Mercurial > repos > iuc > schicexplorer_schiccorrectmatrices
comparison scHicCorrectMatrices.xml @ 1:16dda99bd733 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer commit 72e1e90ac05a32dbd6fc675073429c0086048b18"
| author | iuc |
|---|---|
| date | Tue, 10 Mar 2020 15:14:37 -0400 |
| parents | 104bedd292cd |
| children | 295558e266d0 |
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| 0:104bedd292cd | 1:16dda99bd733 |
|---|---|
| 5 <import>macros.xml</import> | 5 <import>macros.xml</import> |
| 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 --matrix '$matrix_mcooler' | 10 --matrix '$matrix_scooler' |
| 11 --outFileName corrected.mcool | 11 --outFileName corrected.scool |
| 12 --threads @THREADS@ | 12 --threads @THREADS@ |
| 13 ]]></command> | 13 ]]></command> |
| 14 <inputs> | 14 <inputs> |
| 15 <expand macro="matrix_mcooler_macro"/> | 15 <expand macro="matrix_scooler_macro"/> |
| 16 </inputs> | 16 </inputs> |
| 17 <outputs> | 17 <outputs> |
| 18 <data name="outFileName" from_work_dir="corrected.mcool" format="mcool" label="${tool.name} on ${on_string}: KR corrected matrix"/> | 18 <data name="outFileName" from_work_dir="corrected.scool" format="scool" label="${tool.name} on ${on_string}: KR corrected matrix"/> |
| 19 </outputs> | 19 </outputs> |
| 20 <tests> | 20 <tests> |
| 21 <test> | 21 <test> |
| 22 <param name='matrix_mcooler' value='test_matrix.mcool' /> | 22 <param name='matrix_scooler' value='test_matrix.scool' /> |
| 23 <output name="outFileName" ftype="mcool"> | 23 <output name="outFileName" ftype="scool"> |
| 24 <assert_contents> | 24 <assert_contents> |
| 25 <has_h5_keys keys='Diploid_1_CGTACTAG_AAGGAGTA_R1fastqgz, Diploid_1_CGTACTAG_AAGGAGTA_R1fastqgz/bins, | 25 <has_h5_keys keys='Diploid_1_CGTACTAG_AAGGAGTA_R1fastqgz, Diploid_1_CGTACTAG_AAGGAGTA_R1fastqgz/bins, |
| 26 Diploid_1_CGTACTAG_AAGGAGTA_R1fastqgz/bins/chrom, Diploid_1_CGTACTAG_AAGGAGTA_R1fastqgz/bins/end, | 26 Diploid_1_CGTACTAG_AAGGAGTA_R1fastqgz/bins/chrom, Diploid_1_CGTACTAG_AAGGAGTA_R1fastqgz/bins/end, |
| 27 Diploid_1_CGTACTAG_AAGGAGTA_R1fastqgz/bins/start, Diploid_1_CGTACTAG_AAGGAGTA_R1fastqgz/chroms, | 27 Diploid_1_CGTACTAG_AAGGAGTA_R1fastqgz/bins/start, Diploid_1_CGTACTAG_AAGGAGTA_R1fastqgz/chroms, |
| 28 Diploid_1_CGTACTAG_AAGGAGTA_R1fastqgz/chroms/length, Diploid_1_CGTACTAG_AAGGAGTA_R1fastqgz/chroms/name, | 28 Diploid_1_CGTACTAG_AAGGAGTA_R1fastqgz/chroms/length, Diploid_1_CGTACTAG_AAGGAGTA_R1fastqgz/chroms/name, |
| 178 <help><![CDATA[ | 178 <help><![CDATA[ |
| 179 | 179 |
| 180 Correct all matrices | 180 Correct all matrices |
| 181 ==================== | 181 ==================== |
| 182 | 182 |
| 183 scHicCorrectmatrices is a tool to correct with HiCExplorer's KR algorithm all Hi-C matrices stored in the mcool file. | 183 scHicCorrectmatrices is a tool to correct all Hi-C matrices stored in the provided scool file using HiCExplorer's KR algorithm, which is detailed here: |
| 184 https://hicexplorer.readthedocs.io/en/latest/content/tools/hicCorrectMatrix.html | |
| 184 | 185 |
| 185 For more information about scHiCExplorer please consider our documentation on readthedocs.io_ | 186 For more information about scHiCExplorer please consider our documentation on readthedocs.io_ |
| 186 | 187 |
| 187 .. _readthedocs.io: http://schicexplorer.readthedocs.io/ | 188 .. _readthedocs.io: http://schicexplorer.readthedocs.io/ |
| 188 ]]></help> | 189 ]]></help> |