Mercurial > repos > bgruening > hicexplorer_hicnormalize
diff 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 |
line wrap: on
line diff
--- a/hicNormalize.xml Fri Dec 11 20:58:36 2020 +0000 +++ b/hicNormalize.xml Tue Mar 16 15:29:18 2021 +0000 @@ -1,4 +1,4 @@ -<tool id="hicexplorer_hicnormalize" name="@BINARY@" version="@WRAPPER_VERSION@.0"> +<tool id="hicexplorer_hicnormalize" name="@BINARY@" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@"> <description>normalizes a matrix to norm range or smallest read count</description> <macros> <token name="@BINARY@">hicNormalize</token> @@ -28,65 +28,76 @@ ]]> </command> <inputs> - <expand macro='matrix_h5_cooler_multiple_macro'/> + <expand macro='matrix_h5_cooler_multiple_macro' /> <conditional name="normalize_conditional"> <param name='normalize' type='select' label='Normalize matrices'> <option value='norm_range'>0 to 1 range</option> <option value='smallest'>Smallest read count</option> <option value='multiplicative'>Multiply by value</option> </param> - <when value='norm_range'/> - <when value='smallest'/> + <when value='norm_range' /> + <when value='smallest' /> <when value='multiplicative'> - <param name="multiplicativeValue" type="float" value="1.0" label="Multiplicative value"/> + <param name="multiplicativeValue" type="float" value="1.0" label="Multiplicative value" /> </when> </conditional> - <param name="zero_threshold_value" type="float" value="1.0" optional='True' label="Set values below this threshold to zero"/> + <param name="zero_threshold_value" type="float" value="1.0" optional='True' label="Set values below this threshold to zero" /> </inputs> <outputs> <data format='cool' name="normalize_matrix"> - <discover_datasets pattern="__name_and_ext__" directory="output" visible="true"/> + <discover_datasets pattern="__name_and_ext__" directory="output" visible="true" /> <change_format> - <when input_dataset="matrix_h5_cooler_multiple" attribute="ext" value="h5" format="h5"/> + <when input_dataset="matrix_h5_cooler_multiple" attribute="ext" value="h5" format="h5" /> </change_format> </data> </outputs> <tests> <test> - <param name="matrix_h5_cooler_multiple" value="small_test_matrix.cool"/> - <param name='normalize' value='norm_range'/> + <param name="matrix_h5_cooler_multiple" value="small_test_matrix.cool" /> + <param name='normalize' value='norm_range' /> <output name="normalize_matrix"> <discovered_dataset designation="0_norm_small_test_matrix" ftype="cool"> - <assert_contents><has_h5_keys keys="bins,chroms,indexes,pixels"/></assert_contents> + <assert_contents> + <has_h5_keys keys="bins,chroms,indexes,pixels" /> + </assert_contents> </discovered_dataset> </output> </test> <test> - <param name="matrix_h5_cooler_multiple" value="small_test_matrix.cool,small_test_matrix.cool"/> - <param name='normalize' value='smallest'/> + <param name="matrix_h5_cooler_multiple" value="small_test_matrix.cool,small_test_matrix.cool" /> + <param name='normalize' value='smallest' /> <output name="normalize_matrix"> <discovered_dataset designation="0_norm_small_test_matrix" ftype="cool"> - <assert_contents><has_h5_keys keys="bins,chroms,indexes,pixels"/></assert_contents> + <assert_contents> + <has_h5_keys keys="bins,chroms,indexes,pixels" /> + </assert_contents> </discovered_dataset> <discovered_dataset designation="1_norm_small_test_matrix" ftype="cool"> - <assert_contents><has_h5_keys keys="bins,chroms,indexes,pixels"/></assert_contents> + <assert_contents> + <has_h5_keys keys="bins,chroms,indexes,pixels" /> + </assert_contents> </discovered_dataset> </output> </test> <test> - <param name="matrix_h5_cooler_multiple" value="small_test_matrix.h5,small_test_matrix.h5"/> - <param name='normalize' value='smallest'/> + <param name="matrix_h5_cooler_multiple" value="small_test_matrix.h5,small_test_matrix.h5" /> + <param name='normalize' value='smallest' /> <output name="normalize_matrix"> <discovered_dataset designation="0_norm_small_test_matrix" ftype="h5"> - <assert_contents><has_h5_keys keys="intervals,matrix"/></assert_contents> + <assert_contents> + <has_h5_keys keys="intervals,matrix" /> + </assert_contents> </discovered_dataset> <discovered_dataset designation="1_norm_small_test_matrix" ftype="h5"> - <assert_contents><has_h5_keys keys="intervals,matrix"/></assert_contents> + <assert_contents> + <has_h5_keys keys="intervals,matrix" /> + </assert_contents> </discovered_dataset> </output> </test> </tests> <help><![CDATA[ + Normalization of matrices ========================= @@ -105,6 +116,6 @@ .. _readthedocs.io: http://hicexplorer.readthedocs.io/en/latest/index.html .. _`Lieberman-Aiden et al. (2009)`: https://doi.org/10.1126%2Fscience.1181369 -]]></help> +]]> </help> <expand macro="citations" /> </tool>