Mercurial > repos > iuc > schicexplorer_schicnormalize

comparison scHicNormalize.xml @ 1:7c2387e72aac 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 15:14:00 -0400
parents 6eda3d3b562d
children 66e96c3d3c5d
comparison
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0:6eda3d3b562d 1:7c2387e72aac
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 12
13 --outFileName normalized_matrix.mcool 13 --outFileName normalized_matrix.scool
14 14
15 --threads @THREADS@ 15 --threads @THREADS@
16 16
17 17
18 18
19 ]]></command> 19 ]]></command>
20 <inputs> 20 <inputs>
21 21
22 <expand macro="matrix_mcooler_macro"/> 22 <expand macro="matrix_scooler_macro"/>
23 </inputs> 23 </inputs>
24 <outputs> 24 <outputs>
25 <data name="outFileName" from_work_dir="normalized_matrix.mcool" format="mcool" label="${tool.name} on ${on_string}: normalized matrix"/> 25 <data name="outFileName" from_work_dir="normalized_matrix.scool" format="scool" label="${tool.name} on ${on_string}: normalized matrix"/>
26 </outputs> 26 </outputs>
27 <tests> 27 <tests>
28 <test> 28 <test>
29 <param name='matrix_mcooler' value='test_matrix.mcool' /> 29 <param name='matrix_scooler' value='test_matrix.scool' />
30 <output name="outFileName" ftype="mcool"> 30 <output name="outFileName" ftype="scool">
31 <assert_contents> 31 <assert_contents>
32 <has_h5_keys keys='Diploid_1_CGTACTAG_AAGGAGTA_R1fastqgz, Diploid_1_CGTACTAG_AAGGAGTA_R1fastqgz/bins, 32 <has_h5_keys keys='Diploid_1_CGTACTAG_AAGGAGTA_R1fastqgz, Diploid_1_CGTACTAG_AAGGAGTA_R1fastqgz/bins,
33 Diploid_1_CGTACTAG_AAGGAGTA_R1fastqgz/bins/chrom, Diploid_1_CGTACTAG_AAGGAGTA_R1fastqgz/bins/end, 33 Diploid_1_CGTACTAG_AAGGAGTA_R1fastqgz/bins/chrom, Diploid_1_CGTACTAG_AAGGAGTA_R1fastqgz/bins/end,
34 Diploid_1_CGTACTAG_AAGGAGTA_R1fastqgz/bins/start, Diploid_1_CGTACTAG_AAGGAGTA_R1fastqgz/chroms, 34 Diploid_1_CGTACTAG_AAGGAGTA_R1fastqgz/bins/start, Diploid_1_CGTACTAG_AAGGAGTA_R1fastqgz/chroms,
35 Diploid_1_CGTACTAG_AAGGAGTA_R1fastqgz/chroms/length, Diploid_1_CGTACTAG_AAGGAGTA_R1fastqgz/chroms/name, 35 Diploid_1_CGTACTAG_AAGGAGTA_R1fastqgz/chroms/length, Diploid_1_CGTACTAG_AAGGAGTA_R1fastqgz/chroms/name,
186 <help><![CDATA[ 186 <help><![CDATA[
187 187
188 Normalize matrices 188 Normalize matrices
189 ================== 189 ==================
190 190
191 scHicNOrmalize normalizes all read coverages to the lowest read coverage found in a mcool file. 191 scHicNormalize scales the read coverage of all matrices stored in the provided scool file to the matrix displaying the lowest read coverage in the said file.
192 This is a highly parallelized version of HiCExplorer's ̀ hicNormalize`, for more information, you can refer to this page:
193 https://hicexplorer.readthedocs.io/en/latest/content/tools/hicNormalize.html
192 194
193 For more information about scHiCExplorer please consider our documentation on readthedocs.io_ 195 For more information about scHiCExplorer please consider our documentation on readthedocs.io_
194 196
195 .. _readthedocs.io: http://schicexplorer.readthedocs.io/ 197 .. _readthedocs.io: http://schicexplorer.readthedocs.io/
196 ]]></help> 198 ]]></help>