Mercurial > repos > iuc > episcanpy_cluster_embed
changeset 1:f4713992f23a draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit bb79cb8cad3bc1433bff7caf9d7b45e7993dd470
| author | iuc |
|---|---|
| date | Sat, 22 Apr 2023 12:14:16 +0000 |
| parents | 7340d619d7f8 |
| children | |
| files | cluster_embed.xml macros.xml test-data/chrY.h5ad test-data/chrY_norm_peaks.h5ad test-data/chrY_with_transcript_annotation.h5ad |
| diffstat | 5 files changed, 6 insertions(+), 86 deletions(-) [+] |
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--- a/cluster_embed.xml Tue Apr 18 13:19:32 2023 +0000 +++ b/cluster_embed.xml Sat Apr 22 12:14:16 2023 +0000 @@ -46,16 +46,6 @@ corr_method='$method.rank_features_corr_method' ) -#else if $method.method == 'tl.find_genes' -esc.tl.find_genes( - adata, - gtf_file='$method.find_genes_gtf_file', - key_added='$method.find_genes_key_added', - upstream=$method.find_genes_upstream, - feature_type='$method.find_genes_feature_type', - annotation='$method.find_genes_annotation', - raw=$method.find_genes_raw) - #else if $method.method == 'tl.get_n_clusters' esc.tl.getNClusters( adata, @@ -88,7 +78,6 @@ <param argument="method" type="select" label="Method used for Clustering or Embedding"> <option value="pp.lazy">Embedding: Automatically compute PCA coordinates, loadings and variance decomposition, a neighborhood graph of observations, t-distributed stochastic neighborhood embedding (tSNE) Uniform Manifold Approximation and Projection (UMAP), using 'pp.lazy'</option> <option value="tl.rank_features">Rank features for characterizing groups, using 'tl.rank_features'</option> - <option value="tl.find_genes">Embedding: Find genes and add annotations, using 'pp.find_genes'</option> <option value="tl.get_n_clusters">Clustering: Test different settings of louvain to obtain the target number of clusters, using 'tl.getNClusters'</option> <option value="tl.kmeans">Clustering: Compute kmeans clustering using X_pca fits, using 'tl.kmeans'</option> <option value="tl.hc">Clustering: Compute hierarchical clustering using X_pca fits, using 'tl.hc'</option> @@ -213,50 +202,6 @@ <option value="bonferroni">Bonferroni</option> </param> </when> - <when value="tl.find_genes"> - <param name="find_genes_gtf_file" type="data" format="gtf" label="Annotation GTF file" help="(gtf_file)"/> - <param name="find_genes_key_added" value="transcript_annotation" type="text" label="Key added" help="(key_added)"> - <sanitizer invalid_char=""> - <valid initial="string.letters,string.digits"> - <add value="_" /> - <add value="-" /> - <add value="." /> - <add value=" " /> - <add value="," /> - </valid> - </sanitizer> - <validator type="regex">[0-9a-zA-Z_., -]+</validator> - </param> - <param name="find_genes_upstream" value="2000" min="0" type="integer" label="Upstream" help="(upstream)"/> - <param name="find_genes_feature_type" value="transcript" type="text" label="Feature type" help="(feature_type)"> - <sanitizer invalid_char=""> - <valid initial="string.letters,string.digits"> - <add value="_" /> - <add value="-" /> - <add value="." /> - <add value=" " /> - <add value="," /> - </valid> - </sanitizer> - <validator type="regex">[0-9a-zA-Z_., -]+</validator> - </param> - <param name="find_genes_annotation" value="HAVANA" type="text" label="Annotation" help="(annotation)"> - <sanitizer invalid_char=""> - <valid initial="string.letters,string.digits"> - <add value="_" /> - <add value="-" /> - <add value="." /> - <add value=" " /> - <add value="," /> - </valid> - </sanitizer> - <validator type="regex">[0-9a-zA-Z_., -]+</validator> - </param> - <param name="find_genes_raw" type="select" label="Raw?" help="(raw)"> - <option value="True">True</option> - <option value="False" selected="true">False</option> - </param> - </when> <when value="tl.get_n_clusters"> <param name="get_n_clusters_n_cluster" value="14" min="1" type="integer" label="Number of clusters" help="(n_cluster)"/> <param name="get_n_clusters_method" type="select" label="Clustering method to use" help="(method)"> @@ -293,7 +238,7 @@ </outputs> <tests> <test expect_num_outputs="2"> - <!-- test 0- pp.lazy --> + <!-- pp.lazy --> <param name="adata" value="krumsiek11.h5ad" /> <conditional name="method"> <param name="method" value="pp.lazy"/> @@ -322,7 +267,7 @@ <output name="anndata_out" file="krumsiek11.pp.lazy.h5ad" ftype="h5ad" compare="sim_size"/> </test> <test expect_num_outputs="2"> - <!-- test 1- tl.rank_features --> + <!-- tl.rank_features --> <param name="adata" value="krumsiek11.pp.lazy.tl.louvain.h5ad" /> <conditional name="method"> <param name="method" value="tl.rank_features"/> @@ -345,29 +290,8 @@ </assert_contents> </output> </test> - <test expect_num_outputs="2"> - <!-- test 2-tl.find_genes --> - <param name="adata" value="chrY.h5ad" /> - <conditional name="method"> - <param name="method" value="tl.find_genes"/> - <param name="find_genes_gtf_file" value="chrY.gtf"/> - <param name="find_genes_key_added" value="transcript_annotation"/> - <param name="find_genes_upstream" value="2000"/> - <param name="find_genes_feature_type" value="transcript"/> - <param name="find_genes_annotation" value="HAVANA"/> - <param name="find_genes_raw" value="False"/> - </conditional> - <section name="advanced_common"> - <param name="show_log" value="true" /> - </section> - <output name="anndata_out" file="chrY_with_transcript_annotation.h5ad" ftype="h5ad" compare="sim_size"> - <assert_contents> - <has_h5_keys keys="var" /> - </assert_contents> - </output> - </test> <test expect_num_outputs="2"> - <!-- test 3-tl.get_n_clusters --> + <!-- tl.get_n_clusters --> <param name="adata" value="krumsiek11.pp.lazy.tl.louvain.h5ad" /> <conditional name="method"> <param name="method" value="tl.get_n_clusters"/> @@ -386,7 +310,7 @@ <output name="anndata_out" file="krumsiek11.tl.get_n_clusters.h5ad" ftype="h5ad"/> </test> <test expect_num_outputs="2"> - <!-- test 4-tl.kmeans --> + <!-- tl.kmeans --> <param name="adata" value="krumsiek11.pp.lazy.h5ad" /> <conditional name="method"> <param name="method" value="tl.kmeans"/> @@ -398,7 +322,7 @@ <output name="anndata_out" file="krumsiek11.tl.kmeans.h5ad" ftype="h5ad"/> </test> <test expect_num_outputs="2"> - <!-- test 5-tl.hc --> + <!-- tl.hc --> <param name="adata" value="krumsiek11.pp.lazy.h5ad" /> <conditional name="method"> <param name="method" value="tl.hc"/> @@ -420,10 +344,6 @@ More details on the `episcanpy documentation <https://colomemaria.github.io/episcanpy_doc/api/episcanpy.api.pp.lazy.html>`__ -Find and add gene annotations (`tl.find_genes`) -======================================================================================== -This function adds a gene annotation to an AnnData (h5ad) file from annotations file (.annotation.gtf). - Automatically obtain target number of clusters (`tl.getNClusters`) ======================================================================================== This function will test different settings of louvain to obtain the target number of clusters.
--- a/macros.xml Tue Apr 18 13:19:32 2023 +0000 +++ b/macros.xml Sat Apr 22 12:14:16 2023 +0000 @@ -1,6 +1,6 @@ <macros> <token name="@TOOL_VERSION@">0.3.2</token> - <token name="@VERSION_SUFFIX@">0</token> + <token name="@VERSION_SUFFIX@">1</token> <token name="@PROFILE@">21.01</token> <xml name="requirements"> <requirements>