Mercurial > repos > bgruening > hicexplorer_hicconvertformat

comparison hicConvertFormat.xml @ 8:c0737631eea1 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9
author iuc
date Wed, 18 Oct 2023 10:33:29 +0000
parents 2a24ce221cd7
children
comparison
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7:2a24ce221cd7 8:c0737631eea1
37 #if $xml_path.inputFormat_selector == 'optionHicpro': 37 #if $xml_path.inputFormat_selector == 'optionHicpro':
38 --matrices "matrix.hicpro" 38 --matrices "matrix.hicpro"
39 --bedFileHicpro "matrix.bed" 39 --bedFileHicpro "matrix.bed"
40 --inputFormat hicpro 40 --inputFormat hicpro
41 #end if 41 #end if
42 #if $xml_path.inputFormat_selector == 'option2Dtext':
43 --matrices "matrix.2Dtext"
44 #if $xml_path.resolutions:
45 #set $resolutions = ' '.join([ '"%s"' % $resolution for $resolution in str($xml_path.resolutions).split(" ") ])
46 --resolutions $resolutions
47 #end if
48 --chromosomeSizes "chromosomeSizes.txt"
49 --inputFormat 2D-text
50 #end if
42 #if $xml_path.inputFormat_selector == 'optionHic': 51 #if $xml_path.inputFormat_selector == 'optionHic':
43 --matrices "matrix.hic" 52 --matrices "matrix.hic"
44 #if $xml_path.resolutions: 53 #if $xml_path.resolutions:
45 #set $resolutions = ' '.join([ '"%s"' % $resolution for $resolution in str($xml_path.resolutions).split(" ") ]) 54 #set $resolutions = ' '.join([ '"%s"' % $resolution for $resolution in str($xml_path.resolutions).split(" ") ])
46 55
75 84
76 #if $xml_path.inputFormat_selector == 'optionHicpro': 85 #if $xml_path.inputFormat_selector == 'optionHicpro':
77 ln -s '$xml_path.matrixHicpro' "matrix.hicpro" && 86 ln -s '$xml_path.matrixHicpro' "matrix.hicpro" &&
78 ln -s '$xml_path.bedHicpro' "matrix.bed" && 87 ln -s '$xml_path.bedHicpro' "matrix.bed" &&
79 #end if 88 #end if
80 89 #if $xml_path.inputFormat_selector == 'option2Dtext':
90 ln -s '$xml_path.matrix2Dtext' "matrix.2Dtext" &&
91
92 ln -s '$xml_path.chromosomeSizes' "chromosomeSizes.txt" &&
93
94 #end if
81 #if $xml_path.inputFormat_selector == 'optionHic': 95 #if $xml_path.inputFormat_selector == 'optionHic':
82 ln -s '$xml_path.matrixHic' "matrix.hic" && 96 ln -s '$xml_path.matrixHic' "matrix.hic" &&
83 #end if 97 #end if
84 98
85 @BINARY@ 99 @BINARY@
86 @SINGLE_INPUT@ 100 @SINGLE_INPUT@
87 101
88 --outputFormat $outputSingleMultiple_conditional.outputFormat_conditional.outputFormat_selector 102 --outputFormat $outputSingleMultiple_conditional.outputFormat_conditional.outputFormat_selector
89 --outFileName 'matrix.$outputSingleMultiple_conditional.outputFormat_conditional.outputFormat_selector' 103 --outFileName 'matrix.$outputSingleMultiple_conditional.outputFormat_conditional.outputFormat_selector'
104 #if $outputSingleMultiple_conditional.outputFormat_conditional.outputFormat_selector == 'hicpro':
105 --bedFileHicpro intervalls.bed
106 #end if
90 107
91 ### Set up links to matrices to have correct ending 108 ### Set up links to matrices to have correct ending
92 #else if $outputSingleMultiple_conditional.outputSingleMultiple_selector == 'multipleMatrix': 109 #else if $outputSingleMultiple_conditional.outputSingleMultiple_selector == 'multipleMatrix':
93 #if $outputSingleMultiple_conditional.resolutionOrManyToOne_conditional.resolutionOrManyToOne_selector == 'resolution_option': 110 #if $outputSingleMultiple_conditional.resolutionOrManyToOne_conditional.resolutionOrManyToOne_selector == 'resolution_option':
94 #set xml_path = $outputSingleMultiple_conditional.resolutionOrManyToOne_conditional.inputFormat_conditional 111 #set xml_path = $outputSingleMultiple_conditional.resolutionOrManyToOne_conditional.inputFormat_conditional
106 123
107 #if $xml_path.inputFormat_selector == 'optionHicpro': 124 #if $xml_path.inputFormat_selector == 'optionHicpro':
108 ln -s '$xml_path.matrix_h5_cooler' "matrix.hicpro" && 125 ln -s '$xml_path.matrix_h5_cooler' "matrix.hicpro" &&
109 ln -s '$xml_path.bedHicpro' "matrix.bed" && 126 ln -s '$xml_path.bedHicpro' "matrix.bed" &&
110 #end if 127 #end if
128 #if $xml_path.inputFormat_selector == 'option2Dtext':
129 ln -s '$xml_path.chromosomeSizes' "chromosomeSizes.txt" &&
130
131 #end if
111 #if $xml_path.inputFormat_selector == 'optionHic': 132 #if $xml_path.inputFormat_selector == 'optionHic':
112 ln -s '$xml_path.matrix_h5_cooler' "matrix.hic" && 133 ln -s '$xml_path.matrix_h5_cooler' "matrix.hic" &&
113 #end if 134 #end if
114 #else: 135 #else:
115 #set xml_manyToOne = $outputSingleMultiple_conditional.resolutionOrManyToOne_conditional 136 #set xml_manyToOne = $outputSingleMultiple_conditional.resolutionOrManyToOne_conditional
130 #for $counter, $m in enumerate($xml_manyToOne.matrixHomer): 151 #for $counter, $m in enumerate($xml_manyToOne.matrixHomer):
131 ln -s '$m' "${counter}_matrix.homer" && 152 ln -s '$m' "${counter}_matrix.homer" &&
132 #end for 153 #end for
133 #set $m = ' '.join([ '"%s_matrix.homer"' % $counter for $counter, $matrix in enumerate($xml_manyToOne.matrixHomer) ]) 154 #set $m = ' '.join([ '"%s_matrix.homer"' % $counter for $counter, $matrix in enumerate($xml_manyToOne.matrixHomer) ])
134 #end if 155 #end if
135 #if $xml_manyToOne.inputFormat_conditional.inputFormat_selector == 'optionHicpro': 156 #if $xml_manyToOne.inputFormat_conditional.inputFormat_selector == 'option2Dtext':
157 #for $counter, $m in enumerate($xml_manyToOne.matrix2Dtext):
158 ln -s '$m' "${counter}_matrix.matrix2Dtext" &&
159 #end for
160 #set $m = ' '.join([ '"%s_matrix.matrix2Dtext"' % $counter for $counter, $matrix in enumerate($xml_manyToOne.matrix2Dtext) ])
161 #if $xml_manyToOne.resolutions:
162 #set $resolutions = ' '.join([ '"%s"' % $resolution for $resolution in str($xml_manyToOne.resolutions).split(" ") ])
163 --resolutions $resolutions
164 #end if
165 --chromosomeSizes "chromosomeSizes.txt"
166
167 #end if
168 #if $xml_manyToOne.inputFormat_conditional.inputFormat_selector == 'optionHicpro':
136 #for $counter, $m in enumerate($xml_manyToOne.matrixHicpro): 169 #for $counter, $m in enumerate($xml_manyToOne.matrixHicpro):
137 ln -s '$m' "${counter}_matrix.hicpro" && 170 ln -s '$m' "${counter}_matrix.hicpro" &&
138 #end for 171 #end for
139 #set $m = ' '.join([ '"%s_matrix.hicpro"' % $counter for $counter, $matrix in enumerate($xml_manyToOne.matrixHicpro) ]) 172 #set $m = ' '.join([ '"%s_matrix.hicpro"' % $counter for $counter, $matrix in enumerate($xml_manyToOne.matrixHicpro) ])
140 173
169 #if $xml_path.inputFormat_selector == 'optionHicpro': 202 #if $xml_path.inputFormat_selector == 'optionHicpro':
170 --matrices "matrix.hicpro" 203 --matrices "matrix.hicpro"
171 --bedFileHicpro "matrix.bed" 204 --bedFileHicpro "matrix.bed"
172 --inputFormat hicpro 205 --inputFormat hicpro
173 #end if 206 #end if
207 #if $xml_path.inputFormat_selector == 'option2Dtext':
208 --matrices "matrix.2Dtext"
209 --chromosomeSizes "chromosomeSizes.txt"
210 --inputFormat 2D-text
211 #end if
174 #if $xml_path.inputFormat_selector == 'optionHic': 212 #if $xml_path.inputFormat_selector == 'optionHic':
175 --matrices "matrix.hic" 213 --matrices "matrix.hic"
176 --inputFormat hic 214 --inputFormat hic
177 #end if 215 #end if
178 #end if 216 #end if
187 #end if 225 #end if
188 226
189 #if $xml_manyToOne.inputFormat_conditional.inputFormat_selector == 'optionHomer': 227 #if $xml_manyToOne.inputFormat_conditional.inputFormat_selector == 'optionHomer':
190 --inputFormat homer 228 --inputFormat homer
191 #end if 229 #end if
192 230 #if $xml_manyToOne.inputFormat_conditional.inputFormat_selector == 'option2Dtext':
231
232 --inputFormat 2D-text
233 #end if
193 #if $xml_manyToOne.inputFormat_conditional.inputFormat_selector == 'optionHicpro': 234 #if $xml_manyToOne.inputFormat_conditional.inputFormat_selector == 'optionHicpro':
194 --inputFormat hicpro 235 --inputFormat hicpro
195 --bedFileHicpro '$bed' 236 --bedFileHicpro '$bed'
196 #end if 237 #end if
197 238
203 $enforceInteger 244 $enforceInteger
204 245
205 #if $outputSingleMultiple_conditional.outputSingleMultiple_selector == 'singleMatrix': 246 #if $outputSingleMultiple_conditional.outputSingleMultiple_selector == 'singleMatrix':
206 #if $outputSingleMultiple_conditional.outputFormat_conditional.outputFormat_selector == 'ginteractions': 247 #if $outputSingleMultiple_conditional.outputFormat_conditional.outputFormat_selector == 'ginteractions':
207 && mv 'matrix.${outputSingleMultiple_conditional.outputFormat_conditional.outputFormat_selector}.tsv' matrix_out 248 && mv 'matrix.${outputSingleMultiple_conditional.outputFormat_conditional.outputFormat_selector}.tsv' matrix_out
249 #else if $outputSingleMultiple_conditional.outputFormat_conditional.outputFormat_selector == 'hicpro':
250 && mv matrix.hicpro matrix_out
208 #else: 251 #else:
209 && mv 'matrix.$outputSingleMultiple_conditional.outputFormat_conditional.outputFormat_selector' matrix_out 252 && mv 'matrix.$outputSingleMultiple_conditional.outputFormat_conditional.outputFormat_selector' matrix_out
210 #end if 253 #end if
211 #else if $outputSingleMultiple_conditional.outputSingleMultiple_selector == 'multipleMatrix': 254 #else if $outputSingleMultiple_conditional.outputSingleMultiple_selector == 'multipleMatrix':
212 && mv matrix.mcool matrix_out 255 && mv matrix.mcool matrix_out
213 #end if 256 #end if
257
214 ]]> 258 ]]>
215 </command> 259 </command>
216 <inputs> 260 <inputs>
217
218 <conditional name="outputSingleMultiple_conditional"> 261 <conditional name="outputSingleMultiple_conditional">
219 <param name="outputSingleMultiple_selector" type="select" label="Choose output matrix type"> 262 <param name="outputSingleMultiple_selector" type="select" label="Choose output matrix type">
220 <option value="singleMatrix" selected="True">single matrix</option> 263 <option value="singleMatrix" selected="True">single matrix</option>
221 <option value="multipleMatrix">multiple matrix</option> 264 <option value="multipleMatrix">multiple matrix</option>
222 </param> 265 </param>
223 <when value='singleMatrix'> 266 <when value="singleMatrix">
224 <expand macro='convertFormat_single_macro' /> 267 <expand macro="convertFormat_single_macro" />
225 <expand macro='convertFormat_single_output_macro' /> 268 <expand macro="convertFormat_single_output_macro" />
226 </when> 269 </when>
227 <when value='multipleMatrix'> 270 <when value="multipleMatrix">
228 <conditional name="resolutionOrManyToOne_conditional"> 271 <conditional name="resolutionOrManyToOne_conditional">
229 <param name="resolutionOrManyToOne_selector" type="select" label="Choose input file type"> 272 <param name="resolutionOrManyToOne_selector" type="select" label="Choose input file type">
230 <option value='resolution_option' >Create out of one matrix a multi matrix with diffrerent resolutions</option> 273 <option value="resolution_option" >Create out of one matrix a multi matrix with diffrerent resolutions</option>
231 <option value='manyToOne_option'>Create out of n matrices one multi matrix</option> 274 <option value="manyToOne_option">Create out of n matrices one multi matrix</option>
232 </param> 275 </param>
233 <when value='resolution_option'> 276 <when value="resolution_option">
234 <param name='resolutions' type='text' label='To be stored resolutions' help="Resolutions can be specified seperated with a space, e.g. '10000 20000 50000'"> 277 <param name="resolutions" type="text" label="To be stored resolutions" help="Resolutions can be specified seperated with a space, e.g. '10000 20000 50000'">
235 <validator type="expression" message="Only numeric characters and the a space as seperator are allowed.">value.replace(' ', '').isnumeric()</validator> 278 <validator type="expression" message="Only numeric characters and a space as seperator are allowed.">value.replace(' ', '').isnumeric()</validator>
236 </param> 279 </param>
237 <expand macro='convertFormat_single_macro' /> 280 <expand macro="convertFormat_single_macro" />
238 </when> 281 </when>
239 <when value='manyToOne_option'> 282 <when value="manyToOne_option">
240 <expand macro='convertFormat_multiple_macro' /> 283 <expand macro="convertFormat_multiple_macro" />
241 </when> 284 </when>
242 </conditional> 285 </conditional>
243 </when> 286 </when>
244 </conditional> 287 </conditional>
245 <param name='storeAppliedCorrection' type="boolean" truevalue="--store_applied_correction" falsevalue="" label="Store applied correction factors in column count" help="Option only for cool input files" /> 288 <param name="storeAppliedCorrection" type="boolean" truevalue="--store_applied_correction" falsevalue="" label="Store applied correction factors in column count" help="Option only for cool input files" />
246 <param name='enforceInteger' type="boolean" truevalue="--enforce_integer" falsevalue="" label="Enforce integer for count column" help="Option only for cool input files" /> 289 <param name="enforceInteger" type="boolean" truevalue="--enforce_integer" falsevalue="" label="Enforce integer for count column" help="Option only for cool input files" />
247 </inputs> 290 </inputs>
248 <outputs> 291 <outputs>
249 <data name='output_converted_matrix' from_work_dir='matrix_out' format='cool' label='Converted matrix'> 292 <data name="output_converted_matrix" from_work_dir="matrix_out" format="cool" label="Converted matrix in cool format">
250 <filter>outputSingleMultiple_conditional.outputSingleMultiple_selector == 'singleMatrix'</filter> 293 <filter>outputSingleMultiple_conditional['outputSingleMultiple_selector'] == 'singleMatrix'</filter>
251 <change_format> 294 <change_format>
252 <when input="outputSingleMultiple_conditional.outputFormat_conditional.outputFormat_selector" value="h5" format="h5" /> 295 <when input="outputSingleMultiple_conditional.outputFormat_conditional.outputFormat_selector" value="h5" format="h5" />
253 <when input="outputSingleMultiple_conditional.outputFormat_conditional.outputFormat_selector" value="homer" format="zip" /> 296 <when input="outputSingleMultiple_conditional.outputFormat_conditional.outputFormat_selector" value="homer" format="zip" />
254 <when input="outputSingleMultiple_conditional.outputFormat_conditional.outputFormat_selector" value="ginteractions" format="tabular" /> 297 <when input="outputSingleMultiple_conditional.outputFormat_conditional.outputFormat_selector" value="ginteractions" format="tabular" />
298 <when input="outputSingleMultiple_conditional.outputFormat_conditional.outputFormat_selector" value="hicpro" format="tabular" />
255 </change_format> 299 </change_format>
256 </data> 300 </data>
257 <data name='output_converted_matrix_multi' from_work_dir='matrix_out' format='mcool' label='Converted matrix mcool'> 301 <data name="output_converted_matrix_bed" from_work_dir="intervalls.bed" format="tabular" label="Converted matrix in tabular format">
258 <filter>outputSingleMultiple_conditional.outputSingleMultiple_selector == 'multipleMatrix'</filter> 302 <filter>outputSingleMultiple_conditional['outputFormat_conditional']['outputFormat_selector'] == 'hicpro'</filter>
303 </data>
304 <data name="output_converted_matrix_multi" from_work_dir="matrix_out" format="mcool" label="Converted matrix in mcool format">
305 <filter>outputSingleMultiple_conditional['outputSingleMultiple_selector'] == 'multipleMatrix'</filter>
259 </data> 306 </data>
260 </outputs> 307 </outputs>
261 <tests> 308 <tests>
262 <test> 309 <test expect_num_outputs="1">
263 <conditional name='outputSingleMultiple_conditional'> 310 <conditional name="outputSingleMultiple_conditional">
264 <param name='outputSingleMultiple_selector' value='singleMatrix' /> 311 <param name="outputSingleMultiple_selector" value="singleMatrix" />
265 <conditional name='inputFormat_conditional'> 312 <conditional name="inputFormat_conditional">
266 <param name='inputFormat_selector' value='optionCool' /> 313 <param name="inputFormat_selector" value="optionCool" />
267 <param name='matrix_h5_cooler' value='small_test_matrix.cool' /> 314 <param name="matrix_h5_cooler" value="small_test_matrix.cool" />
268 </conditional> 315 </conditional>
269 316
270 <conditional name='outputFormat_conditional'> 317 <conditional name="outputFormat_conditional">
271 <param name='outputFormat_selector' value='h5' /> 318 <param name="outputFormat_selector" value="h5" />
272 </conditional> 319 </conditional>
273 </conditional> 320 </conditional>
274 <output name="output_converted_matrix" ftype="h5"> 321 <output name="output_converted_matrix" ftype="h5">
275 <assert_contents> 322 <assert_contents>
276 <has_h5_keys keys='intervals,matrix,nan_bins' /> 323 <has_h5_keys keys="intervals,matrix,nan_bins" />
277 </assert_contents> 324 </assert_contents>
278 </output> 325 </output>
279 </test> 326 </test>
280 <test> 327 <test expect_num_outputs="1">
281 <conditional name='outputSingleMultiple_conditional'> 328 <conditional name="outputSingleMultiple_conditional">
282 <param name='outputSingleMultiple_selector' value='singleMatrix' /> 329 <param name="outputSingleMultiple_selector" value="singleMatrix" />
283 <conditional name='inputFormat_conditional'> 330 <conditional name="inputFormat_conditional">
284 <param name='inputFormat_selector' value='optionH5' /> 331 <param name="inputFormat_selector" value="option2Dtext" />
285 <param name='matrix_h5_cooler' value='small_test_matrix.h5' /> 332 <param name="matrix2Dtext" value="hicConvertFormat/GSM1436265_RAD21_ENCFF002EMQ.txt" />
286 </conditional> 333 <param name="resolutions" value="10000" />
287 334 <param name="chromosomeSizes" value="hicConvertFormat/hg19.chrom.sizes" />
288 <conditional name='outputFormat_conditional'> 335 </conditional>
289 <param name='outputFormat_selector' value='cool' /> 336
337 <conditional name="outputFormat_conditional">
338 <param name="outputFormat_selector" value="h5" />
339 </conditional>
340 </conditional>
341 <output name="output_converted_matrix" ftype="h5">
342 <assert_contents>
343 <has_h5_keys keys="intervals,matrix" />
344 </assert_contents>
345 </output>
346 </test>
347 <test expect_num_outputs="1">
348 <conditional name="outputSingleMultiple_conditional">
349 <param name="outputSingleMultiple_selector" value="singleMatrix" />
350 <conditional name="inputFormat_conditional">
351 <param name="inputFormat_selector" value="optionH5" />
352 <param name="matrix_h5_cooler" value="small_test_matrix.h5" />
353 </conditional>
354
355 <conditional name="outputFormat_conditional">
356 <param name="outputFormat_selector" value="cool" />
290 </conditional> 357 </conditional>
291 </conditional> 358 </conditional>
292 <output name="output_converted_matrix" ftype="cool"> 359 <output name="output_converted_matrix" ftype="cool">
293 <assert_contents> 360 <assert_contents>
294 <has_h5_keys keys='bins,chroms,indexes,pixels' /> 361 <has_h5_keys keys="bins,chroms,indexes,pixels" />
295 </assert_contents> 362 </assert_contents>
296 </output> 363 </output>
297 </test> 364 </test>
298 <test> 365 <test expect_num_outputs="1">
299 <conditional name='outputSingleMultiple_conditional'> 366 <conditional name="outputSingleMultiple_conditional">
300 <param name='outputSingleMultiple_selector' value='singleMatrix' /> 367 <param name="outputSingleMultiple_selector" value="singleMatrix" />
301 <conditional name='inputFormat_conditional'> 368 <conditional name="inputFormat_conditional">
302 <param name='inputFormat_selector' value='optionCool' /> 369 <param name="inputFormat_selector" value="optionCool" />
303 <param name='matrix_h5_cooler' value='hicConvertFormat/small_test_matrix_chr4.cool' /> 370 <param name="matrix_h5_cooler" value="hicConvertFormat/small_test_matrix_chr4.cool" />
304 </conditional> 371 </conditional>
305 372
306 <conditional name='outputFormat_conditional'> 373 <conditional name="outputFormat_conditional">
307 <param name='outputFormat_selector' value='homer' /> 374 <param name="outputFormat_selector" value="homer" />
308 </conditional> 375 </conditional>
309 </conditional> 376 </conditional>
310 <output name="output_converted_matrix" file="hicConvertFormat/small_test_matrix_chr4.homer" ftype="zip" compare="sim_size" delta="40000" /> 377 <output name="output_converted_matrix" file="hicConvertFormat/small_test_matrix_chr4.homer" ftype="zip" compare="sim_size" delta="40000" />
311 </test> 378 </test>
312 <test> 379 <test expect_num_outputs="1">
313 <conditional name='outputSingleMultiple_conditional'> 380 <conditional name="outputSingleMultiple_conditional">
314 <param name='outputSingleMultiple_selector' value='singleMatrix' /> 381 <param name="outputSingleMultiple_selector" value="singleMatrix" />
315 <conditional name='inputFormat_conditional'> 382 <conditional name="inputFormat_conditional">
316 <param name='inputFormat_selector' value='optionCool' /> 383 <param name="inputFormat_selector" value="optionCool" />
317 <param name='matrix_h5_cooler' value='hicConvertFormat/small_test_matrix_chr4.cool' /> 384 <param name="matrix_h5_cooler" value="hicConvertFormat/small_test_matrix_chr4.cool" />
318 </conditional> 385 </conditional>
319 386
320 <conditional name='outputFormat_conditional'> 387 <conditional name="outputFormat_conditional">
321 <param name='outputFormat_selector' value='ginteractions' /> 388 <param name="outputFormat_selector" value="ginteractions" />
322 </conditional> 389 </conditional>
323 </conditional> 390 </conditional>
324 <output name="output_converted_matrix" file="hicConvertFormat/small_test_matrix_chr4.ginteractions.tsv" ftype="tabular" /> 391 <output name="output_converted_matrix" file="hicConvertFormat/small_test_matrix_chr4.ginteractions.tsv" ftype="tabular" />
325 </test> 392 </test>
326 <test> 393 <test expect_num_outputs="2">
327 <conditional name='outputSingleMultiple_conditional'> 394 <conditional name="outputSingleMultiple_conditional">
328 <param name='outputSingleMultiple_selector' value='multipleMatrix' /> 395 <param name="outputSingleMultiple_selector" value="singleMatrix" />
329 <conditional name='resolutionOrManyToOne_conditional'> 396 <conditional name="inputFormat_conditional">
330 <param name='resolutionOrManyToOne_selector' value='resolution_option' /> 397 <param name="inputFormat_selector" value="optionCool" />
331 <param name='resolutions' value='5000 10000 20000' /> 398 <param name="matrix_h5_cooler" value="hicConvertFormat/small_test_matrix_chr4.cool" />
332 <conditional name='inputFormat_conditional'> 399 </conditional>
333 <param name='inputFormat_selector' value='optionH5' /> 400
334 <param name='matrix_h5_cooler' value='small_test_matrix.h5' /> 401 <conditional name="outputFormat_conditional">
402 <param name="outputFormat_selector" value="hicpro" />
403 </conditional>
404 </conditional>
405 <output name="output_converted_matrix" file="hicConvertFormat/small_test_matrix_chr4.hicpro" ftype="tabular" />
406 <output name="output_converted_matrix_bed" file="hicConvertFormat/small_test_matrix_chr4.bed" ftype="tabular" />
407 </test>
408 <test expect_num_outputs="2">
409 <conditional name="outputSingleMultiple_conditional">
410 <param name="outputSingleMultiple_selector" value="multipleMatrix" />
411 <conditional name="resolutionOrManyToOne_conditional">
412 <param name="resolutionOrManyToOne_selector" value="resolution_option" />
413 <param name="resolutions" value="5000 10000 20000" />
414 <conditional name="inputFormat_conditional">
415 <param name="inputFormat_selector" value="optionH5" />
416 <param name="matrix_h5_cooler" value="small_test_matrix.h5" />
335 </conditional> 417 </conditional>
336 </conditional> 418 </conditional>
337 </conditional> 419 </conditional>
338 <output name="output_converted_matrix" ftype="cool"> 420 <output name="output_converted_matrix_multi" ftype="mcool">
339 <assert_contents> 421 <assert_contents>
340 <has_h5_keys keys='resolutions' /> 422 <has_h5_keys keys="resolutions" />
341 </assert_contents> 423 </assert_contents>
342 </output> 424 </output>
343 </test> 425 </test>
344 </tests> 426 </tests>
345 <help><![CDATA[ 427 <help><![CDATA[