Mercurial > repos > iuc > scanpy_normalize
diff normalize.xml @ 11:c9cb76cf8d6c draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d
author | iuc |
---|---|
date | Wed, 08 Nov 2023 14:49:18 +0000 |
parents | ab55fe8030b6 |
children | 94c19fb1281c |
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--- a/normalize.xml Wed Sep 22 21:12:45 2021 +0000 +++ b/normalize.xml Wed Nov 08 14:49:18 2023 +0000 @@ -1,9 +1,9 @@ <tool id="scanpy_normalize" name="Normalize" version="@galaxy_version@" profile="@profile@"> <description>with scanpy</description> - <expand macro="bio_tools"/> <macros> <import>macros.xml</import> </macros> + <expand macro="bio_tools"/> <expand macro="requirements"/> <expand macro="version_command"/> <command detect_errors="exit_code"><![CDATA[ @@ -126,8 +126,8 @@ <expand macro="anndata_outputs"/> </outputs> <tests> - <test> - <!-- test 0 --> + <test expect_num_outputs="2"> + <!-- test 1 --> <param name="adata" value="krumsiek11.h5ad" /> <conditional name="method"> <param name="method" value="pp.normalize_total"/> @@ -151,8 +151,8 @@ </output> <output name="anndata_out" file="pp.normalize_total.krumsiek11.h5ad" ftype="h5ad" compare="sim_size"/> </test> - <test> - <!-- test 1 --> + <test expect_num_outputs="2"> + <!-- test 2 --> <param name="adata" value="random-randint.h5ad"/> <conditional name="method"> <param name="method" value="pp.recipe_zheng17"/> @@ -171,8 +171,8 @@ </output> <output name="anndata_out" file="pp.recipe_zheng17.random-randint.h5ad" ftype="h5ad" compare="sim_size" delta="1000000" delta_frac="0.15"/> </test> - <test> - <!-- test 2 --> + <test expect_num_outputs="2"> + <!-- test 3 --> <param name="adata" value="paul15_subsample.h5ad" /> <conditional name="method"> <param name="method" value="pp.recipe_weinreb17"/> @@ -199,8 +199,8 @@ </output> <output name="anndata_out" file="pp.recipe_weinreb17.paul15_subsample.updated.h5ad" ftype="h5ad" compare="sim_size"/> </test> - <test> - <!-- test 3 --> + <test expect_num_outputs="2"> + <!-- test 4 --> <param name="adata" value="pp.recipe_zheng17.random-randint.h5ad" /> <conditional name="method"> <param name="method" value="pp.recipe_seurat"/> @@ -228,7 +228,7 @@ Similar functions are used, for example, by Seurat, Cell Ranger or SPRING. More details on the `scanpy documentation -<https://icb-scanpy.readthedocs-hosted.com/en/@version@/api/scanpy.pp.normalize_per_cell.html>`__ +<https://icb-scanpy.readthedocs-hosted.com/en/stable/api/scanpy.pp.normalize_per_cell.html>`__ Normalization and filtering as of Zheng et al. (2017), the Cell Ranger R Kit of 10x Genomics (`pp.recipe_zheng17`) @@ -247,7 +247,7 @@ - scale to unit variance and shift to zero mean More details on the `scanpy documentation -<https://icb-scanpy.readthedocs-hosted.com/en/@version@/api/scanpy.pp.recipe_zheng17.html>`__ +<https://icb-scanpy.readthedocs-hosted.com/en/stable/api/scanpy.pp.recipe_zheng17.html>`__ Normalization and filtering as of Weinreb et al (2017) (`pp.recipe_weinreb17`) @@ -256,7 +256,7 @@ Expects non-logarithmized data. If using logarithmized data, pass `log=False`. More details on the `scanpy documentation -<https://icb-scanpy.readthedocs-hosted.com/en/@version@/api/scanpy.pp.recipe_weinreb17.html>`__ +<https://icb-scanpy.readthedocs-hosted.com/en/stable/api/scanpy.pp.recipe_weinreb17.html>`__ Normalization and filtering as of Seurat et al (2015) (`pp.recipe_seurat`) @@ -267,7 +267,7 @@ Expects non-logarithmized data. If using logarithmized data, pass `log=False`. More details on the `scanpy documentation -<https://icb-scanpy.readthedocs-hosted.com/en/@version@/api/scanpy.pp.recipe_seurat.html>`__ +<https://icb-scanpy.readthedocs-hosted.com/en/stable/api/scanpy.pp.recipe_seurat.html>`__ ]]></help> <expand macro="citations"/>