Mercurial > repos > bgruening > hicexplorer_hicmergematrixbins
comparison hicMergeMatrixBins.xml @ 11:49c8055f6830 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
| author | bgruening |
|---|---|
| date | Mon, 16 Dec 2019 15:46:21 -0500 |
| parents | c14ba4629233 |
| children | 03dd3c16ae4e |
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| 10:6bb9545b7c68 | 11:49c8055f6830 |
|---|---|
| 4 <token name="@BINARY@">hicMergeMatrixBins</token> | 4 <token name="@BINARY@">hicMergeMatrixBins</token> |
| 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 hicMergeMatrixBins | 9 ln -s '$matrix_h5_cooler' 'matrix.$matrix_h5_cooler.ext' && |
| 10 --matrix '$matrix_h5_cooler' | 10 @BINARY@ |
| 11 --matrix 'matrix.$matrix_h5_cooler.ext' | |
| 11 --numBins $numBins | 12 --numBins $numBins |
| 12 $runningWindow | 13 $runningWindow |
| 13 --outFileName matrix.$outputFormat | 14 --outFileName 'matrix.$matrix_h5_cooler.ext' |
| 14 && mv matrix.$outputFormat matrix | 15 && mv 'matrix.$matrix_h5_cooler.ext' matrix |
| 15 | 16 |
| 16 ]]> | 17 ]]> |
| 17 </command> | 18 </command> |
| 18 <inputs> | 19 <inputs> |
| 19 <expand macro='matrix_h5_cooler_macro' /> | 20 <expand macro='matrix_h5_cooler_macro' /> |
| 20 | 21 |
| 21 <param argument="--numBins" type="integer" min="1" value="3" label="Number of bins to merge" /> | 22 <param argument="--numBins" type="integer" min="1" value="3" label="Number of bins to merge" /> |
| 22 <param argument="--runningWindow" type="boolean" falsevalue="" truevalue="--runningWindow" label="Set to merge for using a running window of length --numBins. Usually not set." /> | 23 <param argument="--runningWindow" type="boolean" falsevalue="" truevalue="--runningWindow" label="Set to merge for using a running window of length --numBins. Usually not set." /> |
| 23 <param name='outputFormat' type='select' label="Output file format"> | |
| 24 <option value='h5' selected='true'>HiCExplorer format</option> | |
| 25 <option value="cool">cool</option> | |
| 26 </param> | |
| 27 </inputs> | 24 </inputs> |
| 28 <outputs> | 25 <outputs> |
| 29 <data name="outFileName" from_work_dir="matrix" format="h5"> | 26 <data name="outFileName" from_work_dir="matrix" format="cool"> |
| 30 <change_format> | 27 <change_format> |
| 31 <when input="outputFormat" value="cool" format="cool" /> | 28 <when input_dataset="matrix_h5_cooler" attribute="ext" value="h5" format="h5"/> |
| 32 </change_format> | 29 </change_format> |
| 33 </data> | 30 </data> |
| 34 </outputs> | 31 </outputs> |
| 35 <tests> | 32 <tests> |
| 36 <test> | 33 <test> |
| 37 <param name="matrix_h5_cooler" value="small_test_matrix.h5"/> | 34 <param name="matrix_h5_cooler" value="small_test_matrix.h5"/> |
| 38 <param name="numBins" value="5" /> | 35 <param name="numBins" value="5" /> |
| 39 <output name="outFileName" file="hicMergeMatrixBins_result1.npz.h5" ftype="h5" compare="sim_size" delta="24000" /> | 36 <output name="outFileName" ftype="h5"> |
| 37 <assert_contents> | |
| 38 <has_h5_keys keys='intervals,matrix,nan_bins'/> | |
| 39 </assert_contents> | |
| 40 </output> | |
| 40 </test> | 41 </test> |
| 41 </tests> | 42 </tests> |
| 42 <help><![CDATA[ | 43 <help><![CDATA[ |
| 43 | 44 |
| 44 Change matrix resolution | 45 Change matrix resolution |