| Previous changeset 14:c4209ea387d4 (2024-11-08) |
|
Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 4f6d044223f374ba44a4d46ad77559ca781e6db7 |
|
modified:
macros.xml manipulate.xml test-data/tl.umap.h5ad |
|
added:
test-data/flag_new_key.h5ad |
| b |
| diff -r c4209ea387d4 -r d1e49c3c0aa2 macros.xml --- a/macros.xml Fri Nov 08 21:59:34 2024 +0000 +++ b/macros.xml Sat Jan 11 21:10:19 2025 +0000 |
| b |
| @@ -1,6 +1,6 @@ <macros> <token name="@TOOL_VERSION@">0.10.9</token> - <token name="@VERSION_SUFFIX@">0</token> + <token name="@VERSION_SUFFIX@">1</token> <token name="@PROFILE@">21.09</token> <xml name="requirements"> <requirements> |
| b |
| diff -r c4209ea387d4 -r d1e49c3c0aa2 manipulate.xml --- a/manipulate.xml Fri Nov 08 21:59:34 2024 +0000 +++ b/manipulate.xml Sat Jan 11 21:10:19 2025 +0000 |
| [ |
| b'@@ -37,6 +37,11 @@\n #else\n index_unique=None,\n #end if\n+ #if str($manipulate.uns_merge) != \'None\'\n+ uns_merge=\'$manipulate.uns_merge\',\n+ #else\n+ uns_merge=None,\n+ #end if\n batch_key=\'$manipulate.batch_key\')\n \n #else if $manipulate.function == \'var_names_make_unique\'\n@@ -47,9 +52,30 @@\n \n #else if $manipulate.function == \'rename_categories\'\n #set $categories = [x.strip() for x in str($manipulate.categories).split(\',\')]\n+ #if $manipulate.update_key.new_key == \'no\':\n adata.rename_categories(\n key=\'$manipulate.key\',\n categories=$categories)\n+ #else\n+if \'$manipulate.key\' in adata.obs:\n+ print("changing key in obs")\n+ adata.obs[\'$manipulate.key_name\'] = adata.obs[\'$manipulate.key\']\n+ adata.rename_categories(\n+ key=\'$manipulate.key_name\',\n+ categories=$categories)\n+elif \'$manipulate.key\' in adata.var:\n+ print("changing key in var")\n+ adata.var[\'$manipulate.key_name\'] = adata.var[\'$manipulate.key\']\n+ adata.rename_categories(\n+ key=\'$manipulate.key_name\',\n+ categories=$categories)\n+else:\n+ print("chanigng key in uns")\n+ adata.uns[\'$manipulate.key_name\'] = adata.uns[\'$manipulate.key\']\n+ adata.rename_categories(\n+ key=\'$manipulate.key_name\',\n+ categories=$categories)\n+ #end if\n \n #else if $manipulate.function == \'remove_keys\'\n #if $manipulate.obs_keys\n@@ -65,13 +91,29 @@\n #else if $manipulate.function == \'flag_genes\'\n ## adapted from anndata operations\n #for $flag in $manipulate.gene_flags\n+ #if str($flag.col_in) != \'\':\n+k_cat = adata.var[\'${flag.col_in}\'].str.startswith(\'${flag.startswith}\')\n+ #else:\n k_cat = adata.var_names.str.startswith(\'${flag.startswith}\')\n+ #end if\n if k_cat.sum() > 0:\n- adata.var[\'${flag.col_name}\'] = k_cat\n+ adata.var[\'${flag.col_out}\'] = k_cat\n else:\n print(f\'No genes starting with {\'${flag.startswith}\'} found.\')\n #end for\n \n+#else if $manipulate.function == \'rename_obs\':\n+adata.obs[\'${to_obs}\'] = adata.obs[\'${from_obs}\']\n+#if not $keep_original:\n+del adata.obs[\'${from_obs}\']\n+#end if\n+\n+#else if $manipulate.function == \'rename_var\':\n+adata.var[\'${to_var}\'] = adata.var[\'${from_var}\']\n+#if not $keep_original:\n+del adata.var[\'${from_var}\']\n+#end if\n+\n #else if $manipulate.function == \'strings_to_categoricals\'\n adata.strings_to_categoricals()\n \n@@ -101,54 +143,64 @@\n ad_s = adata[adata.obs.${manipulate.key} == field_value]\n ad_s.write(f"{res_dir}/${manipulate.key}_{s}.h5ad", compression=\'gzip\')\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+#else if $manipulate.function == \'copy_obs\'\n+source_adata = ad.read_h5ad(\'$source_adata\')\n+ #for $key in $manipulate.keys\n+if \'$key.source_key\' in source_adata.obs:\n+ #if str($key.target_key) == \'\':\n+ adata.obs[\'$key.source_key\'] = source_adata.obs[\'$key.source_key\']\n+ #else\n+ adata.obs[\'$key.target_key\'] = source_adata.obs[\'$key.source_key\']\n #end if\n+else:\n+ print(f"Obs column {\'{$key.source_key}\'} not found in source AnnData.")\n+ #end for\n+\n+#else if $manipulate.function == \'copy_uns\'\n+source_adata = ad.read_h5ad(\'$source_adata\')\n+ #for $key in $manipulate.keys\n+if \'$key.source_key\' in source_adata.uns:\n+ #if str($key.target_key) == \'\':\n+ adata.uns[\'$key.source_key\'] = source_adata.uns[\'$key.source_key\']\n+ #else\n+ adata.uns[\'$key.target_key\'] = source_adata.uns[\'$key.source_key\']\n+ #end if\n+else:\n+ print(f"Uns key {\'{$key.source_key}\'} not found in source AnnData.")\n+ #end for\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.fi'..b'unction" value="rename_obs"/>\n+ <param name="from_obs" value="cell_type"/>\n+ <param name="to_obs" value="new_cell_type"/>\n+ <param name="keep_original" value="false"/>\n+ </conditional>\n+ <assert_stdout>\n+ <has_text_matching expression="adata.obs\\[\'new_cell_type\'\\] = adata.obs\\[\'cell_type\'\\]"/>\n+ <has_text_matching expression="del adata.obs\\[\'cell_type\'\\]"/>\n+ <has_text_matching expression="500 \xc3\x97 11"/>\n+ </assert_stdout>\n+ <output name="anndata" ftype="h5ad">\n+ <assert_contents>\n+ <has_h5_keys keys="obs/new_cell_type"/>\n+ <has_h5_keys keys="uns/highlights"/>\n+ <has_h5_keys keys="uns/iroot"/>\n+ </assert_contents>\n+ </output>\n+ </test>\n+ <test expect_num_outputs="1">\n+ <!-- test 22 rename_var -->\n+ <param name="input" value="flag_new_key.h5ad"/>\n+ <conditional name="manipulate">\n+ <param name="function" value="rename_var"/>\n+ <param name="from_var" value="gene_ids"/>\n+ <param name="to_var" value="new_id"/>\n+ <param name="keep_original" value="false"/>\n+ </conditional>\n+ <assert_stdout>\n+ <has_text_matching expression="adata.var\\[\'new_id\'\\] = adata.var\\[\'gene_ids\'\\]"/>\n+ <has_text_matching expression="del adata.var\\[\'gene_ids\'\\]"/>\n+ <has_text_matching expression="199 \xc3\x97 199"/>\n+ </assert_stdout>\n+ <output name="anndata" ftype="h5ad">\n+ <assert_contents>\n+ <has_h5_keys keys="var/feature_types"/>\n+ <has_h5_keys keys="var/test"/>\n+ <has_h5_keys keys="var/new_id"/>\n+ </assert_contents>\n+ </output>\n+ </test>\n </tests>\n <help><![CDATA[\n **What it does**\n \n-This tool takes a AnnData dataset, manipulates it and returns it.\n+This tool takes an AnnData dataset, manipulates it and returns it.\n \n The possible manipulations are:\n \n@@ -638,11 +930,11 @@\n \n - Makes the obs index unique by appending \'1\', \'2\', etc (`obs_names_make_unique method <https://anndata.readthedocs.io/en/latest/generated/anndata.AnnData.obs_names_make_unique.html>`__)\n \n- The first occurance of a non-unique value is ignored.\n+ The first occurrence of a non-unique value is ignored.\n \n - Makes the var index unique by appending \'1\', \'2\', etc (`var_names_make_unique method <https://anndata.readthedocs.io/en/latest/generated/anndata.AnnData.var_names_make_unique.html>`__)\n \n- The first occurance of a non-unique value is ignored.\n+ The first occurrence of a non-unique value is ignored.\n \n - Rename categories of annotation `key` in `obs`, `var` and `uns` (`rename_categories method <https://anndata.readthedocs.io/en/latest/generated/anndata.AnnData.rename_categories.html>`__)\n \n@@ -654,7 +946,7 @@\n \n - Flag genes start with a pattern\n \n- Useful for flagging the mitochoncdrial or ribosomal protein genes\n+ Useful for flagging the mitochondrial or ribosomal protein genes\n \n - Transform string annotations to categoricals (`strings_to_categoricals method <https://anndata.readthedocs.io/en/latest/generated/anndata.AnnData.strings_to_categoricals.html>`__)\n \n@@ -668,7 +960,7 @@\n \n - Split the AnnData object into multiple AnnData objects based on the values of a given obs key\n \n- For example, helps in splitting an anndata objects based on cluster annotation. This function generates a collection with number of elements equal to the number of categories in the input obs key.\n+ For example, helps in splitting an anndata objects based on cluster annotation. This function generates a collection with a number of elements equal to the number of categories in the input obs key.\n \n - Filter data variables or observations, by index or key\n \n' |
| b |
| diff -r c4209ea387d4 -r d1e49c3c0aa2 test-data/flag_new_key.h5ad |
| b |
| Binary file test-data/flag_new_key.h5ad has changed |
| b |
| diff -r c4209ea387d4 -r d1e49c3c0aa2 test-data/tl.umap.h5ad |
| b |
| Binary file test-data/tl.umap.h5ad has changed |