Mercurial > repos > bgruening > hicexplorer_hicconvertformat

comparison hicConvertFormat.xml @ 0:e136f22c2a0f draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
author bgruening
date Mon, 16 Dec 2019 15:28:54 -0500
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children 2f62a87d4017
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-1:000000000000 0:e136f22c2a0f
1 <tool id="hicexplorer_hicconvertformat" name="@BINARY@" version="@WRAPPER_VERSION@.0">
2 <description>Convert between different file formats</description>
3 <macros>
4 <token name="@BINARY@">hicConvertFormat</token>
5 <token name="@SINGLE_INPUT@">
6 #if $xml_path.inputFormat_selector == 'optionCool':
7 --matrices 'matrix.cool'
8 --inputFormat cool
9 #if $xml_path.correctionName:
10 --correction_name '$xml_path.correctionName'
11 #end if
12
13 #if $xml_path.correctionDivision:
14 --correction_division
15 #end if
16
17 #if $xml_path.chromosome:
18 #set $chromosome = ' '.join([ '\'%s\'' % $chrom for $chrom in str($xml_path.chromosome).split(' ') ])
19
20 --chromosome $chromosome
21 #end if
22
23 #if $xml_path.loadRawValues:
24 --load_raw_values
25 #end if
26 #end if
27 #if $xml_path.inputFormat_selector == 'optionH5':
28 --matrices "matrix.h5"
29 --inputFormat h5
30
31 #end if
32 #if $xml_path.inputFormat_selector == 'optionHomer':
33 --matrices "matrix.homer"
34 --inputFormat homer
35
36 #end if
37 #if $xml_path.inputFormat_selector == 'optionHicpro':
38 --matrices "matrix.hicpro"
39 --bedFileHicpro "matrix.bed"
40 --inputFormat hicpro
41 #end if
42 #if $xml_path.inputFormat_selector == 'optionHic':
43 --matrices "matrix.hic"
44 #if $xml_path.resolutions:
45 #set $resolutions = ' '.join([ '"%s"' % $resolution for $resolution in str($xml_path.resolutions).split(" ") ])
46
47 --resolutions $resolutions
48 #end if
49 --inputFormat hic
50 #end if
51 </token>
52 <import>macros.xml</import>
53 </macros>
54
55 <expand macro="requirements" />
56 <command detect_errors="exit_code"><![CDATA[
57
58
59 ## single to single case
60
61
62 #if $outputSingleMultiple_conditional.outputSingleMultiple_selector == 'singleMatrix':
63 #set xml_path = $outputSingleMultiple_conditional.inputFormat_conditional
64
65 #if $xml_path.inputFormat_selector == 'optionCool':
66 ln -s "$xml_path.matrix_h5_cooler" "matrix.cool" &&
67
68 #end if
69 #if $xml_path.inputFormat_selector == 'optionH5':
70 ln -s "$xml_path.matrix_h5_cooler" "matrix.h5" &&
71
72 #end if
73 #if $xml_path.inputFormat_selector == 'optionHomer':
74 ln -s "$xml_path.matrixHomer" "matrix.homer" &&
75
76 #end if
77
78 #if $xml_path.inputFormat_selector == 'optionHicpro':
79 ln -s "$xml_path.matrixHicpro" "matrix.hicpro" &&
80 ln -s "$xml_path.bedHicpro" "matrix.bed" &&
81 #end if
82
83 #if $xml_path.inputFormat_selector == 'optionHic':
84 ln -s "$xml_path.matrixHic" "matrix.hic" &&
85 #end if
86
87
88
89 @BINARY@
90 @SINGLE_INPUT@
91
92
93 --outputFormat $outputSingleMultiple_conditional.outputFormat_conditional.outputFormat_selector
94 --outFileName 'matrix.$outputSingleMultiple_conditional.outputFormat_conditional.outputFormat_selector'
95
96 #if $outputSingleMultiple_conditional.outputFormat_conditional.outputFormat_selector == 'ginteractions':
97 && mv 'matrix.${outputSingleMultiple_conditional.outputFormat_conditional.outputFormat_selector}.tsv' matrix_out
98
99 #else:
100 && mv "matrix.$outputSingleMultiple_conditional.outputFormat_conditional.outputFormat_selector" matrix_out
101 #end if
102 #end if
103
104
105 ### Set up links to matrices to have correct ending
106 #if $outputSingleMultiple_conditional.outputSingleMultiple_selector == 'multipleMatrix':
107 #if $outputSingleMultiple_conditional.resolutionOrManyToOne_conditional.resolutionOrManyToOne_selector == 'resolution_option':
108 #set xml_path = $outputSingleMultiple_conditional.resolutionOrManyToOne_conditional.inputFormat_conditional
109 #if $xml_path.inputFormat_selector == 'optionCool':
110 ln -s "$xml_path.matrix_h5_cooler" "matrix.cool" &&
111 #end if
112
113 #if $xml_path.inputFormat_selector == 'optionH5':
114 ln -s "$xml_path.matrix_h5_cooler" "matrix.h5" &&
115
116 #end if
117
118 #if $xml_path.inputFormat_selector == 'optionHomer':
119 ln -s "$xml_path.matrix_h5_cooler" "matrix.homer" &&
120
121 #end if
122
123 #if $xml_path.inputFormat_selector == 'optionHicpro':
124 ln -s "$xml_path.matrix_h5_cooler" "matrix.hicpro" &&
125 ln -s "$xml_path.bedHicpro" "matrix.bed" &&
126
127 #end if
128 #if $xml_path.inputFormat_selector == 'optionHic':
129 ln -s "$xml_path.matrix_h5_cooler" "matrix.hic" &&
130
131 #end if
132 #else:
133 #set xml_manyToOne = $outputSingleMultiple_conditional.resolutionOrManyToOne_conditional
134 #if $xml_manyToOne.inputFormat_conditional.inputFormat_selector == 'optionCool':
135 #for $counter, $m in enumerate($xml_manyToOne.matrix_h5_cooler_multiple):
136 ln -s '$m' "${counter}_matrix.cool" &&
137 #end for
138 #set $m = ' '.join([ '"%s_matrix"' % $counter for $counter, $matrix in enumerate($xml_manyToOne.matrix_h5_cooler_multiple) ])
139
140 #end if
141 #if $xml_manyToOne.inputFormat_conditional.inputFormat_selector == 'optionH5':
142 #for $counter, $m in enumerate($xml_manyToOne.matrix_h5_cooler_multiple):
143 ln -s '$m' "${counter}_matrix.h5" &&
144 #end for
145 #set $m = ' '.join([ '"%s_matrix"' % $counter for $counter, $matrix in enumerate($xml_manyToOne.matrix_h5_cooler_multiple) ])
146 #end if
147 #if $xml_manyToOne.inputFormat_conditional.inputFormat_selector == 'optionHomer':
148 #for $counter, $m in enumerate($xml_manyToOne.matrixHomer):
149 ln -s '$m' "${counter}_matrix.homer" &&
150 #end for
151 #set $m = ' '.join([ '"%s_matrix.homer"' % $counter for $counter, $matrix in enumerate($xml_manyToOne.matrixHomer) ])
152 #end if
153 #if $xml_manyToOne.inputFormat_conditional.inputFormat_selector == 'optionHicpro':
154 #for $counter, $m in enumerate($xml_manyToOne.matrixHicpro):
155 ln -s '$m' "${counter}_matrix.hicpro" &&
156 #end for
157 #set $m = ' '.join([ '"%s_matrix.hicpro"' % $counter for $counter, $matrix in enumerate($xml_manyToOne.matrixHicpro) ])
158
159 #for $counter, $bed in enumerate($xml_manyToOne.bedHicpro):
160 ln -s '$bed' "${counter}_matrix.bed" &&
161 #end for
162 #set $bed = ' '.join([ '"%s_matrix.bed"' % $counter for $counter, $matrix in enumerate($xml_manyToOne.bedHicpro) ])
163 --bedFileHicpro '$bed'
164 #end if
165 #end if
166
167
168 @BINARY@
169 --outputFormat mcool
170
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(" ") ])
173
174 --resolutions $resolutions
175 #if $xml_path.inputFormat_selector == 'optionCool':
176 --matrices "matrix.cool"
177 --inputFormat cool
178 #end if
179 #if $xml_path.inputFormat_selector == 'optionH5':
180 --matrices "matrix.h5"
181 --inputFormat h5
182
183 #end if
184 #if $xml_path.inputFormat_selector == 'optionHomer':
185 --matrices "matrix.homer"
186 --inputFormat homer
187
188 #end if
189 #if $xml_path.inputFormat_selector == 'optionHicpro':
190 --matrices "matrix.hicpro"
191 --bedFileHicpro "matrix.bed"
192 --inputFormat hicpro
193 #end if
194 #if $xml_path.inputFormat_selector == 'optionHic':
195 --matrices "matrix.hic"
196 --inputFormat hic
197 #end if
198 #end if
199
200 #if $outputSingleMultiple_conditional.resolutionOrManyToOne_conditional.resolutionOrManyToOne_selector == 'manyToOne_option':
201 #if $xml_manyToOne.inputFormat_conditional.inputFormat_selector == 'optionCool':
202 --inputFormat cool
203 #end if
204
205 #if $xml_manyToOne.inputFormat_conditional.inputFormat_selector == 'optionH5':
206 --inputFormat h5
207 #end if
208
209
210 #if $xml_manyToOne.inputFormat_conditional.inputFormat_selector == 'optionHomer':
211 --inputFormat homer
212 #end if
213
214 #if $xml_manyToOne.inputFormat_conditional.inputFormat_selector == 'optionHicpro':
215 --inputFormat hicpro
216 --bedFileHicpro '$bed'
217 #end if
218
219 --matrices $m
220 #end if
221 --outFileName matrix.mcool
222 && mv matrix.mcool matrix_out
223
224 #end if
225
226
227 ]]>
228 </command>
229 <inputs>
230
231 <conditional name="outputSingleMultiple_conditional">
232 <param name="outputSingleMultiple_selector" type="select" label="Choose output matrix type">
233 <option value="singleMatrix" selected="True">single matrix</option>
234 <option value="multipleMatrix">multiple matrix</option>
235 </param>
236 <when value='singleMatrix'>
237 <expand macro='convertFormat_single_macro' />
238 <expand macro='convertFormat_single_output_macro' />
239 </when>
240 <when value='multipleMatrix'>
241 <conditional name="resolutionOrManyToOne_conditional">
242 <param name="resolutionOrManyToOne_selector" type="select" label="Choose input file type">
243 <option value='resolution_option' >Create out of one matrix a multi matrix with diffrerent resolutions</option>
244 <option value='manyToOne_option'>Create out of n matrices one multi matrix </option>
245 </param>
246 <when value='resolution_option'>
247 <param name='resolutions' type='text' label='To be stored resolutions'/>
248 <expand macro='convertFormat_single_macro' />
249 </when>
250 <when value='manyToOne_option'>
251 <expand macro='convertFormat_multiple_macro' />
252 </when>
253 </conditional>
254 <param name='storeAppliedCorrection' type="boolean" truevalue="yes" falsevalue="" label='Store applied correction factors in column count'/>
255 <param name='enforceInteger' type="boolean" truevalue="yes" falsevalue="" label='Enforce integer for count column'/>
256 </when>
257 </conditional>
258 </inputs>
259 <outputs>
260
261 <data name='output_converted_matrix' from_work_dir='matrix_out' format='cool' label='Converted matrix'>
262 <filter>outputSingleMultiple_conditional.outputSingleMultiple_selector == 'singleMatrix'</filter>
263 <change_format>
264 <when input="outputSingleMultiple_conditional.outputFormat_conditional.outputFormat_selector" value="h5" format="h5" />
265 <when input="outputSingleMultiple_conditional.outputFormat_conditional.outputFormat_selector" value="homer" format="zip" />
266 <when input="outputSingleMultiple_conditional.outputFormat_conditional.outputFormat_selector" value="ginteractions" format="tsv" />
267 </change_format>
268 </data>
269 <data name='output_converted_matrix_multi' from_work_dir='matrix_out' format='mcool' label='Converted matrix mcool'>
270 <filter>outputSingleMultiple_conditional.outputSingleMultiple_selector == 'multipleMatrix'</filter>
271 </data>
272 </outputs>
273 <tests>
274 <test>
275 <conditional name='outputSingleMultiple_conditional'>
276 <param name='outputSingleMultiple_selector' value='singleMatrix'/>
277 <conditional name='inputFormat_conditional'>
278 <param name='inputFormat_selector' value='optionCool'/>
279 <param name='matrix_h5_cooler' value='small_test_matrix.cool'/>
280 </conditional>
281
282 <conditional name='outputFormat_conditional'>
283 <param name='outputFormat_selector' value='h5'/>
284 </conditional>
285 </conditional>
286 <output name="output_converted_matrix" ftype="h5">
287 <assert_contents>
288 <has_h5_keys keys='intervals,matrix,nan_bins'/>
289 </assert_contents>
290 </output>
291 </test>
292 <test>
293 <conditional name='outputSingleMultiple_conditional'>
294 <param name='outputSingleMultiple_selector' value='singleMatrix'/>
295 <conditional name='inputFormat_conditional'>
296 <param name='inputFormat_selector' value='optionH5'/>
297 <param name='matrix_h5_cooler' value='small_test_matrix.h5'/>
298 </conditional>
299
300 <conditional name='outputFormat_conditional'>
301 <param name='outputFormat_selector' value='cool'/>
302 </conditional>
303 </conditional>
304 <output name="output_converted_matrix" ftype="cool">
305 <assert_contents>
306 <has_h5_keys keys='bins,chroms,indexes,pixels'/>
307 </assert_contents>
308 </output>
309 </test>
310 <test>
311 <conditional name='outputSingleMultiple_conditional'>
312 <param name='outputSingleMultiple_selector' value='singleMatrix'/>
313 <conditional name='inputFormat_conditional'>
314 <param name='inputFormat_selector' value='optionCool'/>
315 <param name='matrix_h5_cooler' value='hicConvertFormat/small_test_matrix_chr4.cool'/>
316 </conditional>
317
318 <conditional name='outputFormat_conditional'>
319 <param name='outputFormat_selector' value='homer'/>
320 </conditional>
321 </conditional>
322 <output name="output_converted_matrix" file="hicConvertFormat/small_test_matrix_chr4.homer" ftype="zip" compare="sim_size" delta="40000"/>
323 </test>
324 <test>
325 <conditional name='outputSingleMultiple_conditional'>
326 <param name='outputSingleMultiple_selector' value='singleMatrix'/>
327 <conditional name='inputFormat_conditional'>
328 <param name='inputFormat_selector' value='optionCool'/>
329 <param name='matrix_h5_cooler' value='hicConvertFormat/small_test_matrix_chr4.cool'/>
330 </conditional>
331
332 <conditional name='outputFormat_conditional'>
333 <param name='outputFormat_selector' value='ginteractions'/>
334 </conditional>
335 </conditional>
336 <output name="output_converted_matrix" file="hicConvertFormat/small_test_matrix_chr4.ginteractions.tsv" ftype="tsv" compare="sim_size" delta="40000"/>
337
338 </test>
339 <test>
340 <conditional name='outputSingleMultiple_conditional'>
341 <param name='outputSingleMultiple_selector' value='multipleMatrix'/>
342 <conditional name='resolutionOrManyToOne_conditional'>
343 <param name='resolutionOrManyToOne_selector' value='resolution_option'/>
344 <param name='resolutions' value='5000 10000 20000'/>
345 <conditional name='inputFormat_conditional'>
346 <param name='inputFormat_selector' value='optionH5'/>
347 <param name='matrix_h5_cooler' value='small_test_matrix.h5'/>
348 </conditional>
349 </conditional>
350 </conditional>
351 <output name="output_converted_matrix" ftype="cool">
352 <assert_contents>
353 <has_h5_keys keys='resolutions'/>
354 </assert_contents>
355 </output>
356 </test>
357 </tests>
358 <help><![CDATA[
359 Converting between different Hi-C interaction formats
360 =====================================================
361
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
364 from one format with different resolutions and creates a mcool file. Each original file is stored under the path e.g. ::/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
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.
368 HiCPro file format needs an additional bed file as input.
369
370 | For more information about HiCExplorer please consider our documentation on readthedocs.io_
371
372 .. _readthedocs.io: http://hicexplorer.readthedocs.io/en/latest/index.html
373 ]]></help>
374 <expand macro="citations" />
375 </tool>