Mercurial > repos > iuc > schicexplorer_schicmergematrixbins

comparison scHicMergeMatrixBins.xml @ 1:ecae4e42d40a draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer commit 72e1e90ac05a32dbd6fc675073429c0086048b18"
author iuc
date Tue, 10 Mar 2020 15:10:44 -0400
parents 18ac7f83ae0e
children 47ef02546fe9
comparison
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0:18ac7f83ae0e 1:ecae4e42d40a
6 </macros> 6 </macros>
7 <expand macro="requirements" /> 7 <expand macro="requirements" />
8 <command detect_errors="exit_code"><![CDATA[ 8 <command detect_errors="exit_code"><![CDATA[
9 @BINARY@ 9 @BINARY@
10 10
11 --matrix '$matrix_mcooler' 11 --matrix '$matrix_scooler'
12 --numBins $numberOfBins 12 --numBins $numberOfBins
13 13
14 #if $runningWindow: 14 #if $runningWindow:
15 $runningWindow 15 $runningWindow
16 #end if 16 #end if
17 17
18 --outFileName merged_matrices.mcool 18 --outFileName merged_matrices.scool
19 19
20 --threads @THREADS@ 20 --threads @THREADS@
21 21
22 22
23 23
24 ]]></command> 24 ]]></command>
25 <inputs> 25 <inputs>
26 26
27 <expand macro="matrix_mcooler_macro"/> 27 <expand macro="matrix_scooler_macro"/>
28 <param name="numberOfBins" type="integer" value="10" label="Number of bins to merge" help='Number of bins to merge to achieve the desired resolution. For example: To merge a 10kb matrix to 1MB, 10kb * 100 = 1MB i.e. the value needs to be 100.' /> 28 <param name="numberOfBins" type="integer" value="10" label="Number of bins to merge" help='Number of bins to merge to achieve the desired resolution. For example: To merge a 10kb matrix to 1MB, 10kb * 100 = 1MB i.e. the value needs to be 100.' />
29 <param name='runningWindow' type='boolean' truevalue='--runningWindow' label='Running window' help='Set to merge for using a running window of length --numBins. Must be an odd number.'/> 29 <param name='runningWindow' type='boolean' truevalue='--runningWindow' label='Running window' help='Set to merge for using a running window of length --numBins. Must be an odd number.'/>
30 30
31 </inputs> 31 </inputs>
32 <outputs> 32 <outputs>
33 <data name="outFileName" from_work_dir="merged_matrices.mcool" format="mcool" label="${tool.name} on ${on_string}: Adjusted matrix"/> 33 <data name="outFileName" from_work_dir="merged_matrices.scool" format="scool" label="${tool.name} on ${on_string}: Merged matrix"/>
34 </outputs> 34 </outputs>
35 <tests> 35 <tests>
36 <test> 36 <test>
37 <param name='matrix_mcooler' value='test_matrix.mcool' /> 37 <param name='matrix_scooler' value='test_matrix.scool' />
38 <param name='numberOfBins' value='10' /> 38 <param name='numberOfBins' value='10' />
39 <output name="outFileName" ftype="mcool"> 39 <output name="outFileName" ftype="scool">
40 <assert_contents> 40 <assert_contents>
41 <has_h5_keys keys='Diploid_1_CGTACTAG_AAGGAGTA_R1fastqgz, Diploid_1_CGTACTAG_AAGGAGTA_R1fastqgz/bins, 41 <has_h5_keys keys='Diploid_1_CGTACTAG_AAGGAGTA_R1fastqgz, Diploid_1_CGTACTAG_AAGGAGTA_R1fastqgz/bins,
42 Diploid_1_CGTACTAG_AAGGAGTA_R1fastqgz/bins/chrom, Diploid_1_CGTACTAG_AAGGAGTA_R1fastqgz/bins/end, 42 Diploid_1_CGTACTAG_AAGGAGTA_R1fastqgz/bins/chrom, Diploid_1_CGTACTAG_AAGGAGTA_R1fastqgz/bins/end,
43 Diploid_1_CGTACTAG_AAGGAGTA_R1fastqgz/bins/start, Diploid_1_CGTACTAG_AAGGAGTA_R1fastqgz/chroms, 43 Diploid_1_CGTACTAG_AAGGAGTA_R1fastqgz/bins/start, Diploid_1_CGTACTAG_AAGGAGTA_R1fastqgz/chroms,
44 Diploid_1_CGTACTAG_AAGGAGTA_R1fastqgz/chroms/length, Diploid_1_CGTACTAG_AAGGAGTA_R1fastqgz/chroms/name, 44 Diploid_1_CGTACTAG_AAGGAGTA_R1fastqgz/chroms/length, Diploid_1_CGTACTAG_AAGGAGTA_R1fastqgz/chroms/name,
189 Diploid_2_AGGCAGAA_AAGGAGTA_R1fastqgz/pixels/count'/> 189 Diploid_2_AGGCAGAA_AAGGAGTA_R1fastqgz/pixels/count'/>
190 </assert_contents> 190 </assert_contents>
191 </output> 191 </output>
192 </test> 192 </test>
193 <test> 193 <test>
194 <param name='matrix_mcooler' value='test_matrix.mcool' /> 194 <param name='matrix_scooler' value='test_matrix.scool' />
195 <param name='numberOfBins' value='11' /> 195 <param name='numberOfBins' value='11' />
196 <param name='runningWindow' value='true' /> 196 <param name='runningWindow' value='true' />
197 197
198 <output name="outFileName" ftype="mcool"> 198 <output name="outFileName" ftype="scool">
199 <assert_contents> 199 <assert_contents>
200 <has_h5_keys keys='Diploid_1_CGTACTAG_AAGGAGTA_R1fastqgz, Diploid_1_CGTACTAG_AAGGAGTA_R1fastqgz/bins, 200 <has_h5_keys keys='Diploid_1_CGTACTAG_AAGGAGTA_R1fastqgz, Diploid_1_CGTACTAG_AAGGAGTA_R1fastqgz/bins,
201 Diploid_1_CGTACTAG_AAGGAGTA_R1fastqgz/bins/chrom, Diploid_1_CGTACTAG_AAGGAGTA_R1fastqgz/bins/end, 201 Diploid_1_CGTACTAG_AAGGAGTA_R1fastqgz/bins/chrom, Diploid_1_CGTACTAG_AAGGAGTA_R1fastqgz/bins/end,
202 Diploid_1_CGTACTAG_AAGGAGTA_R1fastqgz/bins/start, Diploid_1_CGTACTAG_AAGGAGTA_R1fastqgz/chroms, 202 Diploid_1_CGTACTAG_AAGGAGTA_R1fastqgz/bins/start, Diploid_1_CGTACTAG_AAGGAGTA_R1fastqgz/chroms,
203 Diploid_1_CGTACTAG_AAGGAGTA_R1fastqgz/chroms/length, Diploid_1_CGTACTAG_AAGGAGTA_R1fastqgz/chroms/name, 203 Diploid_1_CGTACTAG_AAGGAGTA_R1fastqgz/chroms/length, Diploid_1_CGTACTAG_AAGGAGTA_R1fastqgz/chroms/name,
353 <help><![CDATA[ 353 <help><![CDATA[
354 354
355 Change the resolution of the scHi-C matrices 355 Change the resolution of the scHi-C matrices
356 ============================================ 356 ============================================
357 357
358 Merges bins from a Hi-C matrix. For example, using a matrix containing 5kb bins, a matrix of 50kb bins can be derived using --numBins 10. 358 **scHicMergeMatrixBins** is used to decrease the resolution of single cell matrices stored in a scool file by merging their adjacent bins. With this tool, you can for example create out of a 5kb
359 359 contact matrix a 50kb one:
360 Number of bins to merge = 10
361 5kb * 10 = 50k
362 Depending on the downstream analyses to perform on single cell Hi-C matrices generated with HiCExplorer, one might need different bin resolutions, for instance during clustering or for plotting small or large regions of consensus matrices.
363 The best practice is to merge bins in uncorrected matrices, and correct the lower resolution matrices using `scHicCorrectMatrices` subsequently.
360 364
361 For more information about scHiCExplorer please consider our documentation on readthedocs.io_ 365 For more information about scHiCExplorer please consider our documentation on readthedocs.io_
362 366
363 .. _readthedocs.io: http://schicexplorer.readthedocs.io/ 367 .. _readthedocs.io: http://schicexplorer.readthedocs.io/
364 ]]></help> 368 ]]></help>