Mercurial > repos > bgruening > hicexplorer_hicnormalize
comparison hicNormalize.xml @ 6:05257e5d5016 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
| author | iuc |
|---|---|
| date | Tue, 16 Mar 2021 15:29:18 +0000 |
| parents | 483e507c8d42 |
| children | 8ad23dfdaabb |
comparison
equal
deleted
inserted
replaced
| 5:b9d7410b6593 | 6:05257e5d5016 |
|---|---|
| 1 <tool id="hicexplorer_hicnormalize" name="@BINARY@" version="@WRAPPER_VERSION@.0"> | 1 <tool id="hicexplorer_hicnormalize" name="@BINARY@" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@"> |
| 2 <description>normalizes a matrix to norm range or smallest read count</description> | 2 <description>normalizes a matrix to norm range or smallest read count</description> |
| 3 <macros> | 3 <macros> |
| 4 <token name="@BINARY@">hicNormalize</token> | 4 <token name="@BINARY@">hicNormalize</token> |
| 5 <import>macros.xml</import> | 5 <import>macros.xml</import> |
| 6 </macros> | 6 </macros> |
| 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><has_h5_keys keys="bins,chroms,indexes,pixels"/></assert_contents> | 60 <assert_contents> |
| 61 <has_h5_keys keys="bins,chroms,indexes,pixels" /> | |
| 62 </assert_contents> | |
| 61 </discovered_dataset> | 63 </discovered_dataset> |
| 62 </output> | 64 </output> |
| 63 </test> | 65 </test> |
| 64 <test> | 66 <test> |
| 65 <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" /> |
| 66 <param name='normalize' value='smallest'/> | 68 <param name='normalize' value='smallest' /> |
| 67 <output name="normalize_matrix"> | 69 <output name="normalize_matrix"> |
| 68 <discovered_dataset designation="0_norm_small_test_matrix" ftype="cool"> | 70 <discovered_dataset designation="0_norm_small_test_matrix" ftype="cool"> |
| 69 <assert_contents><has_h5_keys keys="bins,chroms,indexes,pixels"/></assert_contents> | 71 <assert_contents> |
| 72 <has_h5_keys keys="bins,chroms,indexes,pixels" /> | |
| 73 </assert_contents> | |
| 70 </discovered_dataset> | 74 </discovered_dataset> |
| 71 <discovered_dataset designation="1_norm_small_test_matrix" ftype="cool"> | 75 <discovered_dataset designation="1_norm_small_test_matrix" ftype="cool"> |
| 72 <assert_contents><has_h5_keys keys="bins,chroms,indexes,pixels"/></assert_contents> | 76 <assert_contents> |
| 77 <has_h5_keys keys="bins,chroms,indexes,pixels" /> | |
| 78 </assert_contents> | |
| 73 </discovered_dataset> | 79 </discovered_dataset> |
| 74 </output> | 80 </output> |
| 75 </test> | 81 </test> |
| 76 <test> | 82 <test> |
| 77 <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" /> |
| 78 <param name='normalize' value='smallest'/> | 84 <param name='normalize' value='smallest' /> |
| 79 <output name="normalize_matrix"> | 85 <output name="normalize_matrix"> |
| 80 <discovered_dataset designation="0_norm_small_test_matrix" ftype="h5"> | 86 <discovered_dataset designation="0_norm_small_test_matrix" ftype="h5"> |
| 81 <assert_contents><has_h5_keys keys="intervals,matrix"/></assert_contents> | 87 <assert_contents> |
| 88 <has_h5_keys keys="intervals,matrix" /> | |
| 89 </assert_contents> | |
| 82 </discovered_dataset> | 90 </discovered_dataset> |
| 83 <discovered_dataset designation="1_norm_small_test_matrix" ftype="h5"> | 91 <discovered_dataset designation="1_norm_small_test_matrix" ftype="h5"> |
| 84 <assert_contents><has_h5_keys keys="intervals,matrix"/></assert_contents> | 92 <assert_contents> |
| 93 <has_h5_keys keys="intervals,matrix" /> | |
| 94 </assert_contents> | |
| 85 </discovered_dataset> | 95 </discovered_dataset> |
| 86 </output> | 96 </output> |
| 87 </test> | 97 </test> |
| 88 </tests> | 98 </tests> |
| 89 <help><![CDATA[ | 99 <help><![CDATA[ |
| 100 | |
| 90 Normalization of matrices | 101 Normalization of matrices |
| 91 ========================= | 102 ========================= |
| 92 | 103 |
| 93 **hicNormalize** normalizes either each matrix to a 0 - 1 value range, to the smallest read coverage or with a user given factor. | 104 **hicNormalize** normalizes either each matrix to a 0 - 1 value range, to the smallest read coverage or with a user given factor. |
| 94 | 105 |
| 103 | 114 |
| 104 | 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_ |
| 105 | 116 |
| 106 .. _readthedocs.io: http://hicexplorer.readthedocs.io/en/latest/index.html | 117 .. _readthedocs.io: http://hicexplorer.readthedocs.io/en/latest/index.html |
| 107 .. _`Lieberman-Aiden et al. (2009)`: https://doi.org/10.1126%2Fscience.1181369 | 118 .. _`Lieberman-Aiden et al. (2009)`: https://doi.org/10.1126%2Fscience.1181369 |
| 108 ]]></help> | 119 ]]> </help> |
| 109 <expand macro="citations" /> | 120 <expand macro="citations" /> |
| 110 </tool> | 121 </tool> |