Mercurial > repos > md-anderson-bioinformatics > matrix_manipulation
comparison Matrix_Manipulation.xml @ 1:f1bcd79cd923 draft default tip
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| author | insilico-bob |
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| date | Tue, 27 Nov 2018 14:20:40 -0500 |
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| 0:7f12c81e2083 | 1:f1bcd79cd923 |
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| 1 <?xml version='1.1' encoding='utf-8'?> | |
| 2 <tool id="Matrix_Manipulation" name="Matrix Manipulation" version="1.2.4"> | |
| 3 <description> Data manipulation before heatmap creation</description> | |
| 4 | |
| 5 <command interpreter="bash" detect_errors="aggressive"> | |
| 6 $__tool_directory__/Matrix_Manipulation.sh '$__tool_directory__' '${manipulation.option}' '$p_input' '$output_file' | |
| 7 '${manipulation.extra.choice}' '${manipulation.extra.thresh}' '${manipulation.extra.axis}' | |
| 8 '${manipulation.extra.transpose}' '${manipulation.extra.input2}' '${manipulation.extra.offsetvalue}' '${manipulation.extra.scalevalue}' | |
| 9 | |
| 10 </command> | |
| 11 | |
| 12 <inputs> | |
| 13 <param name="p_input" type="data" format="tabular" label="Input Matrix" /> | |
| 14 <conditional name="manipulation"> | |
| 15 <param name="option" type="select" label="Choose Manipulation Method"> | |
| 16 <option value="Matrix_Validations">Missing or Invalid Data</option> | |
| 17 <option value="Matrix_Filters">Filter Data</option> | |
| 18 <option value="Matrix_Transformations">Transform Data</option> | |
| 19 <option value="Matrix_Multiply">Multiply or Correlate Matrices</option> | |
| 20 <!-- <option value="Matrix_Statistics">View metadata about Heat Map Matrix</option> --> | |
| 21 <!-- <option value="Split_ExcelTabs_IntoFiles">Split Excel tabs into separate tab delimited files</option> --> | |
| 22 </param> | |
| 23 | |
| 24 | |
| 25 <when value="Matrix_Validations"> | |
| 26 <conditional name="extra"> | |
| 27 <param name="choice" type="select" label="Replace Invalid Value with:"> | |
| 28 <option value="Mean">Mean</option> | |
| 29 <option value="Zero">Zero</option> | |
| 30 </param> | |
| 31 <when value="Mean"> | |
| 32 <param name="axis" type="select" label="Choose Axis:"> | |
| 33 <option value="Row">Row</option> | |
| 34 <option value="Column">Column</option> | |
| 35 </param> | |
| 36 | |
| 37 <param name="offsetvalue" type="text" size="10" hidden="true" value="0"/> | |
| 38 <param name="scalevalue" type="text" size="10" hidden="true" value="1.0"/> | |
| 39 <param name="thresh" type="float" size="4" value=".05" hidden="true" /> | |
| 40 <param name="transpose" type="text" size="10" hidden="true" value="n" /> | |
| 41 <param name="input2" type="data" hidden="true" value="$input1" /> | |
| 42 </when> | |
| 43 <when value="Zero"> | |
| 44 <param name="axis" type="text" size="10" hidden="true" value="Row"/> | |
| 45 | |
| 46 <param name="offsetvalue" type="text" size="10" hidden="true" value="0"/> | |
| 47 <param name="scalevalue" type="text" size="10" hidden="true" value="1.0"/> | |
| 48 <param name="thresh" type="float" size="4" value=".05" hidden="true" /> | |
| 49 <param name="transpose" type="text" size="10" hidden="true" value="n" /> | |
| 50 <param name="input2" type="data" hidden="true" value="$input1" /> | |
| 51 </when> | |
| 52 </conditional> | |
| 53 </when> | |
| 54 | |
| 55 | |
| 56 | |
| 57 <when value="Matrix_Filters"> | |
| 58 <conditional name="extra"> | |
| 59 <param name="choice" type="select" label="Filter Criteria:"> | |
| 60 <option value="LowerLimit">Remove row/column if any cell is less than threshold value</option> | |
| 61 <option value="UpperLimit">Remove row/column if any cell is greater than threshold value</option> | |
| 62 <option value="NANlimit">Remove row/column if number of invalid cells exceeds threshold value </option> | |
| 63 <option value="NANpercent">Remove row/column if invalid cells exceeds threshold percent</option> | |
| 64 <!-- <option value="VarianceValue">Remove row/column if Variance is below threshold value</option> --> | |
| 65 <option value="VarianceCount">Remove row/column if Variance is not in top row/column count</option> | |
| 66 <option value="VariancePercent">Remove row/column if Variance is not in top percent</option> | |
| 67 <!-- <option value="MADcount">Remove row/column if Median Absolute Deviation (MAD) is not in top row/column count</option> | |
| 68 <option value="MADpercent">Remove row/column if Median Absolute Deviation (MAD) is not in top percent</option> --> | |
| 69 <!-- <option value="Covariance">Remove row/column if covariance exceeds threshold value</option> | |
| 70 <option value="Median">Remove row/column if Median is less than threshold value</option> | |
| 71 <option value="MADvalue">Remove row/column if Median Absolute Deviation (MAD) is below threshold value</option> | |
| 72 <option value="Mean">Remove row/column if Mean is less than threshold value</option> | |
| 73 <option value="Quantile">Remove row/column if less than Quantile_Cutoff</option> | |
| 74 <option value="GeneList">Keep only these genes</option> | |
| 75 <option value="Histogram">View filter histogram</option> | |
| 76 --> | |
| 77 </param> | |
| 78 <when value="LowerLimit"> | |
| 79 <param name="thresh" type="float" size="5" value="0.01" label="Absolute minimum value" help="Lowest value allowed or row/col removed."/> | |
| 80 <param name="axis" type="select" label="Choose axis to Filter on (Rows or Columns)"> | |
| 81 <option value="Row">Row</option> | |
| 82 <option value="Column">Column</option> | |
| 83 </param> | |
| 84 | |
| 85 <param name="offsetvalue" type="text" size="10" hidden="true" value="0"/> | |
| 86 <param name="scalevalue" type="text" size="10" hidden="true" value="1.0"/> | |
| 87 <param name="transpose" type="text" size="10" hidden="true" value="n" /> | |
| 88 <param name="input2" type="data" hidden="true" value="$input1" /> | |
| 89 </when> | |
| 90 <when value="UpperLimit"> | |
| 91 <param name="thresh" type="float" size="5" value="0.9" label="Absolute maximum value" help="Highest value allowed or row/col removed."/> | |
| 92 <param name="axis" type="select" label="Choose axis to Filter on (Rows or Columns)"> | |
| 93 <option value="Row">Row</option> | |
| 94 <option value="Column">Column</option> | |
| 95 </param> | |
| 96 | |
| 97 <param name="offsetvalue" type="text" size="10" hidden="true" value="0"/> | |
| 98 <param name="scalevalue" type="text" size="10" hidden="true" value="1.0"/> | |
| 99 <param name="transpose" type="text" size="10" hidden="true" value="n" /> | |
| 100 <param name="input2" type="data" hidden="true" value="$input1" /> | |
| 101 </when> | |
| 102 <when value="NANlimit"> | |
| 103 <param name="thresh" type="integer" size="5" value="50" label="Maximum number NANs" help="More NANs per row/col removed."/> | |
| 104 <param name="axis" type="select" label="Choose axis to Filter on (Rows or Columns)"> | |
| 105 <option value="Row">Row</option> | |
| 106 <option value="Column">Column</option> | |
| 107 </param> | |
| 108 | |
| 109 <param name="offsetvalue" type="text" size="10" hidden="true" value="0"/> | |
| 110 <param name="scalevalue" type="text" size="10" hidden="true" value="1.0"/> | |
| 111 <param name="transpose" type="text" size="10" hidden="true" value="n" /> | |
| 112 <param name="input2" type="data" hidden="true" value="$input1" /> | |
| 113 </when> | |
| 114 <when value="NANpercent"> | |
| 115 <param name="thresh" type="integer" size="5" value="20" label="Percent maximum" help="Above percent rows/cols removed."/> | |
| 116 <param name="axis" type="select" label="Choose axis to Filter on (Rows or Columns)"> | |
| 117 <option value="Row">Row</option> | |
| 118 <option value="Column">Column</option> | |
| 119 </param> | |
| 120 | |
| 121 <param name="offsetvalue" type="text" size="10" hidden="true" value="0"/> | |
| 122 <param name="scalevalue" type="text" size="10" hidden="true" value="1.0"/> | |
| 123 <param name="transpose" type="text" size="10" hidden="true" value="n" /> | |
| 124 <param name="input2" type="data" hidden="true" value="$input1" /> | |
| 125 </when> | |
| 126 <when value="VariancePercent"> | |
| 127 <param name="thresh" type="integer" size="5" value="90" label="Percentile minimum" help="Below percentile rows/cols removed."/> | |
| 128 <param name="axis" type="select" label="Choose axis to Filter on (Rows or Columns)"> | |
| 129 <option value="Row">Row</option> | |
| 130 <option value="Column">Column</option> | |
| 131 </param> | |
| 132 | |
| 133 <param name="offsetvalue" type="text" size="10" hidden="true" value="0"/> | |
| 134 <param name="scalevalue" type="text" size="10" hidden="true" value="1.0"/> | |
| 135 <param name="transpose" type="text" size="10" hidden="true" value="n" /> | |
| 136 <param name="input2" type="data" hidden="true" value="$input1" /> | |
| 137 </when> | |
| 138 <when value="VarianceCount"> | |
| 139 <param name="thresh" type="integer" size="5" value="10" label="Number minimum" help="Below threshold rows/cols removed."/> | |
| 140 <param name="axis" type="select" label="Choose axis to Filter on (Rows or Columns)"> | |
| 141 <option value="Row">Row</option> | |
| 142 <option value="Column">Column</option> | |
| 143 </param> | |
| 144 | |
| 145 <param name="offsetvalue" type="text" size="10" hidden="true" value="0"/> | |
| 146 <param name="scalevalue" type="text" size="10" hidden="true" value="1.0"/> | |
| 147 <param name="transpose" type="text" size="10" hidden="true" value="n" /> | |
| 148 <param name="input2" type="data" hidden="true" value="$input1" /> | |
| 149 </when> | |
| 150 <when value="MADpercent"> | |
| 151 <param name="thresh" type="integer" size="5" value="90" label="Percentile minimum" help="Below percentile rows/cols removed."/> | |
| 152 <param name="axis" type="select" label="Choose axis to Filter on (Rows or Columns)"> | |
| 153 <option value="Row">Row</option> | |
| 154 <option value="Column">Column</option> | |
| 155 </param> | |
| 156 | |
| 157 <param name="offsetvalue" type="text" size="10" hidden="true" value="0"/> | |
| 158 <param name="scalevalue" type="text" size="10" hidden="true" value="1.0"/> | |
| 159 <param name="transpose" type="text" size="10" hidden="true" value="n" /> | |
| 160 <param name="input2" type="data" hidden="true" value="$input1" /> | |
| 161 </when> | |
| 162 <when value="MADcount"> | |
| 163 <param name="thresh" type="integer" size="5" value="10" label="Number minimum" help="Below threshold rows/cols removed."/> | |
| 164 <param name="axis" type="select" label="Choose axis to Filter on (Rows or Columns)"> | |
| 165 <option value="Row">Row</option> | |
| 166 <option value="Column">Column</option> | |
| 167 </param> | |
| 168 | |
| 169 <param name="offsetvalue" type="text" size="10" hidden="true" value="0"/> | |
| 170 <param name="scalevalue" type="text" size="10" hidden="true" value="1.0"/> | |
| 171 <param name="transpose" type="text" size="10" hidden="true" value="n" /> | |
| 172 <param name="input2" type="data" hidden="true" value="$input1" /> | |
| 173 </when> | |
| 174 </conditional> | |
| 175 </when> | |
| 176 | |
| 177 | |
| 178 | |
| 179 <when value="Matrix_Transformations"> | |
| 180 <conditional name="extra"> | |
| 181 <param name="choice" type="select" label="Choose Normalization Method"> | |
| 182 <option value="ln_normalization">Log2 Normalization</option> | |
| 183 <option value="log_normalization">Log10 Normalization</option> | |
| 184 <option value="mean_center_normalization">Mean Centered Normalization</option> | |
| 185 <option value="median_center_normalization">Median Centered Normalization</option> | |
| 186 <option value="z_score_normalization">Z-Score Normalization</option> | |
| 187 <option value="add_offset">Add Offset Value</option> | |
| 188 <option value="scale">Scale by Multiple</option> | |
| 189 <option value="divide_by_sum">Divide by Sum</option> | |
| 190 <option value="transpose">Matrix Transpose</option> | |
| 191 </param> | |
| 192 <when value="add_offset"> | |
| 193 <param name="offsetvalue" type="text" size="10" value="0.0" label="Matrix Values offset" help="Add value to each Matrix element."/> | |
| 194 <param name="scalevalue" type="text" size="10" hidden="true" value="1.0"/> | |
| 195 <param name="axis" type="text" size="10" hidden="true" value="Row"/> | |
| 196 | |
| 197 <param name="thresh" type="float" size="4" value=".05" hidden="true" /> | |
| 198 <param name="transpose" type="text" size="10" hidden="true" value="n" /> | |
| 199 <param name="input2" type="data" hidden="true" value="$input1" /> | |
| 200 </when> | |
| 201 <when value="scale"> | |
| 202 <param name="scalevalue" type="text" size="10" value="1.0" label="Matrix Value scaling" help="multiply value with each Matrix element."/> | |
| 203 <param name="offsetvalue" type="text" size="10" hidden="true" value="0"/> | |
| 204 <param name="axis" type="text" size="10" hidden="true" value="Row"/> | |
| 205 | |
| 206 <param name="thresh" type="float" size="4" value=".05" hidden="true" /> | |
| 207 <param name="transpose" type="text" size="10" hidden="true" value="n" /> | |
| 208 <param name="input2" type="data" hidden="true" value="$input1" /> | |
| 209 </when> | |
| 210 <when value="ln_normalization"> | |
| 211 <param name="offsetvalue" type="text" size="10" value="0.0" label="Matrix Values offset" help="Calculate log2 for each Matrix element then add offset."/> | |
| 212 <param name="scalevalue" type="text" size="10" hidden="true" value="1.0"/> | |
| 213 <param name="axis" type="select" label="Choose Axis"> | |
| 214 <option value="Row">Row</option> | |
| 215 <option value="Column">Column</option> | |
| 216 </param> | |
| 217 | |
| 218 <param name="thresh" type="float" size="4" value=".05" hidden="true" /> | |
| 219 <param name="transpose" type="text" size="10" hidden="true" value="n" /> | |
| 220 <param name="input2" type="data" hidden="true" value="$input1" /> | |
| 221 </when> | |
| 222 <when value="log_normalization"> | |
| 223 <param name="offsetvalue" type="text" size="10" value="0.0" label="Matrix Values offset" help="Calculate log10 for each Matrix element then add offset."/> | |
| 224 <param name="scalevalue" type="text" size="10" hidden="true" value="1.0"/> | |
| 225 <param name="axis" type="select" label="Choose Axis"> | |
| 226 <option value="Row">Row</option> | |
| 227 <option value="Column">Column</option> | |
| 228 </param> | |
| 229 | |
| 230 <param name="thresh" type="float" size="4" value=".05" hidden="true" /> | |
| 231 <param name="transpose" type="text" size="10" hidden="true" value="n" /> | |
| 232 <param name="input2" type="data" hidden="true" value="$input1" /> | |
| 233 </when> | |
| 234 <when value="z_score_normalization"> | |
| 235 <param name="offsetvalue" type="text" size="10" hidden="true" value="0"/> | |
| 236 <param name="scalevalue" type="text" size="10" hidden="true" value="1.0"/> | |
| 237 <param name="axis" type="select" label="Choose Axis"> | |
| 238 <option value="Row">Row</option> | |
| 239 <option value="Column">Column</option> | |
| 240 </param> | |
| 241 | |
| 242 <param name="thresh" type="float" size="4" value=".05" hidden="true" /> | |
| 243 <param name="transpose" type="text" size="10" hidden="true" value="n" /> | |
| 244 <param name="input2" type="data" hidden="true" value="$input1" /> | |
| 245 </when> | |
| 246 <when value="mean_center_normalization"> | |
| 247 <param name="offsetvalue" type="text" size="10" hidden="true" value="0"/> | |
| 248 <param name="scalevalue" type="text" size="10" hidden="true" value="1.0"/> | |
| 249 <param name="axis" type="select" label="Choose Axis"> | |
| 250 <option value="Row">Row</option> | |
| 251 <option value="Column">Column</option> | |
| 252 </param> | |
| 253 | |
| 254 <param name="thresh" type="float" size="4" value=".05" hidden="true" /> | |
| 255 <param name="transpose" type="text" size="10" hidden="true" value="n" /> | |
| 256 <param name="input2" type="data" hidden="true" value="$input1" /> | |
| 257 </when> | |
| 258 <when value="median_center_normalization"> | |
| 259 <param name="offsetvalue" type="text" size="10" hidden="true" value="0"/> | |
| 260 <param name="scalevalue" type="text" size="10" hidden="true" value="1.0"/> | |
| 261 <param name="axis" type="select" label="Choose Axis"> | |
| 262 <option value="Row">Row</option> | |
| 263 <option value="Column">Column</option> | |
| 264 </param> | |
| 265 | |
| 266 <param name="thresh" type="float" size="4" value=".05" hidden="true" /> | |
| 267 <param name="transpose" type="text" size="10" hidden="true" value="n" /> | |
| 268 <param name="input2" type="data" hidden="true" value="$input1" /> | |
| 269 </when> | |
| 270 <when value="transpose"> | |
| 271 <param name="offsetvalue" type="text" size="10" hidden="true" value="0"/> | |
| 272 <param name="scalevalue" type="text" size="10" hidden="true" value="1.0"/> | |
| 273 <param name="axis" type="text" size="10" hidden="true" value="neither"/> | |
| 274 | |
| 275 <param name="thresh" type="float" size="4" value=".05" hidden="true" /> | |
| 276 <param name="transpose" type="text" size="10" hidden="true" value="n" /> | |
| 277 <param name="input2" type="data" hidden="true" value="$input1" /> | |
| 278 </when> | |
| 279 <when value="divide_by_sum"> | |
| 280 <param name="offsetvalue" type="text" size="10" hidden="true" value="0"/> | |
| 281 <param name="scalevalue" type="text" size="10" hidden="true" value="1.0"/> | |
| 282 <param name="axis" type="select" label="Choose Axis"> | |
| 283 <option value="Row">Row</option> | |
| 284 <option value="Column">Column</option> | |
| 285 </param> | |
| 286 | |
| 287 <param name="thresh" type="float" size="4" value=".05" hidden="true" /> | |
| 288 <param name="transpose" type="text" size="10" hidden="true" value="n" /> | |
| 289 <param name="input2" type="data" hidden="true" value="$input1" /> | |
| 290 </when> | |
| 291 </conditional> | |
| 292 </when> | |
| 293 | |
| 294 | |
| 295 | |
| 296 <when value="Matrix_Multiply"> | |
| 297 <conditional name="extra"> | |
| 298 <param name="choice" type="select" label="Choose composition type"> | |
| 299 <option value="MatrixMultiply">Matrix Multiplication</option> | |
| 300 <option value="Corr2Matrices">Correlate two matrices</option> | |
| 301 <option value="Corr1Matrix">Correlate one matrix with itself</option> | |
| 302 </param> | |
| 303 <when value="MatrixMultiply"> | |
| 304 <param name="transpose" type="select" label="transpose matrix?"> | |
| 305 <option value="y">Transpose matrix</option> | |
| 306 <option value="n" selected="true">Do Not transpose matrix</option> | |
| 307 </param> | |
| 308 <param name="input2" type="data" format="tabular" label="Second Input Matrix size NxP" /> | |
| 309 | |
| 310 <param name="offsetvalue" type="text" size="10" hidden="true" value="0"/> | |
| 311 <param name="scalevalue" type="text" size="10" hidden="true" value="1.0"/> | |
| 312 <param name="thresh" type="float" size="4" value=".05" hidden="true" /> | |
| 313 <param name="axis" type="text" size="10" hidden="true" value="Row"/> | |
| 314 </when> | |
| 315 <when value="Corr2Matrices"> | |
| 316 <param name="transpose" type="select" label="transpose matrix?"> | |
| 317 <option value="y">Transpose matrix</option> | |
| 318 <option value="n" selected="true">Do Not transpose matrix</option> | |
| 319 </param> | |
| 320 <param name="input2" type="data" format="tabular" label="Second Input Matrix size NxP" /> | |
| 321 | |
| 322 <param name="offsetvalue" type="text" size="10" hidden="true" value="0"/> | |
| 323 <param name="scalevalue" type="text" size="10" hidden="true" value="1.0"/> | |
| 324 <param name="thresh" type="float" size="4" value=".05" hidden="true" /> | |
| 325 <param name="axis" type="text" size="10" hidden="true" value="Row"/> | |
| 326 </when> | |
| 327 <when value="Corr1Matrix"> | |
| 328 <param name="transpose" type="text" size="10" hidden="true" value="n" /> | |
| 329 <param name="input2" type="data" hidden="true" value="$input1" /> | |
| 330 | |
| 331 <param name="offsetvalue" type="text" size="10" hidden="true" value="0"/> | |
| 332 <param name="scalevalue" type="text" size="10" hidden="true" value="1.0"/> | |
| 333 <param name="thresh" type="float" size="4" value=".05" hidden="true" /> | |
| 334 <param name="axis" type="text" size="10" hidden="true" value="Row"/> | |
| 335 </when> | |
| 336 </conditional> | |
| 337 </when> | |
| 338 | |
| 339 | |
| 340 | |
| 341 <when value="Matrix_Statistics"> | |
| 342 <conditional name="extra"> | |
| 343 <param name="choice" type="select" label="Choose Metric to Filter By"> | |
| 344 <option value="Histogram">Plot info about either matrix row/column</option> | |
| 345 </param> | |
| 346 <when value = "Histogram"> | |
| 347 <param name="thresh" type="float" size="4" value=".05" label="Filter Threshold (Value above/below row/column will be Removed)" /> | |
| 348 <param name="axis" type="select" label="Choose axis to Filter on (Rows or Columns)"> | |
| 349 <option value="Row">Row</option> | |
| 350 <option value="Column">Column</option> | |
| 351 </param> | |
| 352 | |
| 353 <param name="offsetvalue" type="text" size="10" hidden="true" value="0"/> | |
| 354 <param name="scalevalue" type="text" size="10" hidden="true" value="1.0"/> | |
| 355 <param name="transpose" type="text" size="10" hidden="true" value="n" /> | |
| 356 <param name="input2" type="data" hidden="true" value="$input1" /> | |
| 357 </when> | |
| 358 </conditional> | |
| 359 </when> | |
| 360 | |
| 361 | |
| 362 | |
| 363 | |
| 364 | |
| 365 | |
| 366 | |
| 367 | |
| 368 <!-- <when value="Split_ExcelTabs_IntoFiles"> | |
| 369 <description>into separate tab delimited files</description> | |
| 370 | |
| 371 <param name="input" type="data" format="txt" label="Input Excel.xls or Excel.xlsx file"> </param> | |
| 372 | |
| 373 <conditional name="extra"> | |
| 374 <param name="choice" type="select" label="Select tab" help="Select tab position or name"> | |
| 375 <option value="tab_number">Tab number</option> | |
| 376 </param> | |
| 377 | |
| 378 '$extra.tabname' | |
| 379 <option value="tab_name">Tab name</option> | |
| 380 <option value="all">All tabs in file</option> | |
| 381 <option value="1">First tab only</option> | |
| 382 </param> | |
| 383 <when value="tab_name"> | |
| 384 <param name="tabname" type="text" size="20" value="" label="Tab Name" help="Spreadsheet Tab Name"> | |
| 385 </param> | |
| 386 </when> | |
| 387 | |
| 388 <when value="tab_number"> | |
| 389 <param name="tabnumber" type="text" size="2" value="1" label="Tab position" help="Integer Tab position from left"> | |
| 390 </param> | |
| 391 </when> | |
| 392 </conditional> | |
| 393 | |
| 394 <outputs> | |
| 395 <data name="output_file" format="tabular" label="Output File Name" help="Name based on Input file name and tab name"/> | |
| 396 </outputs> | |
| 397 </when> --> | |
| 398 | |
| 399 | |
| 400 | |
| 401 </conditional> | |
| 402 </inputs> | |
| 403 <outputs> | |
| 404 <data name="output_file" format="tabular" /> | |
| 405 </outputs> | |
| 406 </tool> |