| Previous changeset 0:0ef28c0963c8 (2019-04-10) Next changeset 2:a56baceb1900 (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:
macros.xml manipulate.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 0ef28c0963c8 -r 19592ec717ef macros.xml --- a/macros.xml Wed Apr 10 03:25:05 2019 -0400 +++ b/macros.xml Wed Oct 16 06:26:45 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 0ef28c0963c8 -r 19592ec717ef manipulate.xml --- a/manipulate.xml Wed Apr 10 03:25:05 2019 -0400 +++ b/manipulate.xml Wed Oct 16 06:26:45 2019 -0400 |
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| b'@@ -50,11 +50,76 @@\n key=\'$manipulate.key\',\n categories=$categories)\n \n-#else if $manipulate.function == \'transpose\'\n-adata.transpose()\n-\n #else if $manipulate.function == \'strings_to_categoricals\'\n adata.strings_to_categoricals()\n+\n+#else if $manipulate.function == \'transpose\'\n+adata = adata.transpose()\n+\n+#else if $manipulate.function == \'add_annotation\'\n+import pandas as pd\n+extra_annot_t = pd.read_csv(\'$manipulate.new_annot\', sep=\'\\t\').reset_index(drop=True)\n+ #if $manipulate.var_obs == \'var\'\n+var_index = adata.var_names\n+var = pd.concat([adata.var.reset_index(drop=True), extra_annot_t], axis=1)\n+var.index = var_index\n+adata.var = var\n+ #else if $manipulate.var_obs == \'obs\'\n+obs_index = adata.obs.index\n+obs = pd.concat([adata.obs.reset_index(drop=True), extra_annot_t], axis=1)\n+obs.index = obs_index\n+adata.obs = obs\n+ #end if\n+\n+#else if $manipulate.function == \'filter\'\n+ #if $manipulate.filter.filter == \'key\'\n+ #if $manipulate.var_obs == \'var\'\n+filtered = adata.var[\'$manipulate.filter.key\']\n+ #else if $manipulate.var_obs == \'obs\'\n+filtered = adata.obs[\'$manipulate.filter.key\']\n+ #end if\n+\n+ #if $manipulate.filter.filter_key.type == \'number\'\n+ #if $manipulate.filter.filter_key.filter == \'equal\'\n+filtered = filtered == $manipulate.filter.filter_key.value\n+ #else if $manipulate.filter.filter_key.filter == \'equal\'\n+filtered = filtered != $manipulate.filter.filter_key.value\n+ #else if $manipulate.filter.filter_key.filter == \'less\'\n+filtered = filtered < $manipulate.filter.filter_key.value\n+ #else if $manipulate.filter.filter_key.filter == \'less_or_equal\'\n+filtered = filtered <= $manipulate.filter.filter_key.value\n+ #else if $manipulate.filter.filter_key.filter == \'greater\'\n+filtered = filtered > $manipulate.filter.filter_key.value\n+ #else if $manipulate.filter.filter_key.filter == \'greater_or_equal\'\n+filtered = filtered >= $manipulate.filter.filter_key.value\n+ #end if\n+ #else if $manipulate.filter.filter_key.type == \'text\'\n+ #if $manipulate.filter.filter_key.filter == \'equal\'\n+filtered = filtered == \'$manipulate.filter.filter_key.value\'\n+ #else\n+filtered = filtered != \'$manipulate.filter.filter_key.value\'\n+ #end if\n+ #else if $manipulate.filter.filter_key.type == \'boolean\'\n+filtered = filtered == $manipulate.filter.filter_key.value\n+ #end if\n+\n+ #else if $manipulate.filter.filter == \'index\'\n+ #if str($manipulate.filter.index.format) == \'file\'\n+with open(\'$manipulate.filter.index.file\', \'r\') as filter_f:\n+ filters = [str(x.strip()) for x in filter_f.readlines()]\n+filtered = filters\n+ #else\n+ #set $filters = [str(x.strip()) for x in $manipulate.filter.index.text.split(\',\')]\n+filtered = $filters\n+ #end if\n+ #end if\n+print(filtered)\n+\n+ #if $manipulate.var_obs == \'var\'\n+adata = adata[:,filtered]\n+ #else if $manipulate.var_obs == \'obs\'\n+adata = adata[filtered, :]\n+ #end if\n #end if\n \n adata.write(\'anndata.h5ad\')\n@@ -70,6 +135,8 @@\n <option value="rename_categories">Rename categories of annotation</option>\n <option value="strings_to_categoricals">Transform string annotations to categoricals</option>\n <option value="transpose">Transpose the data matrix, leaving observations and variables interchanged</option>\n+ <option value="add_annotation">Add new annotation(s) for observations or variables</option>\n+ <option value="filter">Filter observations or variables</option>\n </param>\n <when value="concatenate">\n <param name="other_adatas" type="data" format="h5ad" multiple="true" label="Annotated data matrix to add"/>\n@@ -97,13 +164,78 @@\n </when>\n <when value="strings_to_categoricals"/>\n <when value="transpose"/>\n+ <when value="add_annotation">\n+ '..b'5ad"/>\n <conditional name="manipulate">\n <param name="function" value="rename_categories"/>\n@@ -158,6 +293,7 @@\n <output name="anndata" value="manipulate.rename_categories.h5ad" ftype="h5ad" compare="sim_size"/>\n </test>\n <test>\n+ <!-- test 5 -->\n <param name="input" value="krumsiek11.h5ad"/>\n <conditional name="manipulate">\n <param name="function" value="strings_to_categoricals"/>\n@@ -168,6 +304,7 @@\n <output name="anndata" value="manipulate.strings_to_categoricals.h5ad" ftype="h5ad" compare="sim_size"/>\n </test>\n <test>\n+ <!-- test 6 -->\n <param name="input" value="krumsiek11.h5ad"/>\n <conditional name="manipulate">\n <param name="function" value="transpose"/>\n@@ -177,6 +314,60 @@\n </assert_stdout>\n <output name="anndata" value="manipulate.transpose.h5ad" ftype="h5ad" compare="sim_size"/>\n </test>\n+ <test>\n+ <!-- test 7 -->\n+ <param name="input" value="krumsiek11.h5ad"/>\n+ <conditional name="manipulate">\n+ <param name="function" value="add_annotation"/>\n+ <param name="var_obs" value="var"/>\n+ <param name="new_annot" value="var_add_annotation.tabular"/>\n+ </conditional>\n+ <output name="anndata" value="manipulate.add_annotation_var.h5ad" ftype="h5ad" compare="sim_size"/>\n+ </test>\n+ <test>\n+ <!-- test 8 -->\n+ <param name="input" value="krumsiek11.h5ad"/>\n+ <conditional name="manipulate">\n+ <param name="function" value="add_annotation"/>\n+ <param name="var_obs" value="obs"/>\n+ <param name="new_annot" value="obs_add_annotation.tabular"/>\n+ </conditional>\n+ <output name="anndata" value="manipulate.add_annotation_obs.h5ad" ftype="h5ad" compare="sim_size"/>\n+ </test>\n+ <test>\n+ <!-- test 9 -->\n+ <param name="input" value="krumsiek11.h5ad"/>\n+ <conditional name="manipulate">\n+ <param name="function" value="filter"/>\n+ <param name="var_obs" value="var"/>\n+ <conditional name="filter">\n+ <param name="filter" value="index"/>\n+ <conditional name="index">\n+ <param name="format" value="text"/>\n+ <param name="text" value="Gata2,EKLF"/>\n+ </conditional>\n+ </conditional>\n+ </conditional>\n+ <output name="anndata" value="manipulate.filter_var_index.h5ad" ftype="h5ad" compare="sim_size"/>\n+ </test>\n+ <test>\n+ <!-- test 10 -->\n+ <param name="input" value="krumsiek11.h5ad"/>\n+ <conditional name="manipulate">\n+ <param name="function" value="filter"/>\n+ <param name="var_obs" value="obs"/>\n+ <conditional name="filter">\n+ <param name="filter" value="key"/>\n+ <param name="key" value="cell_type"/>\n+ <conditional name="filter_key">\n+ <param name="type" value="text"/>\n+ <param name="filter" value="equal"/>\n+ <param name="value" value="progenitor"/>\n+ </conditional>\n+ </conditional>\n+ </conditional>\n+ <output name="anndata" value="manipulate.filter_obs_key.h5ad" ftype="h5ad" compare="sim_size"/>\n+ </test>\n </tests>\n <help><![CDATA[\n **What it does**\n@@ -211,6 +402,10 @@\n \n Data matrix is transposed, observations and variables are interchanged.\n \n+- Add annotation for variables or observations \n+\n+- Filter data variables or observations, by index or key\n+\n @HELP@\n ]]></help>\n <expand macro="citations"/>\n' |
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| diff -r 0ef28c0963c8 -r 19592ec717ef test-data/manipulate.filter_var_index.h5ad |
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| diff -r 0ef28c0963c8 -r 19592ec717ef 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 06:26:45 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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| diff -r 0ef28c0963c8 -r 19592ec717ef 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 06:26:45 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 |