Mercurial > repos > bgruening > hicexplorer_hicconvertformat

comparison hicConvertFormat.xml @ 2:2f62a87d4017 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 4b602d427e0fc0da5353a4510798349de98e4ae4"
author iuc
date Wed, 11 Mar 2020 16:59:15 -0400
parents e136f22c2a0f
children 3e598b8e72e7
comparison
equal deleted inserted replaced
1:3b15581e7ca7 2:2f62a87d4017
26 #end if 26 #end if
27 #if $xml_path.inputFormat_selector == 'optionH5': 27 #if $xml_path.inputFormat_selector == 'optionH5':
28 --matrices "matrix.h5" 28 --matrices "matrix.h5"
29 --inputFormat h5 29 --inputFormat h5
30 30
31 #end if 31 #end if
32 #if $xml_path.inputFormat_selector == 'optionHomer': 32 #if $xml_path.inputFormat_selector == 'optionHomer':
33 --matrices "matrix.homer" 33 --matrices "matrix.homer"
34 --inputFormat homer 34 --inputFormat homer
35 35
36 #end if 36 #end if
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 == 'optionHic': 42 #if $xml_path.inputFormat_selector == 'optionHic':
43 --matrices "matrix.hic" 43 --matrices "matrix.hic"
44 #if $xml_path.resolutions: 44 #if $xml_path.resolutions:
45 #set $resolutions = ' '.join([ '"%s"' % $resolution for $resolution in str($xml_path.resolutions).split(" ") ]) 45 #set $resolutions = ' '.join([ '"%s"' % $resolution for $resolution in str($xml_path.resolutions).split(" ") ])
46 46
47 --resolutions $resolutions 47 --resolutions $resolutions
48 #end if 48 #end if
49 --inputFormat hic 49 --inputFormat hic
50 #end if 50 #end if
51 </token> 51 </token>
52 <import>macros.xml</import> 52 <import>macros.xml</import>
53 </macros> 53 </macros>
54 54
55 <expand macro="requirements" /> 55 <expand macro="requirements" />
56 <command detect_errors="exit_code"><![CDATA[ 56 <command detect_errors="exit_code"><![CDATA[
57 57
58 58
59 ## single to single case 59 ## single to single case
60 60
61 61
62 #if $outputSingleMultiple_conditional.outputSingleMultiple_selector == 'singleMatrix': 62 #if $outputSingleMultiple_conditional.outputSingleMultiple_selector == 'singleMatrix':
63 #set xml_path = $outputSingleMultiple_conditional.inputFormat_conditional 63 #set xml_path = $outputSingleMultiple_conditional.inputFormat_conditional
64 64
65 #if $xml_path.inputFormat_selector == 'optionCool': 65 #if $xml_path.inputFormat_selector == 'optionCool':
66 ln -s "$xml_path.matrix_h5_cooler" "matrix.cool" && 66 ln -s "$xml_path.matrix_h5_cooler" "matrix.cool" &&
67 67
68 #end if 68 #end if
69 #if $xml_path.inputFormat_selector == 'optionH5': 69 #if $xml_path.inputFormat_selector == 'optionH5':
70 ln -s "$xml_path.matrix_h5_cooler" "matrix.h5" && 70 ln -s "$xml_path.matrix_h5_cooler" "matrix.h5" &&
71 71
72 #end if 72 #end if
73 #if $xml_path.inputFormat_selector == 'optionHomer': 73 #if $xml_path.inputFormat_selector == 'optionHomer':
74 ln -s "$xml_path.matrixHomer" "matrix.homer" && 74 ln -s "$xml_path.matrixHomer" "matrix.homer" &&
75 75
76 #end if 76 #end if
77 77
78 #if $xml_path.inputFormat_selector == 'optionHicpro': 78 #if $xml_path.inputFormat_selector == 'optionHicpro':
79 ln -s "$xml_path.matrixHicpro" "matrix.hicpro" && 79 ln -s "$xml_path.matrixHicpro" "matrix.hicpro" &&
80 ln -s "$xml_path.bedHicpro" "matrix.bed" && 80 ln -s "$xml_path.bedHicpro" "matrix.bed" &&
81 #end if 81 #end if
82 82
83 #if $xml_path.inputFormat_selector == 'optionHic': 83 #if $xml_path.inputFormat_selector == 'optionHic':
84 ln -s "$xml_path.matrixHic" "matrix.hic" && 84 ln -s "$xml_path.matrixHic" "matrix.hic" &&
85 #end if 85 #end if
86 86
87 87
88 88
89 @BINARY@ 89 @BINARY@
90 @SINGLE_INPUT@ 90 @SINGLE_INPUT@
91 91
92 92
93 --outputFormat $outputSingleMultiple_conditional.outputFormat_conditional.outputFormat_selector 93 --outputFormat $outputSingleMultiple_conditional.outputFormat_conditional.outputFormat_selector
94 --outFileName 'matrix.$outputSingleMultiple_conditional.outputFormat_conditional.outputFormat_selector' 94 --outFileName 'matrix.$outputSingleMultiple_conditional.outputFormat_conditional.outputFormat_selector'
95 95
96 #if $outputSingleMultiple_conditional.outputFormat_conditional.outputFormat_selector == 'ginteractions': 96 #if $outputSingleMultiple_conditional.outputFormat_conditional.outputFormat_selector == 'ginteractions':
97 && mv 'matrix.${outputSingleMultiple_conditional.outputFormat_conditional.outputFormat_selector}.tsv' matrix_out 97 && mv 'matrix.${outputSingleMultiple_conditional.outputFormat_conditional.outputFormat_selector}.tsv' matrix_out
99 #else: 99 #else:
100 && mv "matrix.$outputSingleMultiple_conditional.outputFormat_conditional.outputFormat_selector" matrix_out 100 && mv "matrix.$outputSingleMultiple_conditional.outputFormat_conditional.outputFormat_selector" matrix_out
101 #end if 101 #end if
102 #end if 102 #end if
103 103
104 104
105 ### Set up links to matrices to have correct ending 105 ### Set up links to matrices to have correct ending
106 #if $outputSingleMultiple_conditional.outputSingleMultiple_selector == 'multipleMatrix': 106 #if $outputSingleMultiple_conditional.outputSingleMultiple_selector == 'multipleMatrix':
107 #if $outputSingleMultiple_conditional.resolutionOrManyToOne_conditional.resolutionOrManyToOne_selector == 'resolution_option': 107 #if $outputSingleMultiple_conditional.resolutionOrManyToOne_conditional.resolutionOrManyToOne_selector == 'resolution_option':
108 #set xml_path = $outputSingleMultiple_conditional.resolutionOrManyToOne_conditional.inputFormat_conditional 108 #set xml_path = $outputSingleMultiple_conditional.resolutionOrManyToOne_conditional.inputFormat_conditional
109 #if $xml_path.inputFormat_selector == 'optionCool': 109 #if $xml_path.inputFormat_selector == 'optionCool':
153 #if $xml_manyToOne.inputFormat_conditional.inputFormat_selector == 'optionHicpro': 153 #if $xml_manyToOne.inputFormat_conditional.inputFormat_selector == 'optionHicpro':
154 #for $counter, $m in enumerate($xml_manyToOne.matrixHicpro): 154 #for $counter, $m in enumerate($xml_manyToOne.matrixHicpro):
155 ln -s '$m' "${counter}_matrix.hicpro" && 155 ln -s '$m' "${counter}_matrix.hicpro" &&
156 #end for 156 #end for
157 #set $m = ' '.join([ '"%s_matrix.hicpro"' % $counter for $counter, $matrix in enumerate($xml_manyToOne.matrixHicpro) ]) 157 #set $m = ' '.join([ '"%s_matrix.hicpro"' % $counter for $counter, $matrix in enumerate($xml_manyToOne.matrixHicpro) ])
158 158
159 #for $counter, $bed in enumerate($xml_manyToOne.bedHicpro): 159 #for $counter, $bed in enumerate($xml_manyToOne.bedHicpro):
160 ln -s '$bed' "${counter}_matrix.bed" && 160 ln -s '$bed' "${counter}_matrix.bed" &&
161 #end for 161 #end for
162 #set $bed = ' '.join([ '"%s_matrix.bed"' % $counter for $counter, $matrix in enumerate($xml_manyToOne.bedHicpro) ]) 162 #set $bed = ' '.join([ '"%s_matrix.bed"' % $counter for $counter, $matrix in enumerate($xml_manyToOne.bedHicpro) ])
163 --bedFileHicpro '$bed' 163 --bedFileHicpro '$bed'
164 #end if 164 #end if
165 #end if 165 #end if
166 166
167 167
168 @BINARY@ 168 @BINARY@
169 --outputFormat mcool 169 --outputFormat mcool
170 170
171 #if $outputSingleMultiple_conditional.resolutionOrManyToOne_conditional.resolutionOrManyToOne_selector == 'resolution_option': 171 #if $outputSingleMultiple_conditional.resolutionOrManyToOne_conditional.resolutionOrManyToOne_selector == 'resolution_option':
172 #set $resolutions = ' '.join([ '"%s"' % $resolution for $resolution in str($outputSingleMultiple_conditional.resolutionOrManyToOne_conditional.resolutions).split(" ") ]) 172 #set $resolutions = ' '.join([ '"%s"' % $resolution for $resolution in str($outputSingleMultiple_conditional.resolutionOrManyToOne_conditional.resolutions).split(" ") ])
173 173
178 #end if 178 #end if
179 #if $xml_path.inputFormat_selector == 'optionH5': 179 #if $xml_path.inputFormat_selector == 'optionH5':
180 --matrices "matrix.h5" 180 --matrices "matrix.h5"
181 --inputFormat h5 181 --inputFormat h5
182 182
183 #end if 183 #end if
184 #if $xml_path.inputFormat_selector == 'optionHomer': 184 #if $xml_path.inputFormat_selector == 'optionHomer':
185 --matrices "matrix.homer" 185 --matrices "matrix.homer"
186 --inputFormat homer 186 --inputFormat homer
187 187
188 #end if 188 #end if
189 #if $xml_path.inputFormat_selector == 'optionHicpro': 189 #if $xml_path.inputFormat_selector == 'optionHicpro':
190 --matrices "matrix.hicpro" 190 --matrices "matrix.hicpro"
191 --bedFileHicpro "matrix.bed" 191 --bedFileHicpro "matrix.bed"
192 --inputFormat hicpro 192 --inputFormat hicpro
193 #end if 193 #end if
194 #if $xml_path.inputFormat_selector == 'optionHic': 194 #if $xml_path.inputFormat_selector == 'optionHic':
195 --matrices "matrix.hic" 195 --matrices "matrix.hic"
196 --inputFormat hic 196 --inputFormat hic
197 #end if 197 #end if
198 #end if 198 #end if
199 199
200 #if $outputSingleMultiple_conditional.resolutionOrManyToOne_conditional.resolutionOrManyToOne_selector == 'manyToOne_option': 200 #if $outputSingleMultiple_conditional.resolutionOrManyToOne_conditional.resolutionOrManyToOne_selector == 'manyToOne_option':
201 #if $xml_manyToOne.inputFormat_conditional.inputFormat_selector == 'optionCool': 201 #if $xml_manyToOne.inputFormat_conditional.inputFormat_selector == 'optionCool':
202 --inputFormat cool 202 --inputFormat cool
230 230
231 <conditional name="outputSingleMultiple_conditional"> 231 <conditional name="outputSingleMultiple_conditional">
232 <param name="outputSingleMultiple_selector" type="select" label="Choose output matrix type"> 232 <param name="outputSingleMultiple_selector" type="select" label="Choose output matrix type">
233 <option value="singleMatrix" selected="True">single matrix</option> 233 <option value="singleMatrix" selected="True">single matrix</option>
234 <option value="multipleMatrix">multiple matrix</option> 234 <option value="multipleMatrix">multiple matrix</option>
235 </param> 235 </param>
236 <when value='singleMatrix'> 236 <when value='singleMatrix'>
237 <expand macro='convertFormat_single_macro' /> 237 <expand macro='convertFormat_single_macro' />
238 <expand macro='convertFormat_single_output_macro' /> 238 <expand macro='convertFormat_single_output_macro' />
239 </when> 239 </when>
240 <when value='multipleMatrix'> 240 <when value='multipleMatrix'>
276 <param name='outputSingleMultiple_selector' value='singleMatrix'/> 276 <param name='outputSingleMultiple_selector' value='singleMatrix'/>
277 <conditional name='inputFormat_conditional'> 277 <conditional name='inputFormat_conditional'>
278 <param name='inputFormat_selector' value='optionCool'/> 278 <param name='inputFormat_selector' value='optionCool'/>
279 <param name='matrix_h5_cooler' value='small_test_matrix.cool'/> 279 <param name='matrix_h5_cooler' value='small_test_matrix.cool'/>
280 </conditional> 280 </conditional>
281 281
282 <conditional name='outputFormat_conditional'> 282 <conditional name='outputFormat_conditional'>
283 <param name='outputFormat_selector' value='h5'/> 283 <param name='outputFormat_selector' value='h5'/>
284 </conditional> 284 </conditional>
285 </conditional> 285 </conditional>
286 <output name="output_converted_matrix" ftype="h5"> 286 <output name="output_converted_matrix" ftype="h5">
294 <param name='outputSingleMultiple_selector' value='singleMatrix'/> 294 <param name='outputSingleMultiple_selector' value='singleMatrix'/>
295 <conditional name='inputFormat_conditional'> 295 <conditional name='inputFormat_conditional'>
296 <param name='inputFormat_selector' value='optionH5'/> 296 <param name='inputFormat_selector' value='optionH5'/>
297 <param name='matrix_h5_cooler' value='small_test_matrix.h5'/> 297 <param name='matrix_h5_cooler' value='small_test_matrix.h5'/>
298 </conditional> 298 </conditional>
299 299
300 <conditional name='outputFormat_conditional'> 300 <conditional name='outputFormat_conditional'>
301 <param name='outputFormat_selector' value='cool'/> 301 <param name='outputFormat_selector' value='cool'/>
302 </conditional> 302 </conditional>
303 </conditional> 303 </conditional>
304 <output name="output_converted_matrix" ftype="cool"> 304 <output name="output_converted_matrix" ftype="cool">
312 <param name='outputSingleMultiple_selector' value='singleMatrix'/> 312 <param name='outputSingleMultiple_selector' value='singleMatrix'/>
313 <conditional name='inputFormat_conditional'> 313 <conditional name='inputFormat_conditional'>
314 <param name='inputFormat_selector' value='optionCool'/> 314 <param name='inputFormat_selector' value='optionCool'/>
315 <param name='matrix_h5_cooler' value='hicConvertFormat/small_test_matrix_chr4.cool'/> 315 <param name='matrix_h5_cooler' value='hicConvertFormat/small_test_matrix_chr4.cool'/>
316 </conditional> 316 </conditional>
317 317
318 <conditional name='outputFormat_conditional'> 318 <conditional name='outputFormat_conditional'>
319 <param name='outputFormat_selector' value='homer'/> 319 <param name='outputFormat_selector' value='homer'/>
320 </conditional> 320 </conditional>
321 </conditional> 321 </conditional>
322 <output name="output_converted_matrix" file="hicConvertFormat/small_test_matrix_chr4.homer" ftype="zip" compare="sim_size" delta="40000"/> 322 <output name="output_converted_matrix" file="hicConvertFormat/small_test_matrix_chr4.homer" ftype="zip" compare="sim_size" delta="40000"/>
326 <param name='outputSingleMultiple_selector' value='singleMatrix'/> 326 <param name='outputSingleMultiple_selector' value='singleMatrix'/>
327 <conditional name='inputFormat_conditional'> 327 <conditional name='inputFormat_conditional'>
328 <param name='inputFormat_selector' value='optionCool'/> 328 <param name='inputFormat_selector' value='optionCool'/>
329 <param name='matrix_h5_cooler' value='hicConvertFormat/small_test_matrix_chr4.cool'/> 329 <param name='matrix_h5_cooler' value='hicConvertFormat/small_test_matrix_chr4.cool'/>
330 </conditional> 330 </conditional>
331 331
332 <conditional name='outputFormat_conditional'> 332 <conditional name='outputFormat_conditional'>
333 <param name='outputFormat_selector' value='ginteractions'/> 333 <param name='outputFormat_selector' value='ginteractions'/>
334 </conditional> 334 </conditional>
335 </conditional> 335 </conditional>
336 <output name="output_converted_matrix" file="hicConvertFormat/small_test_matrix_chr4.ginteractions.tsv" ftype="tsv" compare="sim_size" delta="40000"/> 336 <output name="output_converted_matrix" file="hicConvertFormat/small_test_matrix_chr4.ginteractions.tsv" ftype="tsv" compare="sim_size" delta="40000"/>
337 337
338 </test> 338 </test>
339 <test> 339 <test>
340 <conditional name='outputSingleMultiple_conditional'> 340 <conditional name='outputSingleMultiple_conditional'>
341 <param name='outputSingleMultiple_selector' value='multipleMatrix'/> 341 <param name='outputSingleMultiple_selector' value='multipleMatrix'/>
342 <conditional name='resolutionOrManyToOne_conditional'> 342 <conditional name='resolutionOrManyToOne_conditional'>
359 Converting between different Hi-C interaction formats 359 Converting between different Hi-C interaction formats
360 ===================================================== 360 =====================================================
361 361
362 Conversion of Hi-C matrices of different file formats. We support the conversion of hic to cool format via hic2cool, 362 Conversion of Hi-C matrices of different file formats. We support the conversion of hic to cool format via hic2cool,
363 and homer, HicPro, h5 and cool format to h5, cool, homer or ginteractions format. Moreover, hicConvertFormat accepts multiple input files 363 and homer, HicPro, h5 and cool format to h5, cool, homer or ginteractions format. Moreover, hicConvertFormat accepts multiple input files
364 from one format with different resolutions and creates a mcool file. Each original file is stored under the path e.g. ::/resolutions/10000. 364 from one format with different resolutions and creates a mcool file. Each original file is stored under a path, e.g. matrix.mcool::/resolutions/10000.
365 A batch computation is possible, the number of input files and output files needs to match, all input files need to be of the same format type and 365 A batch computation is possible, the number of input files and output files needs to match, all input files need to be of the same format type and
366 all output files too. 366 all output files too.
367 For input and output of cooler files special options are available, for all other formats they will be ignored. 367 For input and output of cooler files, special options are available, for all other formats they will be ignored.
368 HiCPro file format needs an additional bed file as input. 368 HiCPro file format needs an additional bed file as input.
369 369
370 | For more information about HiCExplorer please consider our documentation on readthedocs.io_ 370 | For more information about HiCExplorer please consider our documentation on readthedocs.io_
371 371
372 .. _readthedocs.io: http://hicexplorer.readthedocs.io/en/latest/index.html 372 .. _readthedocs.io: http://hicexplorer.readthedocs.io/en/latest/index.html