| Previous changeset 0:b2a6ce371781 (2019-04-10) Next changeset 2:6a1a3dab235a (2019-12-12) |
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Commit message:
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" |
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modified:
inspect.xml macros.xml |
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added:
test-data/manipulate.add_annotation_obs.h5ad test-data/manipulate.add_annotation_var.h5ad test-data/manipulate.filter_obs_key.h5ad test-data/manipulate.filter_var_index.h5ad test-data/obs_add_annotation.tabular test-data/pp.neighbors_umap_euclidean.recipe_weinreb17.paul15_subsample.h5ad test-data/pp.pca.krumsiek11.h5ad test-data/tl.diffmap.h5ad test-data/tl.draw_graph.h5ad test-data/tl.paga.neighbors_gauss_braycurtis.recipe_weinreb17.paul15_subsample.h5ad test-data/tl.rank_genes_groups.krumsiek11.h5ad test-data/tl.tsne.h5ad test-data/tl.umap.h5ad test-data/var_add_annotation.tabular |
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| diff -r b2a6ce371781 -r 05304c5c195d inspect.xml --- a/inspect.xml Wed Apr 10 03:25:39 2019 -0400 +++ b/inspect.xml Wed Oct 16 06:27:55 2019 -0400 |
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| b'@@ -11,20 +11,27 @@\n <configfiles>\n <configfile name="script_file"><![CDATA[\n @CMD_imports@\n+import pandas as pd\n+from scipy import io\n+\n+pd.options.display.precision = 15\n \n adata = ad.read(\'$input\')\n \n #if $inspect.info == \'general\'\n with open(\'$general\', \'w\') as f:\n print(adata, file=f)\n+\n #else if $inspect.info == \'X\'\n adata.to_df().to_csv(\'$X\', sep=\'\\t\')\n+\n #else if $inspect.info == \'obs\'\n adata.obs.to_csv(\'$obs\', sep=\'\\t\')\n+\n #else if $inspect.info == \'var\'\n adata.var.to_csv(\'$var\', sep=\'\\t\')\n+\n #else if $inspect.info == \'chunk_X\'\n-import pandas as pd\n #if $inspect.chunk.info == \'random\'\n X = adata.chunk_X(select=$inspect.chunk.size, replace=$inspect.chunk.replace)\n #else\n@@ -32,6 +39,45 @@\n X = adata.chunk_X(select=$select)\n #end if\n pd.DataFrame(X).to_csv(\'$chunk_X\', sep=\'\\t\')\n+\n+#else if $inspect.info == \'uns\'\n+ #if $inspect.uns_info == \'neighbors\'\n+io.mmwrite(\'uns_neighbors_connectivities.mtx\', adata.uns[\'neighbors\'][\'connectivities\'])\n+io.mmwrite(\'uns_neighbors_distances.mtx\', adata.uns[\'neighbors\'][\'distances\'])\n+ #else if $inspect.uns_info == \'paga\'\n+io.mmwrite(\'uns_paga_connectivities.mtx\', adata.uns[\'paga\'][\'connectivities\'])\n+io.mmwrite(\'uns_paga_connectivities_tree.mtx\', adata.uns[\'paga\'][\'connectivities_tree\'])\n+ #else if $inspect.uns_info == \'pca\'\n+pd.DataFrame(adata.uns[\'pca\'][\'variance\']).to_csv("$uns_pca_variance", sep="\\t", index = False)\n+pd.DataFrame(adata.uns[\'pca\'][\'variance_ratio\']).to_csv("$uns_pca_variance_ratio", sep="\\t", index = False)\n+ #else if $inspect.uns_info == \'rank_genes_groups\'\n+pd.DataFrame(adata.uns[\'rank_genes_groups\'][\'logfoldchanges\']).to_csv("$uns_rank_genes_groups_logfoldchanges", sep="\\t", index = False)\n+pd.DataFrame(adata.uns[\'rank_genes_groups\'][\'names\']).to_csv("$uns_rank_genes_groups_names", sep="\\t", index = False)\n+pd.DataFrame(adata.uns[\'rank_genes_groups\'][\'pvals\']).to_csv("$uns_rank_genes_groups_pvals", sep="\\t", index = False)\n+pd.DataFrame(adata.uns[\'rank_genes_groups\'][\'pvals_adj\']).to_csv("$uns_rank_genes_groups_pvals_adj", sep="\\t", index = False)\n+pd.DataFrame(adata.uns[\'rank_genes_groups\'][\'scores\']).to_csv("$uns_rank_genes_groups_scores", sep="\\t", index = False)\n+ #end if\n+\n+#else if $inspect.info == \'obsm\'\n+ #if $inspect.obsm_info == \'X_pca\' \n+pd.DataFrame(adata.obsm[\'X_pca\']).to_csv("$obsm_X_pca", sep="\\t", index = False)\n+ #else if $inspect.obsm_info == \'X_umap\' \n+pd.DataFrame(adata.obsm[\'X_umap\']).to_csv("$obsm_X_umap", sep="\\t", index = False)\n+ #else if $inspect.obsm_info == \'X_tsne\' \n+pd.DataFrame(adata.obsm[\'X_tsne\']).to_csv("$obsm_X_tsne", sep="\\t", index = False)\n+ #else if $inspect.obsm_info == \'X_draw_graph\'\n+for key in adata.obsm.keys():\n+ if key.startswith(\'X_draw_graph\'):\n+ pd.DataFrame(adata.obsm[key]).to_csv(key, sep="\\t", index = False)\n+ #else if $inspect.obsm_info == \'X_diffmap\'\n+pd.DataFrame(adata.obsm[\'X_diffmap\']).to_csv("$obsm_X_diffmap", sep="\\t", index = False)\n+ #end if\n+\n+#else if $inspect.info == \'varm\'\n+ #if $inspect.varm_info == \'PCs\' \n+pd.DataFrame(adata.varm[\'PCs\']).to_csv("$varm_PCs", sep="\\t", index = False)\n+ #end if\n+\n #end if\n ]]></configfile>\n </configfiles>\n@@ -42,16 +88,40 @@\n <option value="general">General information about the object</option>\n <option value="X">The full data matrix</option>\n <option value="chunk_X">A chunk of the data matrix</option>\n- <option value="obs">Key-indexed observations annotation</option>\n- <option value="var">Key-indexed annotation of variables/features</option>\n- <!--<option value="uns">Unstructured annotation</option>!-->\n+ <option value="obs">Key-indexed observations annotation (obs)</option>\n+ <option value="var">Key-indexed annotation of variables/features (var)</option>\n+ <option value="uns">Unstructured annotation (uns)</option>\n+ <option value="obsm'..b'msiek11.h5ad"/>\n+ <conditional name="inspect">\n+ <param name="info" value="obsm"/>\n+ <param name="obsm_info" value="X_pca"/>\n+ </conditional>\n+ <output name="obsm_X_pca">\n+ <assert_contents>\n+ <has_text_matching expression="0.00030471283" />\n+ <has_text_matching expression="3.4109413e-05" />\n+ <has_text_matching expression="-0.6401007" />\n+ <has_n_columns n="10" />\n+ </assert_contents>\n+ </output>\n+ </test>\n+ <test>\n+ <!-- test 12: obsm_info, X_umap -->\n+ <param name="input" value="tl.umap.h5ad"/>\n+ <conditional name="inspect">\n+ <param name="info" value="obsm"/>\n+ <param name="obsm_info" value="X_umap"/>\n+ </conditional>\n+ <output name="obsm_X_umap">\n+ <assert_contents>\n+ <has_text text="1.664" />\n+ <has_text text="5.425" />\n+ <has_text text="-1.748" />\n+ <has_text text="-9.714" />\n+ <has_n_columns n="2" />\n+ </assert_contents>\n+ </output>\n+ </test>\n+ <test>\n+ <!-- test 13: obsm_info, X_tsne -->\n+ <param name="input" value="tl.tsne.h5ad"/>\n+ <conditional name="inspect">\n+ <param name="info" value="obsm"/>\n+ <param name="obsm_info" value="X_tsne"/>\n+ </conditional>\n+ <output name="obsm_X_tsne">\n+ <assert_contents>\n+ <has_text text="14.301989" />\n+ <has_text text="-19.447426" />\n+ <has_n_columns n="2" />\n+ </assert_contents>\n+ </output>\n+ </test>\n+ <test>\n+ <!-- test 14: obsm_info, X_draw_graph -->\n+ <param name="input" value="tl.draw_graph.h5ad"/>\n+ <conditional name="inspect">\n+ <param name="info" value="obsm"/>\n+ <param name="obsm_info" value="X_draw_graph"/>\n+ </conditional>\n+ <output_collection name="obsm_X_draw_graph">\n+ <element name="fr">\n+ <assert_contents>\n+ <has_text text="-39.77" />\n+ <has_text text="-24.83" />\n+ <has_text text="-34.34" />\n+ <has_text text="-22.34" />\n+ <has_n_columns n="2" />\n+ </assert_contents>\n+ </element>\n+ </output_collection>\n+ </test>\n+ <test>\n+ <!-- test 15: obsm_info, X_diffmap -->\n+ <param name="input" value="tl.diffmap.h5ad"/>\n+ <conditional name="inspect">\n+ <param name="info" value="obsm"/>\n+ <param name="obsm_info" value="X_diffmap"/>\n+ </conditional>\n+ <output name="obsm_X_diffmap">\n+ <assert_contents>\n+ <has_text text="0.1006" />\n+ <has_text text="-0.0619" />\n+ <has_n_columns n="15" />\n+ </assert_contents>\n+ </output>\n+ </test>\n+ <test>\n+ <!-- test 16: varm_info, PCs -->\n+ <param name="input" value="pp.pca.krumsiek11.h5ad"/>\n+ <conditional name="inspect">\n+ <param name="info" value="varm"/>\n+ <param name="varm_info" value="PCs"/>\n+ </conditional>\n+ <output name="varm_PCs">\n+ <assert_contents>\n+ <has_text_matching expression="0.2352" />\n+ <has_text_matching expression="-0.0492" />\n+ <has_n_columns n="10" />\n+ </assert_contents>\n+ </output>\n+ </test>\n </tests>\n <help><![CDATA[\n **What it does**\n' |
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| diff -r b2a6ce371781 -r 05304c5c195d macros.xml --- a/macros.xml Wed Apr 10 03:25:39 2019 -0400 +++ b/macros.xml Wed Oct 16 06:27:55 2019 -0400 |
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| @@ -1,11 +1,11 @@ <macros> - <token name="@VERSION@">0.6.19</token> + <token name="@VERSION@">0.6.22.post1</token> <token name="@GALAXY_VERSION@">galaxy0</token> <xml name="requirements"> <requirements> <requirement type="package" version="@VERSION@">anndata</requirement> - <requirement type="package" version="1.4">scanpy</requirement> <requirement type="package" version="2.0.17">loompy</requirement> + <requirement type="package" version="2.9.0">h5py</requirement> <yield /> </requirements> </xml> |
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| diff -r b2a6ce371781 -r 05304c5c195d test-data/manipulate.add_annotation_obs.h5ad |
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| diff -r b2a6ce371781 -r 05304c5c195d test-data/obs_add_annotation.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/obs_add_annotation.tabular Wed Oct 16 06:27:55 2019 -0400 |
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| @@ -0,0 +1,641 @@ +annot1 annot2 +0 progenitor +1 progenitor +2 progenitor +3 progenitor +4 progenitor +5 progenitor +6 progenitor +7 progenitor +8 progenitor +9 progenitor +10 progenitor +11 progenitor +12 progenitor +13 progenitor +14 progenitor +15 progenitor +16 progenitor +17 progenitor +18 progenitor +19 progenitor +20 progenitor +21 progenitor +22 progenitor +23 progenitor +24 progenitor +25 progenitor +26 progenitor +27 progenitor +28 progenitor +29 progenitor +30 progenitor +31 progenitor +32 progenitor +33 progenitor +34 progenitor +35 progenitor +36 progenitor +37 progenitor +38 progenitor +39 progenitor +40 progenitor +41 progenitor +42 progenitor +43 progenitor +44 progenitor +45 progenitor +46 progenitor +47 progenitor +48 progenitor +49 progenitor +50 progenitor +51 progenitor +52 progenitor +53 progenitor +54 progenitor +55 progenitor +56 progenitor +57 progenitor +58 progenitor +59 progenitor +60 progenitor +61 progenitor +62 progenitor +63 progenitor +64 progenitor 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progenitor +31 progenitor +32 progenitor +33 progenitor +34 progenitor +35 progenitor +36 progenitor +37 progenitor +38 progenitor +39 progenitor +40 progenitor +41 progenitor +42 progenitor +43 progenitor +44 progenitor +45 progenitor +46 progenitor +47 progenitor +48 progenitor +49 progenitor +50 progenitor +51 progenitor +52 progenitor +53 progenitor +54 progenitor +55 progenitor +56 progenitor +57 progenitor +58 progenitor +59 progenitor +60 progenitor +61 progenitor +62 progenitor +63 progenitor +64 progenitor +65 progenitor +66 progenitor +67 progenitor +68 progenitor +69 progenitor +70 progenitor +71 progenitor +72 progenitor +73 progenitor +74 progenitor +75 progenitor +76 progenitor +77 progenitor +78 progenitor +79 progenitor +80 Neu +81 Neu +82 Neu +83 Neu +84 Neu +85 Neu +86 Neu +87 Neu +88 Neu +89 Neu +90 Neu +91 Neu +92 Neu +93 Neu +94 Neu +95 Neu +96 Neu +97 Neu +98 Neu +99 Neu +100 Neu +101 Neu +102 Neu +103 Neu +104 Neu +105 Neu +106 Neu +107 Neu +108 Neu +109 Neu +110 Neu +111 Neu +112 Neu +113 Neu +114 Neu +115 Neu +116 Neu +117 Neu +118 Neu +119 Neu +120 Neu +121 Neu +122 Neu +123 Neu +124 Neu +125 Neu +126 Neu +127 Neu +128 Neu +129 Neu +130 Neu +131 Neu +132 Neu +133 Neu +134 Neu +135 Neu +136 Neu +137 Neu +138 Neu +139 Neu +140 Neu +141 Neu +142 Neu +143 Neu +144 Neu +145 Neu +146 Neu +147 Neu +148 Neu +149 Neu +150 Neu +151 Neu +152 Neu +153 Neu +154 Neu +155 Neu +156 Neu +157 Neu +158 Neu +159 Neu |
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| diff -r b2a6ce371781 -r 05304c5c195d test-data/var_add_annotation.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/var_add_annotation.tabular Wed Oct 16 06:27:55 2019 -0400 |
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| @@ -0,0 +1,12 @@ +annot1 annot2 +1 a +2 b +3 c +4 d +5 e +6 f +7 g +8 h +9 i +10 j +11 k |