Mercurial > repos > bgruening > hicexplorer_hiccomparematrices
comparison hicCompareMatrices.xml @ 0:a0ab04565c73 draft
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
| author | bgruening |
|---|---|
| date | Wed, 07 Mar 2018 03:37:57 -0500 |
| parents | |
| children | 08e157ceda6f |
comparison
equal
deleted
inserted
replaced
| -1:000000000000 | 0:a0ab04565c73 |
|---|---|
| 1 <tool id="hicexplorer_hiccomparematrices" name="@BINARY@" version="@WRAPPER_VERSION@.0"> | |
| 2 <description>normalize and compare two HiC matricies</description> | |
| 3 <macros> | |
| 4 <token name="@BINARY@">hicCompareMatrices</token> | |
| 5 <import>macros.xml</import> | |
| 6 </macros> | |
| 7 <expand macro="requirements" /> | |
| 8 <command detect_errors="exit_code"><![CDATA[ | |
| 9 | |
| 10 @BINARY@ | |
| 11 --matrices '$matrix1' '$matrix2' | |
| 12 --operation $operation | |
| 13 --outFileName matrix.$outputFormat | |
| 14 | |
| 15 && mv matrix.$outputFormat matrix | |
| 16 ]]> | |
| 17 </command> | |
| 18 <inputs> | |
| 19 <param name='matrix1' type="data" format="h5,cool" | |
| 20 label="First matrix"/> | |
| 21 <param name='matrix2' type="data" format="h5,cool" | |
| 22 label="Second matrix to compare against the first"/> | |
| 23 | |
| 24 <param name='operation' type='select' label="Operation to be used for the comparison"> | |
| 25 <option value='diff'>diff</option> | |
| 26 <option value="ratio">ratio</option> | |
| 27 <option value="log2ratio">log2ratio</option> | |
| 28 </param> | |
| 29 <param name='outputFormat' type='select' label="Output file format"> | |
| 30 <option value='h5'>HiCExplorer format</option> | |
| 31 <option value="cool">cool</option> | |
| 32 </param> | |
| 33 </inputs> | |
| 34 <outputs> | |
| 35 <data name="outFileName" from_work_dir="matrix" format="h5" label="${tool.name} MATRIX on ${on_string}"> | |
| 36 <change_format> | |
| 37 <when input="outputFormat" value="cool" format="cool" /> | |
| 38 </change_format> | |
| 39 </data> | |
| 40 </outputs> | |
| 41 <tests> | |
| 42 <test> | |
| 43 <param name="matrix1" value="small_test_matrix.h5"/> | |
| 44 <param name="matrix2" value="small_test_matrix.h5"/> | |
| 45 <param name="operation" value='log2ratio' /> | |
| 46 <param name="outputFormat" value="h5" /> | |
| 47 <output name="outFileName" file="compare_matrices_log2ratio.h5" ftype="h5" compare="sim_size" delta='2000'/> | |
| 48 </test> | |
| 49 <test> | |
| 50 <param name="matrix1" value="pearson_small_50kb.cool"/> | |
| 51 <param name="matrix2" value="pearson_small_50kb.cool"/> | |
| 52 <param name="operation" value='ratio' /> | |
| 53 <param name="outputFormat" value="cool" /> | |
| 54 <output name="outFileName" file="compare_matrices_pearson_ratio.cool" ftype="cool" compare="sim_size" delta='2000'/> | |
| 55 </test> | |
| 56 | |
| 57 </tests> | |
| 58 <help><![CDATA[ | |
| 59 Comparison of HiC matrices | |
| 60 ========================== | |
| 61 `hicCompareMatrices` takes two matrices, normalizes them and appliesthe given operation. To | |
| 62 normalize the matrices each element is divided by sum of the matrix. | |
| 63 | |
| 64 Input | |
| 65 ----- | |
| 66 - the matricies to be compared | |
| 67 | |
| 68 | |
| 69 | |
| 70 | For more information about HiCExplorer please consider our documentation on readthedocs.io_ | |
| 71 | |
| 72 .. _readthedocs.io: http://hicexplorer.readthedocs.io/en/latest/index.html | |
| 73 ]]></help> | |
| 74 <expand macro="citations" /> | |
| 75 </tool> |