Mercurial > repos > bgruening > hicexplorer_hicnormalize
diff hicNormalize.xml @ 8:6d042c96aceb draft
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 | f34ab9882252 |
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--- a/hicNormalize.xml Tue Jan 10 18:40:25 2023 +0000 +++ b/hicNormalize.xml Wed Oct 18 10:21:43 2023 +0000 @@ -28,23 +28,23 @@ ]]> </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 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='multiplicative'> + <when value="norm_range" /> + <when value="smallest" /> + <when value="multiplicative"> <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"> + <data format="cool" name="normalize_matrix"> <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" /> @@ -54,7 +54,7 @@ <tests> <test> <param name="matrix_h5_cooler_multiple" value="small_test_matrix.cool" /> - <param name='normalize' value='norm_range' /> + <param name="normalize" value="norm_range" /> <output name="normalize_matrix"> <discovered_dataset designation="0_norm_small_test_matrix" ftype="cool"> <assert_contents> @@ -65,7 +65,7 @@ </test> <test> <param name="matrix_h5_cooler_multiple" value="small_test_matrix.cool,small_test_matrix.cool" /> - <param name='normalize' value='smallest' /> + <param name="normalize" value="smallest" /> <output name="normalize_matrix"> <discovered_dataset designation="0_norm_small_test_matrix" ftype="cool"> <assert_contents> @@ -81,7 +81,7 @@ </test> <test> <param name="matrix_h5_cooler_multiple" value="small_test_matrix.h5,small_test_matrix.h5" /> - <param name='normalize' value='smallest' /> + <param name="normalize" value="smallest" /> <output name="normalize_matrix"> <discovered_dataset designation="0_norm_small_test_matrix" ftype="h5"> <assert_contents> @@ -115,7 +115,7 @@ | For more information about HiCExplorer please consider our documentation on readthedocs.io_ .. _readthedocs.io: http://hicexplorer.readthedocs.io/en/latest/index.html -.. _`Lieberman-Aiden et al. (2009)`: https://doi.org/10.1126/science.1181369 +.. _`Lieberman-Aiden et al. (2009)`: https://pubmed.ncbi.nlm.nih.gov/19815776/ ]]> </help> <expand macro="citations" /> </tool>