \"\\\"/srv/galaxy/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\", \"__page__\": 0}",
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0
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128 "tool_version": "1.0.3",
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129 "type": "tool",
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130 "user_outputs": []
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131 },
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132 "4": {
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1
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133 "annotation": "Clusters annotated proximal genes into operons. Parameter to be set: op_gap. Genes separated by a gap smaller than op_gap are clustered (suggested value: 10 to 150).",
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0
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134 "id": 4,
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135 "input_connections": {
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136 "formatType|inputFileName": {
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137 "id": 2,
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138 "output_name": "outputFile"
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139 }
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140 },
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141 "inputs": [
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142 {
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1
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143 "description": "runtime parameter for tool clusterize",
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0
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144 "name": "distance"
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145 }
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146 ],
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1
|
147 "name": "clusterize",
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0
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148 "outputs": [
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149 {
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150 "name": "outputFileGff",
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151 "type": "gff3"
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152 }
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153 ],
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154 "position": {
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1
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155 "left": 700,
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156 "top": 200.00001525878906
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0
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157 },
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158 "post_job_actions": {
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159 "RenameDatasetActionoutputFileGff": {
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160 "action_arguments": {
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1
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161 "newname": "Annotation with operon-like features"
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0
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162 },
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163 "action_type": "RenameDatasetAction",
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164 "output_name": "outputFileGff"
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165 }
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166 },
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167 "tool_errors": null,
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168 "tool_id": "toolshed.g2.bx.psu.edu/repos/yufei-luo/s_mart/MergingDataClusterize/1.0.0",
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1
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169 "tool_state": "{\"normalize\": \"\\\"False\\\"\", \"__page__\": 0, \"formatType\": \"{\\\"inputFileName\\\": null, \\\"__current_case__\\\": 1, \\\"FormatInputFileName\\\": \\\"gff\\\"}\", \"distance\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"colinear\": \"\\\"True\\\"\", \"chromInfo\": \"\\\"/srv/galaxy/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\"}",
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0
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170 "tool_version": "1.0.0",
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171 "type": "tool",
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172 "user_outputs": []
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173 },
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174 "5": {
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1
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175 "annotation": "Clusters overlapping or proximal reads to produce read clusters. Parameter to be set: clust_gap. Reads separated by a gap smaller than clust_gap are clustered (suggested value: 0 to 20 ; a value of 0 will cluster only overlapping reads while a value of 20 will cluster reads even if they are 20-nt apart)",
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0
|
176 "id": 5,
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177 "input_connections": {
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178 "formatType|inputFileName": {
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179 "id": 3,
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180 "output_name": "output1"
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181 }
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182 },
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183 "inputs": [
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184 {
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1
|
185 "description": "runtime parameter for tool clusterize",
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0
|
186 "name": "distance"
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|
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187 }
|
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188 ],
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1
|
189 "name": "clusterize",
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0
|
190 "outputs": [
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191 {
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192 "name": "outputFileGff",
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193 "type": "gff3"
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194 }
|
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195 ],
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196 "position": {
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1
|
197 "left": 662,
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198 "top": 505.00001525878906
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0
|
199 },
|
|
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200 "post_job_actions": {
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201 "RenameDatasetActionoutputFileGff": {
|
|
|
202 "action_arguments": {
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1
|
203 "newname": "Read clusters (with exon)"
|
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0
|
204 },
|
|
|
205 "action_type": "RenameDatasetAction",
|
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206 "output_name": "outputFileGff"
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207 }
|
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208 },
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209 "tool_errors": null,
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210 "tool_id": "toolshed.g2.bx.psu.edu/repos/yufei-luo/s_mart/MergingDataClusterize/1.0.0",
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1
|
211 "tool_state": "{\"normalize\": \"\\\"False\\\"\", \"__page__\": 0, \"formatType\": \"{\\\"inputFileName\\\": null, \\\"__current_case__\\\": 4, \\\"FormatInputFileName\\\": \\\"sam\\\"}\", \"distance\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"colinear\": \"\\\"True\\\"\", \"chromInfo\": \"\\\"/srv/galaxy/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\"}",
|
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0
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212 "tool_version": "1.0.0",
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213 "type": "tool",
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214 "user_outputs": []
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215 },
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216 "6": {
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1
|
217 "annotation": "Technical step: suppresses unwanted \"exon\" features created by the previous clustering step.",
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0
|
218 "id": 6,
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219 "input_connections": {
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1
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220 "inputFile": {
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0
|
221 "id": 4,
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222 "output_name": "outputFileGff"
|
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1
|
223 }
|
|
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224 },
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225 "inputs": [],
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226 "name": "remove exon lines",
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227 "outputs": [
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228 {
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229 "name": "outputFile",
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230 "type": "gff3"
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231 }
|
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232 ],
|
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233 "position": {
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234 "left": 892,
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235 "top": 221.00001525878906
|
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236 },
|
|
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237 "post_job_actions": {
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238 "RenameDatasetActionoutputFile": {
|
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239 "action_arguments": {
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240 "newname": "Annotation with operon-like (without exon)"
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241 },
|
|
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242 "action_type": "RenameDatasetAction",
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243 "output_name": "outputFile"
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244 }
|
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245 },
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246 "tool_errors": null,
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247 "tool_id": "toolshed.g2.bx.psu.edu/repos/yufei-luo/s_mart/removeExonLines/1.0.0",
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248 "tool_state": "{\"__page__\": 0, \"chromInfo\": \"\\\"/srv/galaxy/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\", \"inputFile\": \"null\"}",
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249 "tool_version": "1.0.0",
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250 "type": "tool",
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251 "user_outputs": []
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252 },
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253 "7": {
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254 "annotation": "Technical step: suppresses unwanted \"exon\" features created by the previous clustering step.",
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255 "id": 7,
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256 "input_connections": {
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257 "inputFile": {
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0
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258 "id": 5,
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259 "output_name": "outputFileGff"
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260 }
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261 },
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1
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262 "inputs": [],
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263 "name": "remove exon lines",
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264 "outputs": [
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0
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265 {
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1
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266 "name": "outputFile",
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267 "type": "gff3"
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0
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268 }
|
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269 ],
|
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1
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270 "position": {
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271 "left": 892,
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272 "top": 505.00001525878906
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273 },
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274 "post_job_actions": {
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275 "RenameDatasetActionoutputFile": {
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276 "action_arguments": {
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277 "newname": "Read clusters"
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278 },
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279 "action_type": "RenameDatasetAction",
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280 "output_name": "outputFile"
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281 }
|
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282 },
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283 "tool_errors": null,
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284 "tool_id": "toolshed.g2.bx.psu.edu/repos/yufei-luo/s_mart/removeExonLines/1.0.0",
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285 "tool_state": "{\"__page__\": 0, \"chromInfo\": \"\\\"/srv/galaxy/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\", \"inputFile\": \"null\"}",
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286 "tool_version": "1.0.0",
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287 "type": "tool",
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288 "user_outputs": []
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289 },
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290 "8": {
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291 "annotation": "Technical step: orders the features by increasing positions.",
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292 "id": 8,
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293 "input_connections": {
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294 "formatType|inputFileName": {
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295 "id": 6,
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296 "output_name": "outputFile"
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297 }
|
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298 },
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299 "inputs": [],
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300 "name": "collapse reads",
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0
|
301 "outputs": [
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302 {
|
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303 "name": "outputFileGff",
|
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304 "type": "gff3"
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305 }
|
|
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306 ],
|
|
|
307 "position": {
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|
1
|
308 "left": 1072,
|
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309 "top": 261.00001525878906
|
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310 },
|
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311 "post_job_actions": {
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312 "RenameDatasetActionoutputFileGff": {
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313 "action_arguments": {
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314 "newname": "Annotation list with operon-like feature"
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315 },
|
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316 "action_type": "RenameDatasetAction",
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317 "output_name": "outputFileGff"
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318 }
|
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319 },
|
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320 "tool_errors": null,
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|
321 "tool_id": "toolshed.g2.bx.psu.edu/repos/yufei-luo/s_mart/collapseReads/1.0.0",
|
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|
322 "tool_state": "{\"__page__\": 0, \"formatType\": \"{\\\"inputFileName\\\": null, \\\"__current_case__\\\": 3, \\\"FormatInputFileName\\\": \\\"gff3\\\"}\", \"chromInfo\": \"\\\"/srv/galaxy/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\", \"strand\": \"\\\"False\\\"\"}",
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323 "tool_version": "1.0.0",
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324 "type": "tool",
|
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325 "user_outputs": []
|
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326 },
|
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|
327 "9": {
|
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|
328 "annotation": "Selects read clusters that form new independent annotations. Parameter to be set: RNA_gap. Read clusters at a distance from existing annotations larger than RNA_gap are selected (suggested value: 25).",
|
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329 "id": 9,
|
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330 "input_connections": {
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331 "formatType2|inputFileName2": {
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332 "id": 8,
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333 "output_name": "outputFileGff"
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334 },
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335 "formatType|inputFileName1": {
|
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336 "id": 7,
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337 "output_name": "outputFile"
|
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338 }
|
|
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339 },
|
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340 "inputs": [
|
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341 {
|
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|
342 "description": "runtime parameter for tool compare overlapping small query",
|
|
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343 "name": "OptionDistance"
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|
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344 }
|
|
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345 ],
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346 "name": "compare overlapping small query",
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347 "outputs": [
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348 {
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349 "name": "outputFileGff",
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350 "type": "gff3"
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351 }
|
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352 ],
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353 "position": {
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|
354 "left": 1197,
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355 "top": 521.0000152587891
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356 },
|
|
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357 "post_job_actions": {
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358 "RenameDatasetActionoutputFileGff": {
|
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359 "action_arguments": {
|
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360 "newname": "Read clusters not overlapping annotation"
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361 },
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362 "action_type": "RenameDatasetAction",
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363 "output_name": "outputFileGff"
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364 }
|
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365 },
|
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366 "tool_errors": null,
|
|
|
367 "tool_id": "toolshed.g2.bx.psu.edu/repos/yufei-luo/s_mart/CompareOverlappingSmallQuery/1.0.0",
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419 "11": {
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420 "annotation": "Selection of read clusters that are antisense of an extended annotation. This step produces a first list of antisense candidates.",
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462 "id": 12,
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501 "13": {
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502 "annotation": "Technical step: merging of annotations and their overlapping read clusters. This will be used to extend annotation.",
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513 },
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514 "inputs": [],
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515 "name": "Concatenate datasets",
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516 "outputs": [
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543 "annotation": "Filters antisense RNAs based on their size. Parameter to be set: as_min_size. as_min_size is the minimal size for calling an antisense RNA (suggestion: 50).",
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544 "id": 14,
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584 "15": {
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585 "annotation": "Filters small RNAs based on their size. Parameter to be set: sRNA_min_size. sRNA_min_size is the minimal size for calling a small RNA (suggestion: 50).",
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626 "16": {
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627 "annotation": "Extend annotations with overlapping or proximal read clusters in the same direction. Parameter to be set: RNA_gap. Read cluster and annotations separated by a gap smaller than RNA_gap are clustered. Caution: use the same RNA_gap value as previous step!",
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628 "id": 16,
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668 "17": {
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669 "annotation": "Filters antisense RNA candidates based on their number of overlapping reads. Parameter to be set: as_min_reads. Antisense RNAs with a number of reads higher than as_min_reads are selected (suggested value: 22).",
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677 "inputs": [
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678 {
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1406 }
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1407 },
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1408 "inputs": [],
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1409 "name": "Extract features",
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1411 {
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1444 },
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1475 "id": 38,
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1477 "inputFile": {
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1486 "name": "outputFile",
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1510 "39": {
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1511 "annotation": "Technical step: change feature name from urt5 to 5_extension",
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1516 "output_name": "out_file1"
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1517 }
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1518 },
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1519 "inputs": [],
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1520 "name": "change GFF features",
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1545 "user_outputs": []
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1548 "annotation": "Filters 5' extensions based on their size. Parameter to be set: 5_extension_min_size. 5' extensions larger than 5_extension_min_size are selected (suggestion value: 50).",
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1549 "id": 40,
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1550 "input_connections": {
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1558 "description": "runtime parameter for tool restrict from size",
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1559 "name": "OptionMin"
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1560 }
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1561 ],
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1564 {
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1565 "name": "outputFileGff",
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1566 "type": "gff3"
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1629 "user_outputs": []
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1641 "name": "colorGff",
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1644 "name": "outputFile",
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