Mercurial > repos > bgruening > hicexplorer_hicnormalize
comparison hicNormalize.xml @ 8:6d042c96aceb draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9
| author | iuc |
|---|---|
| date | Wed, 18 Oct 2023 10:21:43 +0000 |
| parents | 8ad23dfdaabb |
| children |
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| 7:8ad23dfdaabb | 8:6d042c96aceb |
|---|---|
| 26 | 26 |
| 27 --outFileName $m_out | 27 --outFileName $m_out |
| 28 ]]> | 28 ]]> |
| 29 </command> | 29 </command> |
| 30 <inputs> | 30 <inputs> |
| 31 <expand macro='matrix_h5_cooler_multiple_macro' /> | 31 <expand macro="matrix_h5_cooler_multiple_macro" /> |
| 32 <conditional name="normalize_conditional"> | 32 <conditional name="normalize_conditional"> |
| 33 <param name='normalize' type='select' label='Normalize matrices'> | 33 <param name="normalize" type="select" label="Normalize matrices"> |
| 34 <option value='norm_range'>0 to 1 range</option> | 34 <option value="norm_range">0 to 1 range</option> |
| 35 <option value='smallest'>Smallest read count</option> | 35 <option value="smallest">Smallest read count</option> |
| 36 <option value='multiplicative'>Multiply by value</option> | 36 <option value="multiplicative">Multiply by value</option> |
| 37 </param> | 37 </param> |
| 38 <when value='norm_range' /> | 38 <when value="norm_range" /> |
| 39 <when value='smallest' /> | 39 <when value="smallest" /> |
| 40 <when value='multiplicative'> | 40 <when value="multiplicative"> |
| 41 <param name="multiplicativeValue" type="float" value="1.0" label="Multiplicative value" /> | 41 <param name="multiplicativeValue" type="float" value="1.0" label="Multiplicative value" /> |
| 42 </when> | 42 </when> |
| 43 </conditional> | 43 </conditional> |
| 44 <param name="zero_threshold_value" type="float" value="1.0" optional='True' label="Set values below this threshold to zero" /> | 44 <param name="zero_threshold_value" type="float" value="1.0" optional="True" label="Set values below this threshold to zero" /> |
| 45 </inputs> | 45 </inputs> |
| 46 <outputs> | 46 <outputs> |
| 47 <data format='cool' name="normalize_matrix"> | 47 <data format="cool" name="normalize_matrix"> |
| 48 <discover_datasets pattern="__name_and_ext__" directory="output" visible="true" /> | 48 <discover_datasets pattern="__name_and_ext__" directory="output" visible="true" /> |
| 49 <change_format> | 49 <change_format> |
| 50 <when input_dataset="matrix_h5_cooler_multiple" attribute="ext" value="h5" format="h5" /> | 50 <when input_dataset="matrix_h5_cooler_multiple" attribute="ext" value="h5" format="h5" /> |
| 51 </change_format> | 51 </change_format> |
| 52 </data> | 52 </data> |
| 53 </outputs> | 53 </outputs> |
| 54 <tests> | 54 <tests> |
| 55 <test> | 55 <test> |
| 56 <param name="matrix_h5_cooler_multiple" value="small_test_matrix.cool" /> | 56 <param name="matrix_h5_cooler_multiple" value="small_test_matrix.cool" /> |
| 57 <param name='normalize' value='norm_range' /> | 57 <param name="normalize" value="norm_range" /> |
| 58 <output name="normalize_matrix"> | 58 <output name="normalize_matrix"> |
| 59 <discovered_dataset designation="0_norm_small_test_matrix" ftype="cool"> | 59 <discovered_dataset designation="0_norm_small_test_matrix" ftype="cool"> |
| 60 <assert_contents> | 60 <assert_contents> |
| 61 <has_h5_keys keys="bins,chroms,indexes,pixels" /> | 61 <has_h5_keys keys="bins,chroms,indexes,pixels" /> |
| 62 </assert_contents> | 62 </assert_contents> |
| 63 </discovered_dataset> | 63 </discovered_dataset> |
| 64 </output> | 64 </output> |
| 65 </test> | 65 </test> |
| 66 <test> | 66 <test> |
| 67 <param name="matrix_h5_cooler_multiple" value="small_test_matrix.cool,small_test_matrix.cool" /> | 67 <param name="matrix_h5_cooler_multiple" value="small_test_matrix.cool,small_test_matrix.cool" /> |
| 68 <param name='normalize' value='smallest' /> | 68 <param name="normalize" value="smallest" /> |
| 69 <output name="normalize_matrix"> | 69 <output name="normalize_matrix"> |
| 70 <discovered_dataset designation="0_norm_small_test_matrix" ftype="cool"> | 70 <discovered_dataset designation="0_norm_small_test_matrix" ftype="cool"> |
| 71 <assert_contents> | 71 <assert_contents> |
| 72 <has_h5_keys keys="bins,chroms,indexes,pixels" /> | 72 <has_h5_keys keys="bins,chroms,indexes,pixels" /> |
| 73 </assert_contents> | 73 </assert_contents> |
| 79 </discovered_dataset> | 79 </discovered_dataset> |
| 80 </output> | 80 </output> |
| 81 </test> | 81 </test> |
| 82 <test> | 82 <test> |
| 83 <param name="matrix_h5_cooler_multiple" value="small_test_matrix.h5,small_test_matrix.h5" /> | 83 <param name="matrix_h5_cooler_multiple" value="small_test_matrix.h5,small_test_matrix.h5" /> |
| 84 <param name='normalize' value='smallest' /> | 84 <param name="normalize" value="smallest" /> |
| 85 <output name="normalize_matrix"> | 85 <output name="normalize_matrix"> |
| 86 <discovered_dataset designation="0_norm_small_test_matrix" ftype="h5"> | 86 <discovered_dataset designation="0_norm_small_test_matrix" ftype="h5"> |
| 87 <assert_contents> | 87 <assert_contents> |
| 88 <has_h5_keys keys="intervals,matrix" /> | 88 <has_h5_keys keys="intervals,matrix" /> |
| 89 </assert_contents> | 89 </assert_contents> |
| 113 _________________ | 113 _________________ |
| 114 | 114 |
| 115 | For more information about HiCExplorer please consider our documentation on readthedocs.io_ | 115 | For more information about HiCExplorer please consider our documentation on readthedocs.io_ |
| 116 | 116 |
| 117 .. _readthedocs.io: http://hicexplorer.readthedocs.io/en/latest/index.html | 117 .. _readthedocs.io: http://hicexplorer.readthedocs.io/en/latest/index.html |
| 118 .. _`Lieberman-Aiden et al. (2009)`: https://doi.org/10.1126/science.1181369 | 118 .. _`Lieberman-Aiden et al. (2009)`: https://pubmed.ncbi.nlm.nih.gov/19815776/ |
| 119 ]]> </help> | 119 ]]> </help> |
| 120 <expand macro="citations" /> | 120 <expand macro="citations" /> |
| 121 </tool> | 121 </tool> |