| Previous changeset 12:94c19fb1281c (2023-11-17) Next changeset 14:d844935c906c (2024-05-18) |
|
Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 3974c0ff86bb1d6633281f29dfb4c605a74e1e6e |
|
modified:
macros.xml normalize.xml |
|
added:
test-data/external.pp.magic.all_genes.krumsiek11.h5ad test-data/external.pp.magic.pca_only.krumsiek11.h5ad |
| b |
| diff -r 94c19fb1281c -r 7b9fafe32c86 macros.xml --- a/macros.xml Fri Nov 17 09:16:03 2023 +0000 +++ b/macros.xml Thu Mar 14 15:37:29 2024 +0000 |
| b |
| @@ -1,6 +1,6 @@ <macros> <token name="@TOOL_VERSION@">1.9.6</token> - <token name="@VERSION_SUFFIX@">1</token> + <token name="@VERSION_SUFFIX@">2</token> <token name="@profile@">22.05</token> <xml name="requirements"> <requirements> @@ -11,6 +11,7 @@ <requirement type="package" version="1.5.3">pandas</requirement> <requirement type="package" version="3.7">matplotlib</requirement> <requirement type="package" version="0.12.2">seaborn</requirement> + <requirement type="package" version="3.0.0">magic-impute</requirement> <yield /> </requirements> </xml> |
| b |
| diff -r 94c19fb1281c -r 7b9fafe32c86 normalize.xml --- a/normalize.xml Fri Nov 17 09:16:03 2023 +0000 +++ b/normalize.xml Thu Mar 14 15:37:29 2024 +0000 |
| [ |
| b'@@ -1,5 +1,5 @@\n <tool id="scanpy_normalize" name="Normalize" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@profile@">\n- <description>with scanpy</description>\n+ <description>and impute with scanpy</description>\n <macros>\n <import>macros.xml</import>\n </macros>\n@@ -65,6 +65,29 @@\n plot=False,\n copy=False)\n \n+#else if $method.method == "external.pp.magic"\n+sc.external.pp.magic(\n+ adata=adata,\n+ name_list=\'$method.name_list\',\n+ knn=$method.knn,\n+ #if str($method.decay) != \'\'\n+ decay=$method.decay,\n+ #end if\n+ #if str($method.knn_max) != \'\'\n+ knn_max=$method.knn_max,\n+ #end if\n+ #if $method.t == -1\n+ t=\'auto\',\n+ #else\n+ t=$method.t,\n+ #end if\n+ #if str($method.n_pca) != \'\'\n+ n_pca=$method.n_pca,\n+ #end if\n+ solver=\'$method.solver\',\n+ knn_dist=\'$method.knn_dist\',\n+ random_state=$method.random_state,\n+ copy=False)\n #end if\n \n @CMD_anndata_write_outputs@\n@@ -79,6 +102,7 @@\n <option value="pp.recipe_zheng17">Normalization and filtering as of Zheng et al. (2017), using \'pp.recipe_zheng17\'</option>\n <option value="pp.recipe_weinreb17">Normalization and filtering as of Weinreb et al (2017), using \'pp.recipe_weinreb17\'</option>\n <option value="pp.recipe_seurat">Normalization and filtering as of Seurat et al (2015), using \'pp.recipe_seurat\'</option>\n+ <option value="external.pp.magic">Denoising using Markov Affinity-based Graph Imputation of Cells (MAGIC) API \'external.pp.magic\'</option>\n </param>\n <when value="pp.normalize_total">\n <param argument="target_sum" type="float" value="" optional="true" label="Target sum" help="If not provided, after normalization, each observation (cell) has a total count equal to the median of the total counts (cells) before normalization."/>\n@@ -119,6 +143,29 @@\n <when value="pp.recipe_seurat">\n <expand macro="param_log"/>\n </when>\n+ <when value="external.pp.magic">\n+ <param name="name_list" type="select" label="Denoised genes to return" help="Selecting all genes may require a large amount of memory">\n+ <option value="all_genes">All genes</option>\n+ <option value="pca_only">PCA only</option>\n+ </param>\n+ <param argument="knn" type="integer" min="1" value="5" label="Number of nearest neighbors on which to build kernel" help=""/>\n+ <param argument="decay" type="integer" optional="true" value="1" label="Set decay rate of kernel tails" \n+ help="If not set, alpha decaying kernel is not used" />\n+ <param argument="knn_max" type="integer" min="1" optional="true" value="" label="Maximum number of nearest neighbors with nonzero connection"\n+ help="If not set, will be set to 3 * knn" />\n+ <param argument="t" type="integer" min="-1" value="3" label="Power to which the diffusion operator is powered. This sets the level of diffusion"\n+ help="If \xe2\x80\x98-1\xe2\x80\x99, this parameter is selected according to the Procrustes disparity of the diffused data." />\n+ <param argument="n_pca" type="integer" value="100" optional="true" label="Number of principal components to use for calculating neighborhoods"\n+ help="For extremely large datasets, using n_pca less than 20 allows neighborhoods to be calculated in roughly log(n_samples) time. If not set, no PCA is performed." />\n+ <param name="solver" type="select" label="Which solver to use" help="Selecting all genes may require a large amount of memory">\n+ <option value="exact">"exact", the implementation described in van Dijk et al. (2018) </option>\n+ <option value="approximate">"approximate", is faster that performs imputation in the PCA space and then projects back to t'..b' <expand macro="distance_metric_options"/>\n+ </param>\n+ <expand macro="param_random_state"/>\n+ </when>\n </conditional>\n <expand macro="inputs_common_advanced"/>\n </inputs>\n@@ -217,6 +264,53 @@\n </output>\n <output name="anndata_out" file="pp.recipe_seurat.recipe_zheng17.h5ad" ftype="h5ad" compare="sim_size" delta="1000000" delta_frac="0.25"/>\n </test>\n+ <test expect_num_outputs="2">\n+ <!-- test 5 -->\n+ <param name="adata" value="krumsiek11.h5ad" />\n+ <conditional name="method">\n+ <param name="method" value="external.pp.magic"/>\n+ <param name="name_list" value="all_genes"/>\n+ <param name="t" value="-1"/>\n+ <param name="n_pca" value="5"/>\n+ </conditional>\n+ <section name="advanced_common">\n+ <param name="show_log" value="true" />\n+ </section>\n+ <output name="hidden_output">\n+ <assert_contents>\n+ <has_text_matching expression="external.pp.magic"/>\n+ <has_text_matching expression="name_list=\'all_genes\'"/>\n+ <has_text_matching expression="t=\'auto\'"/>\n+ <has_text_matching expression="n_pca=5"/>\n+ </assert_contents>\n+ </output>\n+ <output name="anndata_out" file="external.pp.magic.all_genes.krumsiek11.h5ad" ftype="h5ad" compare="sim_size"/>\n+ </test>\n+ <test expect_num_outputs="2">\n+ <!-- test 6 -->\n+ <param name="adata" value="krumsiek11.h5ad" />\n+ <conditional name="method">\n+ <param name="method" value="external.pp.magic"/>\n+ <param name="name_list" value="pca_only"/>\n+ <param name="t" value="3"/>\n+ <param name="n_pca" value="5"/>\n+ </conditional>\n+ <section name="advanced_common">\n+ <param name="show_log" value="true" />\n+ </section>\n+ <output name="hidden_output">\n+ <assert_contents>\n+ <has_text_matching expression="external.pp.magic"/>\n+ <has_text_matching expression="name_list=\'pca_only\'"/>\n+ <has_text_matching expression="t=3"/>\n+ <has_text_matching expression="n_pca=5"/>\n+ </assert_contents>\n+ </output>\n+ <output name="anndata_out" file="external.pp.magic.pca_only.krumsiek11.h5ad" ftype="h5ad" compare="sim_size"/>\n+ <assert_stdout>\n+ <has_text text="X_magic"/>\n+ </assert_stdout>\n+ </test>\n </tests>\n <help><![CDATA[\n Normalize total counts per cell (`pp.normalize_per_cell`)\n@@ -269,6 +363,20 @@\n More details on the `scanpy documentation\n <https://icb-scanpy.readthedocs-hosted.com/en/stable/api/scanpy.pp.recipe_seurat.html>`__\n \n+\n+Markov Affinity-based Graph Imputation of Cells (MAGIC) as of Van Dijk D et al. (2018) (`external.pp.magic`)\n+============================================================================================================\n+\n+MAGIC is an algorithm for denoising and transcript recover of single cells applied to single-cell sequencing data. MAGIC builds a graph from the data and uses diffusion to smooth out noise and recover the data manifold.\n+\n+The algorithm implemented here has changed primarily in two ways compared to the algorithm described in Van Dijk D et al. (2018). \n+\n+- Firstly, we use the adaptive kernel described in Moon et al, (2019) for improved stability.\n+- Secondly, data diffusion is applied in the PCA space, rather than the data space, for speed and memory improvements.\n+\n+More details on the `scanpy documentation\n+<https://icb-scanpy.readthedocs-hosted.com/en/stable/api/scanpy.external.pp.magic.html>`__\n+\n ]]></help>\n <expand macro="citations"/>\n </tool>\n' |
| b |
| diff -r 94c19fb1281c -r 7b9fafe32c86 test-data/external.pp.magic.all_genes.krumsiek11.h5ad |
| b |
| Binary file test-data/external.pp.magic.all_genes.krumsiek11.h5ad has changed |
| b |
| diff -r 94c19fb1281c -r 7b9fafe32c86 test-data/external.pp.magic.pca_only.krumsiek11.h5ad |
| b |
| Binary file test-data/external.pp.magic.pca_only.krumsiek11.h5ad has changed |