1#@UGENE_WORKFLOW 2#This sample describes how to search for TFBS with different methods and how to write the results into one output file. 3# 4#First, the schema reads sequences input by a user. Then, each sequence goes to searching TFBS elements. At that time two reading elements reads the matrix and model for TFBS searching and transfering this data into TFBS searching elements. After that the TFBS searching elements searches TFBS in the input sequences. After that the two data flows multiplexes into one output data flow. And finally, the multiplexed data are written into file, specified by a user. 5# 6#You can configure the parameters of Search for TFBS with Weight Matrix, Search TFBS with SITECON and Multiplexer elements. 7# 8#To try out this sample, add the input files to the Read Sequence element, select the Read Weight Matrix, Read SITECON model and select name and location of the output file in the Write Sequence element and run the schema. 9# 10 11workflow "Search for tfbs"{ 12 read-sequence { 13 type:read-sequence; 14 name:"Read Sequence"; 15 } 16 write-sequence { 17 type:write-sequence; 18 name:"Write Sequence"; 19 document-format:genbank; 20 url-out:tfbs.gb; 21 } 22 multiplexer { 23 type:multiplexer; 24 name:Multiplexer; 25 } 26 sitecon-search { 27 type:sitecon-search; 28 name:"Search for TFBS with SITECON"; 29 result-name:sitecon; 30 } 31 wmatrix-search { 32 type:wmatrix-search; 33 name:"Search for TFBS with Weight Matrix"; 34 result-name:weight_matrix; 35 } 36 sitecon-read { 37 type:sitecon-read; 38 name:"Read SITECON Model"; 39 } 40 wmatrix-read { 41 type:wmatrix-read; 42 name:"Read Weight Matrix"; 43 } 44 45 46 .actor-bindings { 47 multiplexer.output-data->write-sequence.in-sequence 48 sitecon-search.out-annotations->multiplexer.input-data-2 49 wmatrix-search.out-annotations->multiplexer.input-data-1 50 sitecon-read.out-sitecon->sitecon-search.in-sitecon 51 wmatrix-read.out-wmatrix->wmatrix-search.in-wmatrix 52 read-sequence.out-sequence->wmatrix-search.in-sequence 53 read-sequence.out-sequence->sitecon-search.in-sequence 54 } 55 56 read-sequence.annotations->write-sequence.in-sequence.annotations 57 sitecon-search.annotations->write-sequence.in-sequence.annotations 58 wmatrix-search.annotations->write-sequence.in-sequence.annotations 59 read-sequence.sequence->write-sequence.in-sequence.sequence 60 read-sequence.sequence->sitecon-search.in-sequence.sequence 61 sitecon-read.sitecon-model->sitecon-search.in-sitecon.sitecon-model 62 read-sequence.sequence->wmatrix-search.in-sequence.sequence 63 wmatrix-read.wmatrix->wmatrix-search.in-wmatrix.wmatrix 64 65 .meta { 66 visual { 67 read-sequence { 68 pos:"-892 -468"; 69 style:ext; 70 bg-color-ext:"0 128 128 64"; 71 bounds:"-30 -30 150.25 44"; 72 out-sequence.angle:357.083; 73 } 74 write-sequence { 75 pos:"-159.25 -474"; 76 style:ext; 77 bg-color-ext:"0 128 128 64"; 78 bounds:"-30 -30 149.25 50"; 79 in-sequence.angle:190.701; 80 } 81 multiplexer { 82 pos:"-408 -524"; 83 style:ext; 84 bg-color-ext:"0 128 128 64"; 85 bounds:"-30 -30 150 149"; 86 input-data-1.angle:236.31; 87 input-data-2.angle:249.034; 88 output-data.angle:339.809; 89 } 90 sitecon-search { 91 pos:"-646 -418"; 92 style:ext; 93 bg-color-ext:"0 128 128 64"; 94 bounds:"-30 -30 150 149"; 95 in-sequence.angle:244.622; 96 in-sitecon.angle:290.726; 97 out-annotations.angle:339.044; 98 } 99 wmatrix-search { 100 pos:"-645 -629"; 101 style:ext; 102 bg-color-ext:"0 128 128 64"; 103 bounds:"-30 -30 150 150"; 104 in-sequence.angle:241.557; 105 in-wmatrix.angle:27.613; 106 out-annotations.angle:338.819; 107 } 108 sitecon-read { 109 pos:"-645 -211"; 110 style:ext; 111 bg-color-ext:"0 128 128 64"; 112 bounds:"-30 -30 150 40"; 113 out-sitecon.angle:28.0725; 114 } 115 wmatrix-read { 116 pos:"-643 -728"; 117 style:ext; 118 bg-color-ext:"0 128 128 64"; 119 bounds:"-30 -30 146 41"; 120 out-wmatrix.angle:323.393; 121 } 122 read-sequence.out-sequence->wmatrix-search.in-sequence { 123 text-pos:"-57.5 -26"; 124 } 125 read-sequence.out-sequence->sitecon-search.in-sequence { 126 text-pos:"-57.5 4"; 127 } 128 multiplexer.output-data->write-sequence.in-sequence { 129 text-pos:"-24 -75"; 130 } 131 sitecon-search.out-annotations->multiplexer.input-data-2 { 132 text-pos:"-10 36"; 133 } 134 wmatrix-search.out-annotations->multiplexer.input-data-1 { 135 text-pos:"-10 -69"; 136 } 137 sitecon-read.out-sitecon->sitecon-search.in-sitecon { 138 text-pos:"78 -10"; 139 } 140 wmatrix-read.out-wmatrix->wmatrix-search.in-wmatrix { 141 text-pos:"13.5 -11"; 142 } 143 } 144 wizard { 145 name:"Search for tfbs Wizard"; 146 help-page-id:16122698; 147 auto-run: true; 148 page { 149 id:1; 150 next:2; 151 title:"Input sequence(s)"; 152 parameters-area { 153 read-sequence.url-in { 154 type:datasets; 155 } 156 } 157 } 158 page { 159 id:2; 160 next:3; 161 title:"Search for TFBS parameters"; 162 parameters-area { 163 group { 164 title:"Weight Matrix parameters"; 165 label-size:120; 166 wmatrix-read.url-in { 167 label:"Weight Matrix"; 168 } 169 wmatrix-search.result-name { 170 } 171 wmatrix-search.strand { 172 } 173 wmatrix-search.min-score { 174 } 175 } 176 group { 177 title:"SITECON parameters"; 178 label-size:120; 179 sitecon-read.url-in { 180 label:"SITECON Model"; 181 } 182 sitecon-search.result-name { 183 } 184 sitecon-search.strand { 185 } 186 sitecon-search.min-score { 187 } 188 sitecon-search.err1 { 189 } 190 sitecon-search.err2 { 191 } 192 } 193 } 194 } 195 page { 196 id:3; 197 title:"Output data"; 198 parameters-area { 199 group { 200 title:"Output data"; 201 label-size:120; 202 write-sequence.url-out { 203 label:"Result file"; 204 } 205 write-sequence.accumulate { 206 label:"Accumulate results"; 207 } 208 } 209 } 210 } 211 } 212 } 213} 214