Mercurial > repos > sauria > hifive
comparison hifive.xml @ 0:0a9c76d80e33 draft
planemo upload for repository https://github.com/bxlab/galaxy_tools/suites/suite_hifive commit abaefa638db82abe90f335d783c9503dce28944f-dirty
| author | sauria |
|---|---|
| date | Fri, 05 Jun 2015 14:09:00 -0400 |
| parents | |
| children | cb4f92e6fd4e |
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| -1:000000000000 | 0:0a9c76d80e33 |
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| 1 <?xml version="1.0"?> | |
| 2 <tool id="hifive" name="hifive" version="@WRAPPER_VERSION@.0"> | |
| 3 <description>manipulate, analyze, and plot HiC and 5C chromatin interaction data</description> | |
| 4 <macros> | |
| 5 <import>hifive_macros.xml</import> | |
| 6 </macros> | |
| 7 <expand macro="requirements"/> | |
| 8 <expand macro="stdio"/> | |
| 9 <command><![CDATA[ | |
| 10 hifive | |
| 11 | |
| 12 $command.command_select | |
| 13 | |
| 14 #if str( $command.command_select ) == "hic-complete": | |
| 15 @HIC_NORMALIZE@ | |
| 16 @HIC_FEND@ | |
| 17 @HIC_SEQUENCE@ | |
| 18 @HIC_CHROMOSOMES@ | |
| 19 @HIC_PROJECT@ | |
| 20 @HIC_RANGE@ | |
| 21 -o $hic_comp_fends $hic_comp_data $hic_comp_project | |
| 22 #end if | |
| 23 #if str( $command.command_select ) == "fends": | |
| 24 @HIC_FEND@ | |
| 25 $hic_fend_output | |
| 26 #end if | |
| 27 #if str( $command.command_select ) == "hic-data": | |
| 28 @HIC_SEQUENCE@ | |
| 29 $fends $hic_data_output | |
| 30 #end if | |
| 31 #if str( $command.command_select ) == "hic-project": | |
| 32 @HIC_CHROMOSOMES@ | |
| 33 @HIC_PROJECT@ | |
| 34 @HIC_RANGE@ | |
| 35 $hic_data $hic_project_output | |
| 36 #end if | |
| 37 #if str( $command.command_select ) == "hic-normalize": | |
| 38 @HIC_NORMALIZE@ | |
| 39 @HIC_CHROMOSOMES@ | |
| 40 @HIC_RANGE@ | |
| 41 -o $hic_norm_output | |
| 42 $hic_project | |
| 43 #end if | |
| 44 #if str( $command.command_select ) == "hic-heatmap": | |
| 45 @HIC_CHROMOSOMES@ | |
| 46 $command.trans1 | |
| 47 @BINSIZE@ | |
| 48 @HIC_DATATYPE@ | |
| 49 @HIC_DYNAMIC@ | |
| 50 #if str( $command.image.generate ) == "yes": | |
| 51 @IMAGE@ | |
| 52 -i $hic_hm_image | |
| 53 #end if | |
| 54 $hic_project $hic_hm_output | |
| 55 #end if | |
| 56 #if str( $command.command_select ) == "hic-interval": | |
| 57 -c $command.chrom | |
| 58 #if $command.start: | |
| 59 -s $command.start | |
| 60 #end if | |
| 61 #if $command.stop: | |
| 62 -e $command.stop | |
| 63 #end if | |
| 64 #if $command.maxdist: | |
| 65 -m $command.maxdist | |
| 66 #end if | |
| 67 @BINSIZE@ | |
| 68 @HIC_DATATYPE@ | |
| 69 @HIC_DYNAMIC@ | |
| 70 #if str( $command.image.generate ) == "yes": | |
| 71 @IMAGE@ | |
| 72 @ROTATE@ | |
| 73 -i $hic_int_image | |
| 74 #end if | |
| 75 $hic_project $hic_int_output | |
| 76 #end if | |
| 77 #if str( $command.command_select ) == "5c-complete": | |
| 78 @5C_NORMALIZE@ | |
| 79 @5C_SEQUENCE@ | |
| 80 @5C_REGIONS@ | |
| 81 @5C_PROJECT@ | |
| 82 @5C_RANGE@ | |
| 83 -o $fivec_comp_frags $fivec_comp_data $fivec_comp_project | |
| 84 @5C_FRAGMENT@ | |
| 85 #end if | |
| 86 #if str( $command.command_select ) == "fragments": | |
| 87 @5C_FRAGMENT@ | |
| 88 $fivec_frag_output | |
| 89 #end if | |
| 90 #if str( $command.command_select ) == "5c-data": | |
| 91 @5C_SEQUENCE@ | |
| 92 $fragments $fivec_data_output | |
| 93 #end if | |
| 94 #if str( $command.command_select ) == "5c-project": | |
| 95 @5C_REGIONS@ | |
| 96 @5C_PROJECT@ | |
| 97 @5C_RANGE@ | |
| 98 $fivec_data $fivec_project_output | |
| 99 #end if | |
| 100 #if str( $command.command_select ) == "5c-normalize": | |
| 101 @5C_NORMALIZE@ | |
| 102 @5C_REGIONS@ | |
| 103 @5C_RANGE@ | |
| 104 -o $fivec_norm_output | |
| 105 $fivec_project | |
| 106 #end if | |
| 107 #if str( $command.command_select ) == "5c-heatmap": | |
| 108 @5C_REGIONS@ | |
| 109 $command.trans2 | |
| 110 @BINSIZE@ | |
| 111 @5C_DATATYPE@ | |
| 112 @5C_DYNAMIC@ | |
| 113 #if str( $command.image.generate ) == "yes": | |
| 114 @IMAGE@ | |
| 115 -i $fivec_hm_image | |
| 116 #end if | |
| 117 $fivec_project $fivec_hm_output | |
| 118 #end if | |
| 119 #if str( $command.command_select ) == "5c-interval": | |
| 120 -c $command.region | |
| 121 #if $command.start: | |
| 122 -s $command.start | |
| 123 #end if | |
| 124 #if $command.stop: | |
| 125 -e $command.stop | |
| 126 #end if | |
| 127 @BINSIZE@ | |
| 128 @5C_DATATYPE@ | |
| 129 @5C_DYNAMIC@ | |
| 130 #if str( $command.image.generate ) == "yes": | |
| 131 @IMAGE@ | |
| 132 @ROTATE@ | |
| 133 -i $fivec_int_image | |
| 134 #end if | |
| 135 $fivec_project $fivec_int_output | |
| 136 #end if | |
| 137 -q | |
| 138 | |
| 139 ]]></command> | |
| 140 <inputs> | |
| 141 <conditional name="command"> | |
| 142 <param name="command_select" type="select" label="Select action to perform"> | |
| 143 <option value="hic-complete">Complete HiC analysis</option> | |
| 144 <option value="5c-complete">Complete 5C analysis</option> | |
| 145 <option value="fends">Create HiC fend set</option> | |
| 146 <option value="hic-data">Create HiC data set</option> | |
| 147 <option value="hic-project">Create HiC project</option> | |
| 148 <option value="hic-normalize">Normalize HiC project</option> | |
| 149 <option value="hic-heatmap">Create HiC heatmap set</option> | |
| 150 <option value="hic-interval">Extract HiC interval</option> | |
| 151 <option value="fragments">Create 5C fragment set</option> | |
| 152 <option value="5c-data">Create 5C data set</option> | |
| 153 <option value="5c-project">Create 5C project</option> | |
| 154 <option value="5c-normalize">Normalize 5C project</option> | |
| 155 <option value="5c-heatmap">Create 5C heatmap set</option> | |
| 156 <option value="5c-interval">Extract 5C interval</option> | |
| 157 </param> | |
| 158 <when value="hic-complete"> | |
| 159 <expand macro="hic_fend_xml"/> | |
| 160 <expand macro="hic_sequence_xml"/> | |
| 161 <expand macro="hic_chromosomes_xml"/> | |
| 162 <expand macro="hic_project_xml"/> | |
| 163 <expand macro="hic_range_xml"/> | |
| 164 <expand macro="hic_normalize_xml"/> | |
| 165 </when> | |
| 166 <when value="fends"> | |
| 167 <expand macro="hic_fend_xml"/> | |
| 168 </when> | |
| 169 <when value="hic-data"> | |
| 170 <param format="h5" name="fends" type="data" label="HiFive fend file" optional="False"/> | |
| 171 <expand macro="hic_sequence_xml"/> | |
| 172 </when> | |
| 173 <when value="hic-project"> | |
| 174 <param format="h5" name="hic_data" type="data" label="HiFive HiC data file" optional="False"/> | |
| 175 <expand macro="hic_chromosomes_xml"/> | |
| 176 <expand macro="hic_project_xml"/> | |
| 177 <expand macro="hic_range_xml"/> | |
| 178 </when> | |
| 179 <when value="hic-normalize"> | |
| 180 <param format="h5" name="hic_project" type="data" label="HiFive HiC project file" optional="False"/> | |
| 181 <expand macro="hic_chromosomes_xml"/> | |
| 182 <expand macro="hic_range_xml"/> | |
| 183 <expand macro="hic_normalize_xml"/> | |
| 184 </when> | |
| 185 <when value="hic-heatmap"> | |
| 186 <param name="hic_project" type="data" format="h5" label="HiFive HiC project file" optional="False"/> | |
| 187 <expand macro="hic_chromosomes_xml"/> | |
| 188 <param type="select" name="trans1" label="Calculate and include trans interactions"> | |
| 189 <option value="-t">yes</option> | |
| 190 <option value="">no</option> | |
| 191 </param> | |
| 192 <expand macro="binsize_xml"/> | |
| 193 <expand macro="hic_datatype_xml"/> | |
| 194 <expand macro="dynamic_xml"/> | |
| 195 <conditional name="image"> | |
| 196 <param name="generate" type="select" label="Generate image"> | |
| 197 <option value="yes">yes</option> | |
| 198 <option value="no">no</option> | |
| 199 </param> | |
| 200 <when value="yes"> | |
| 201 <expand macro="image_xml"/> | |
| 202 </when> | |
| 203 <when value="no"/> | |
| 204 </conditional> | |
| 205 </when> | |
| 206 <when value="hic-interval"> | |
| 207 <param name="hic_project" type="data" format="h5" label="HiFive HiC project file" optional="False"/> | |
| 208 <param type="text" name="chrom" size="10" label="Chromosome" optional="False"> | |
| 209 <validator type="empty_field" /> | |
| 210 </param> | |
| 211 <param type="integer" name="start" value="0" label="Starting coordinate" optional="True"> | |
| 212 <validator type="in_range" min="0"/> | |
| 213 </param> | |
| 214 <param type="integer" name="stop" value="0" label="Stopping coordinate" optional="True"> | |
| 215 <validator type="in_range" min="0"/> | |
| 216 </param> | |
| 217 <expand macro="binsize_xml"/> | |
| 218 <param type="integer" name="maxdist" value="0" label="Maximum interaction distance" optional="True" help="A value of zero will include all interaction distances that fall between the start and stop coordinates."> | |
| 219 <validator type="in_range" min="0"/> | |
| 220 </param> | |
| 221 <expand macro="hic_datatype_xml"/> | |
| 222 <expand macro="dynamic_xml"/> | |
| 223 <conditional name="image"> | |
| 224 <param name="generate" type="select" label="Generate image"> | |
| 225 <option value="yes">yes</option> | |
| 226 <option value="no">no</option> | |
| 227 </param> | |
| 228 <when value="yes"> | |
| 229 <expand macro="image_xml"/> | |
| 230 <expand macro="rotate_xml"/> | |
| 231 </when> | |
| 232 <when value="no"/> | |
| 233 </conditional> | |
| 234 </when> | |
| 235 <when value="5c-complete"> | |
| 236 <expand macro="5c_fragment_xml"/> | |
| 237 <expand macro="5c_sequence_xml"/> | |
| 238 <expand macro="5c_regions_xml"/> | |
| 239 <expand macro="5c_project_xml"/> | |
| 240 <expand macro="5c_range_xml"/> | |
| 241 <expand macro="5c_normalize_xml"/> | |
| 242 </when> | |
| 243 <when value="fragments"> | |
| 244 <expand macro="5c_fragment_xml"/> | |
| 245 </when> | |
| 246 <when value="5c-data"> | |
| 247 <param format="h5" name="fragments" type="data" label="HiFive fragment file" optional="False"/> | |
| 248 <expand macro="5c_sequence_xml"/> | |
| 249 </when> | |
| 250 <when value="5c-project"> | |
| 251 <param format="h5" name="fivec_data" type="data" label="HiFive 5C data file" optional="False"/> | |
| 252 <expand macro="5c_regions_xml"/> | |
| 253 <expand macro="5c_project_xml"/> | |
| 254 <expand macro="5c_range_xml"/> | |
| 255 </when> | |
| 256 <when value="5c-normalize"> | |
| 257 <param format="h5" name="fivec_project" type="data" label="HiFive 5C project file" optional="False"/> | |
| 258 <expand macro="5c_regions_xml"/> | |
| 259 <expand macro="5c_range_xml"/> | |
| 260 <expand macro="5c_normalize_xml"/> | |
| 261 </when> | |
| 262 <when value="5c-heatmap"> | |
| 263 <param name="fivec_project" type="data" format="h5" label="HiFive 5C project file" optional="False"/> | |
| 264 <expand macro="5c_regions_xml"/> | |
| 265 <param type="select" name="trans2" label="Calculate and include trans interactions"> | |
| 266 <option value="-t">yes</option> | |
| 267 <option value="">no</option> | |
| 268 </param> | |
| 269 <expand macro="binsize_xml"/> | |
| 270 <expand macro="5c_datatype_xml"/> | |
| 271 <expand macro="dynamic_xml"/> | |
| 272 <conditional name="image"> | |
| 273 <param name="generate" type="select" label="Generate image"> | |
| 274 <option value="yes">yes</option> | |
| 275 <option value="no">no</option> | |
| 276 </param> | |
| 277 <when value="yes"> | |
| 278 <expand macro="image_xml"/> | |
| 279 </when> | |
| 280 <when value="no"/> | |
| 281 </conditional> | |
| 282 </when> | |
| 283 <when value="5c-interval"> | |
| 284 <param name="fivec_project" type="data" format="h5" label="HiFive 5C project file" optional="False"/> | |
| 285 <param type="integer" name="region" value="" label="Region" optional="False"> | |
| 286 <validator type="empty_field" /> | |
| 287 </param> | |
| 288 <param type="integer" name="start" value="0" label="Starting coordinate" optional="True"> | |
| 289 <validator type="in_range" min="0"/> | |
| 290 </param> | |
| 291 <param type="integer" name="stop" value="0" label="Stopping coordinate" optional="True"> | |
| 292 <validator type="in_range" min="0"/> | |
| 293 </param> | |
| 294 <expand macro="binsize_xml"/> | |
| 295 <expand macro="5c_datatype_xml"/> | |
| 296 <expand macro="dynamic_xml"/> | |
| 297 <conditional name="image"> | |
| 298 <param name="generate" type="select" label="Generate image"> | |
| 299 <option value="yes">yes</option> | |
| 300 <option value="no">no</option> | |
| 301 </param> | |
| 302 <when value="yes"> | |
| 303 <expand macro="image_xml"/> | |
| 304 <expand macro="rotate_xml"/> | |
| 305 </when> | |
| 306 <when value="no"/> | |
| 307 </conditional> | |
| 308 </when> | |
| 309 </conditional> | |
| 310 </inputs> | |
| 311 <outputs> | |
| 312 <data format="h5" name="hic_comp_fends" label="${tool.name} on ${on_string}: HiC fends"> | |
| 313 <filter>(command["command_select"] == "hic-complete")</filter> | |
| 314 </data> | |
| 315 <data format="h5" name="hic_comp_data" label="${tool.name} on ${on_string}: HiC data"> | |
| 316 <filter>(command["command_select"] == "hic-complete")</filter> | |
| 317 </data> | |
| 318 <data format="h5" name="hic_comp_project" label="${tool.name} on ${on_string}: HiC project ${command.analysis.algorithm}"> | |
| 319 <filter>(command["command_select"] == "hic-complete")</filter> | |
| 320 </data> | |
| 321 <data format="h5" name="hic_fend_output" label="${tool.name} on ${on_string}: HiC fends"> | |
| 322 <filter>(command["command_select"] == "fends")</filter> | |
| 323 </data> | |
| 324 <data format="h5" name="hic_data_output" label="${tool.name} on ${on_string}: HiC data"> | |
| 325 <filter>(command["command_select"] == "hic-data")</filter> | |
| 326 </data> | |
| 327 <data format="h5" name="hic_project_output" label="${tool.name} on ${on_string}: HiC project"> | |
| 328 <filter>(command["command_select"] == "hic-project")</filter> | |
| 329 </data> | |
| 330 <data format="h5" name="hic_norm_output" label="${tool.name} on ${on_string}: HiC project ${command.analysis.algorithm}"> | |
| 331 <filter>(command["command_select"] == "hic-normalize")</filter> | |
| 332 </data> | |
| 333 <data format="h5" name="hic_hm_output" label="${tool.name} on ${on_string}: HiC heatmap HDF5"> | |
| 334 <filter>(command["command_select"] == "hic-heatmap")</filter> | |
| 335 </data> | |
| 336 <data format="png" name="hic_hm_image" label="${tool.name} on ${on_string}: HiC heatmap PNG"> | |
| 337 <filter>(command["command_select"] == "hic-heatmap")</filter> | |
| 338 <filter>(command["image"]["generate"] == "yes")</filter> | |
| 339 </data> | |
| 340 <data format="chrint" name="hic_int_output" label="${tool.name} on ${on_string}: HiC interval"> | |
| 341 <filter>(command["command_select"] == "hic-interval")</filter> | |
| 342 </data> | |
| 343 <data format="png" name="hic_int_image" label="${tool.name} on ${on_string}: HiC interval PNG"> | |
| 344 <filter>(command["command_select"] == "hic-interval")</filter> | |
| 345 <filter>(command["image"]["generate"] == "yes")</filter> | |
| 346 </data> | |
| 347 <data format="h5" name="fivec_comp_frags" label="${tool.name} on ${on_string}: 5C frags"> | |
| 348 <filter>(command["command_select"] == "5c-complete")</filter> | |
| 349 </data> | |
| 350 <data format="h5" name="fivec_comp_data" label="${tool.name} on ${on_string}: 5C data"> | |
| 351 <filter>(command["command_select"] == "5c-complete")</filter> | |
| 352 </data> | |
| 353 <data format="h5" name="fivec_comp_project" label="${tool.name} on ${on_string}: 5C project ${command.analysis.algorithm}"> | |
| 354 <filter>(command["command_select"] == "5c-complete")</filter> | |
| 355 </data> | |
| 356 <data format="h5" name="fivec_frag_output" label="${tool.name} on ${on_string}: 5C frags"> | |
| 357 <filter>(command["command_select"] == "fragments")</filter> | |
| 358 </data> | |
| 359 <data format="h5" name="fivec_data_output" label="${tool.name} on ${on_string}: 5C data"> | |
| 360 <filter>(command["command_select"] == "5c-data")</filter> | |
| 361 </data> | |
| 362 <data format="h5" name="fivec_project_output" label="${tool.name} on ${on_string}: 5C project"> | |
| 363 <filter>(command["command_select"] == "5c-project")</filter> | |
| 364 </data> | |
| 365 <data format="h5" name="fivec_norm_output" label="${tool.name} on ${on_string}: 5C project ${command.analysis.algorithm}"> | |
| 366 <filter>(command["command_select"] == "5c-normalize")</filter> | |
| 367 </data> | |
| 368 <data format="h5" name="fivec_hm_output" label="${tool.name} on ${on_string}: 5C heatmap HDF5"> | |
| 369 <filter>(command["command_select"] == "5c-heatmap")</filter> | |
| 370 </data> | |
| 371 <data format="png" name="fivec_hm_image" label="${tool.name} on ${on_string}: 5C heatmap PNG"> | |
| 372 <filter>(command["command_select"] == "5c-heatmap")</filter> | |
| 373 <filter>(command["image"]["generate"] == "yes")</filter> | |
| 374 </data> | |
| 375 <data format="chrint" name="fivec_int_output" label="${tool.name} on ${on_string}: 5C interval"> | |
| 376 <filter>(command["command_select"] == "5c-interval")</filter> | |
| 377 </data> | |
| 378 <data format="png" name="fivec_int_image" label="${tool.name} on ${on_string}: 5C interval PNG"> | |
| 379 <filter>(command["command_select"] == "5c-interval")</filter> | |
| 380 <filter>(command["image"]["generate"] == "yes")</filter> | |
| 381 </data> | |
| 382 </outputs> | |
| 383 <tests> | |
| 384 </tests> | |
| 385 <help><![CDATA[ | |
| 386 @COMMAND_HELP@ | |
| 387 @HIC_HELP@ | |
| 388 @5C_HELP@ | |
| 389 ]]></help> | |
| 390 </tool> |