/var/lib/mobyle/programs/epestfind.xml is in mobyle-programs 5.1.2-1.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 256 257 258 259 260 261 262 263 264 265 266 267 268 269 270 271 272 273 274 275 276 277 278 279 280 281 282 283 284 285 286 287 288 289 290 291 292 293 294 295 296 297 298 299 300 301 302 303 304 305 306 307 308 309 310 311 312 313 314 315 316 317 318 319 320 321 322 323 324 325 326 327 328 329 330 331 332 333 334 335 336 337 338 339 340 341 342 343 344 345 346 347 348 349 350 351 352 353 354 355 356 357 358 359 360 361 362 363 364 365 366 367 368 369 370 371 372 373 374 375 376 377 378 379 380 381 382 383 384 385 386 387 388 389 390 391 392 393 394 395 396 397 398 399 400 401 402 403 404 405 406 407 408 409 410 411 412 413 414 415 416 417 418 419 420 421 422 423 424 425 426 427 428 429 430 431 432 433 434 435 436 437 438 439 440 441 442 443 444 445 446 447 448 449 450 451 452 453 454 455 456 457 458 459 460 461 462 463 464 465 466 467 468 469 470 471 472 473 474 475 476 477 478 479 480 481 482 483 484 485 486 487 488 489 490 491 492 493 494 495 496 497 498 499 500 501 502 | <?xml version="1.0" encoding="ISO-8859-1"?>
<!-- XML Authors: Corinne Maufrais and Nicolas Joly, -->
<!-- 'Biological Software and Databases' Group, Institut Pasteur, Paris. -->
<!-- Distributed under LGPLv2 License. Please refer to the COPYING.LIB document. -->
<program>
<head>
<name>epestfind</name>
<package>
<name>EMBOSS</name>
<version>6.3.1</version>
<doc>
<title>EMBOSS</title>
<description>
<text lang="en">European Molecular Biology Open Software Suite</text>
</description>
<authors>Rice,P. Longden,I. and Bleasby, A.</authors>
<reference>EMBOSS: The European Molecular Biology Open Software Suite (2000) Rice,P. Longden,I. and Bleasby, A. Trends in Genetics 16, (6) pp276--277</reference>
<sourcelink>http://emboss.sourceforge.net/download</sourcelink>
<homepagelink>http://emboss.sourceforge.net</homepagelink>
</doc>
</package>
<doc>
<title>epestfind</title>
<description>
<text lang="en">Finds PEST motifs as potential proteolytic cleavage sites</text>
</description>
<doclink>http://bioweb2.pasteur.fr/docs/EMBOSS/epestfind.html</doclink>
<doclink>http://emboss.sourceforge.net/docs/themes</doclink>
</doc>
<category>sequence:protein:motifs</category>
<command>epestfind</command>
</head>
<parameters>
<paragraph>
<name>e_input</name>
<prompt lang="en">Input section</prompt>
<parameters>
<parameter issimple="1" ismandatory="1">
<name>e_sequence</name>
<prompt lang="en">sequence option</prompt>
<type>
<biotype>Protein</biotype>
<datatype>
<class>Sequence</class>
</datatype>
<dataFormat>EMBL</dataFormat>
<dataFormat>FASTA</dataFormat>
<dataFormat>GCG</dataFormat>
<dataFormat>GENBANK</dataFormat>
<dataFormat>NBRF</dataFormat>
<dataFormat>CODATA</dataFormat>
<dataFormat>RAW</dataFormat>
<dataFormat>SWISSPROT</dataFormat>
<dataFormat>GFF</dataFormat>
<card>1,1</card>
</type>
<format>
<code proglang="python">("", " -sequence=" + str(value))[value is not None]</code>
</format>
<argpos>1</argpos>
<comment>
<text lang="en">Protein sequence USA to be analysed.</text>
</comment>
</parameter>
<parameter>
<name>e_mwdata</name>
<prompt lang="en">Molecular weights data file</prompt>
<type>
<datatype>
<class>MolecularWeights</class>
<superclass>AbstractText</superclass>
</datatype>
</type>
<format>
<code proglang="python">("", " -mwdata=" + str(value))[value is not None ]</code>
</format>
<argpos>2</argpos>
</parameter>
</parameters>
</paragraph>
<paragraph>
<name>e_required</name>
<prompt lang="en">Required section</prompt>
<parameters>
<parameter issimple="1" ismandatory="1">
<name>e_window</name>
<prompt lang="en">Window length (value greater than or equal to 2)</prompt>
<type>
<datatype>
<class>Integer</class>
</datatype>
</type>
<vdef>
<value>10</value>
</vdef>
<format>
<code proglang="python">("", " -window=" + str(value))[value is not None and value!=vdef]</code>
</format>
<ctrl>
<message>
<text lang="en">Value greater than or equal to 2 is required</text>
</message>
<code proglang="python">value >= 2</code>
</ctrl>
<argpos>3</argpos>
<comment>
<text lang="en">Minimal distance between positively charged amino acids.</text>
</comment>
</parameter>
<parameter issimple="1" ismandatory="1">
<name>e_order</name>
<prompt lang="en">Sort order of results</prompt>
<type>
<datatype>
<class>Choice</class>
</datatype>
</type>
<vdef>
<value>3</value>
</vdef>
<vlist>
<velem>
<value>1</value>
<label>Length</label>
</velem>
<velem>
<value>2</value>
<label>Position</label>
</velem>
<velem>
<value>3</value>
<label>Score</label>
</velem>
</vlist>
<format>
<code proglang="python">("", " -order=" + str(value))[value is not None and value!=vdef]</code>
</format>
<argpos>4</argpos>
<comment>
<text lang="en">Name of the output file which holds the results of the analysis. Results may be sorted by length, position and score.</text>
</comment>
</parameter>
</parameters>
</paragraph>
<paragraph>
<name>e_additional</name>
<prompt lang="en">Additional section</prompt>
<parameters>
<parameter>
<name>e_threshold</name>
<prompt lang="en">Threshold score (value from -55.0 to +55.0)</prompt>
<type>
<datatype>
<class>Float</class>
</datatype>
</type>
<vdef>
<value>+5.0</value>
</vdef>
<format>
<code proglang="python">("", " -threshold=" + str(value))[value is not None and value!=vdef]</code>
</format>
<ctrl>
<message>
<text lang="en">Value greater than or equal to -55.0 is required</text>
</message>
<code proglang="python">value >= -55.0</code>
</ctrl>
<ctrl>
<message>
<text lang="en">Value less than or equal to +55.0 is required</text>
</message>
<code proglang="python">value <= +55.0</code>
</ctrl>
<argpos>5</argpos>
<comment>
<text lang="en">Threshold value to discriminate weak from potential PEST motifs. Valid PEST motifs are discriminated into 'poor' and 'potential' motifs depending on this threshold score. By default, the default value is set to +5.0 based on experimental data. Alterations are not recommended since significance is a matter of biology, not mathematics.</text>
</comment>
</parameter>
</parameters>
</paragraph>
<paragraph>
<name>e_advanced</name>
<prompt lang="en">Advanced section</prompt>
<parameters>
<parameter>
<name>e_mono</name>
<prompt lang="en">Use monoisotopic weights</prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<vdef>
<value>0</value>
</vdef>
<format>
<code proglang="python">("", " -mono")[ bool(value) ]</code>
</format>
<argpos>6</argpos>
</parameter>
<parameter>
<name>e_potential</name>
<prompt lang="en">Display potential pest motifs</prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<vdef>
<value>1</value>
</vdef>
<format>
<code proglang="python">(" -nopotential", "")[ bool(value) ]</code>
</format>
<argpos>7</argpos>
<comment>
<text lang="en">Decide whether potential PEST motifs should be printed.</text>
</comment>
</parameter>
<parameter>
<name>e_poor</name>
<prompt lang="en">Display poor pest motifs</prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<vdef>
<value>1</value>
</vdef>
<format>
<code proglang="python">(" -nopoor", "")[ bool(value) ]</code>
</format>
<argpos>8</argpos>
<comment>
<text lang="en">Decide whether poor PEST motifs should be printed.</text>
</comment>
</parameter>
<parameter>
<name>e_invalid</name>
<prompt lang="en">Display invalid pest motifs</prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<vdef>
<value>0</value>
</vdef>
<format>
<code proglang="python">("", " -invalid")[ bool(value) ]</code>
</format>
<argpos>9</argpos>
<comment>
<text lang="en">Decide whether invalid PEST motifs should be printed.</text>
</comment>
</parameter>
<parameter>
<name>e_map</name>
<prompt lang="en">Display pest motifs map</prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<vdef>
<value>1</value>
</vdef>
<format>
<code proglang="python">(" -nomap", "")[ bool(value) ]</code>
</format>
<argpos>10</argpos>
<comment>
<text lang="en">Decide whether PEST motifs should be mapped to sequence.</text>
</comment>
</parameter>
</parameters>
</paragraph>
<paragraph>
<name>e_output</name>
<prompt lang="en">Output section</prompt>
<parameters>
<parameter>
<name>e_outfile</name>
<prompt lang="en">Name of the output file (e_outfile)</prompt>
<type>
<datatype>
<class>Filename</class>
</datatype>
</type>
<vdef>
<value>epestfind.e_outfile</value>
</vdef>
<format>
<code proglang="python">("" , " -outfile=" + str(value))[value is not None]</code>
</format>
<argpos>11</argpos>
<comment>
<text lang="en">Name of file to which results will be written.</text>
</comment>
</parameter>
<parameter isout="1">
<name>e_outfile_out</name>
<prompt lang="en">outfile_out option</prompt>
<type>
<datatype>
<class>EpestfindReport</class>
<superclass>Report</superclass>
</datatype>
</type>
<filenames>
<code proglang="python">e_outfile</code>
</filenames>
</parameter>
<parameter issimple="1" ismandatory="1">
<name>e_graph</name>
<prompt lang="en">Choose the e_graph output format</prompt>
<type>
<datatype>
<class>Choice</class>
</datatype>
</type>
<vdef>
<value>png</value>
</vdef>
<vlist>
<velem>
<value>png</value>
<label>Png</label>
</velem>
<velem>
<value>gif</value>
<label>Gif</label>
</velem>
<velem>
<value>cps</value>
<label>Cps</label>
</velem>
<velem>
<value>ps</value>
<label>Ps</label>
</velem>
<velem>
<value>meta</value>
<label>Meta</label>
</velem>
<velem>
<value>data</value>
<label>Data</label>
</velem>
</vlist>
<format>
<code proglang="python">(" -graph=" + str(vdef), " -graph=" + str(value))[value is not None and value!=vdef]</code>
</format>
<argpos>12</argpos>
</parameter>
<parameter>
<name>xy_goutfile</name>
<prompt lang="en">Name of the output graph</prompt>
<type>
<datatype>
<class>Filename</class>
</datatype>
</type>
<vdef>
<value>epestfind_xygraph</value>
</vdef>
<format>
<code proglang="python">("" , " -goutfile=" + str(value))[value is not None]</code>
</format>
<argpos>13</argpos>
</parameter>
<parameter isout="1">
<name>xy_outgraph_png</name>
<prompt lang="en">Graph file</prompt>
<type>
<datatype>
<class>Picture</class>
<superclass>Binary</superclass>
</datatype>
</type>
<precond>
<code proglang="python">e_graph == "png"</code>
</precond>
<filenames>
<code proglang="python">"*.png"</code>
</filenames>
</parameter>
<parameter isout="1">
<name>xy_outgraph_gif</name>
<prompt lang="en">Graph file</prompt>
<type>
<datatype>
<class>Picture</class>
<superclass>Binary</superclass>
</datatype>
</type>
<precond>
<code proglang="python">e_graph == "gif"</code>
</precond>
<filenames>
<code proglang="python">"*.gif"</code>
</filenames>
</parameter>
<parameter isout="1">
<name>xy_outgraph_ps</name>
<prompt lang="en">Graph file</prompt>
<type>
<datatype>
<class>PostScript</class>
<superclass>Binary</superclass>
</datatype>
</type>
<precond>
<code proglang="python">e_graph == "ps" or e_graph == "cps"</code>
</precond>
<filenames>
<code proglang="python">"*.ps"</code>
</filenames>
</parameter>
<parameter isout="1">
<name>xy_outgraph_meta</name>
<prompt lang="en">Graph file</prompt>
<type>
<datatype>
<class>Picture</class>
<superclass>Binary</superclass>
</datatype>
</type>
<precond>
<code proglang="python">e_graph == "meta"</code>
</precond>
<filenames>
<code proglang="python">"*.meta"</code>
</filenames>
</parameter>
<parameter isout="1">
<name>xy_outgraph_data</name>
<prompt lang="en">Graph file</prompt>
<type>
<datatype>
<class>Text</class>
</datatype>
</type>
<precond>
<code proglang="python">e_graph == "data"</code>
</precond>
<filenames>
<code proglang="python">"*.dat"</code>
</filenames>
</parameter>
</parameters>
</paragraph>
<parameter ishidden="1">
<name>auto</name>
<prompt lang="en">Turn off any prompting</prompt>
<type>
<datatype>
<class>String</class>
</datatype>
</type>
<format>
<code proglang="python">" -auto -stdout"</code>
</format>
<argpos>14</argpos>
</parameter>
</parameters>
</program>
|