Mercurial > repos > iuc > anndata_manipulate
changeset 13:7e8c677a7b71 draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
| author | iuc |
|---|---|
| date | Sat, 14 Sep 2024 19:58:00 +0000 |
| parents | ed4996a16f7f |
| children | |
| files | macros.xml manipulate.xml test-data/addloomout1.loom test-data/addloomout3.loom test-data/converted.loom.test test-data/export.krumsiek11.loom test-data/import.csv.h5ad test-data/import.loom.krumsiek11.h5ad test-data/import.mtx.legacy_10x.h5ad test-data/import.mtx.no_10x.h5ad test-data/import.mtx.v3_10x.h5ad test-data/import.tsv.h5ad test-data/import.umi_tools.h5ad test-data/krumsiek11.h5ad test-data/manipulate.add_annotation_obs.h5ad test-data/manipulate.add_annotation_var.h5ad test-data/manipulate.concatenate.h5ad test-data/manipulate.filter_obs_key.h5ad test-data/manipulate.filter_var_index.h5ad test-data/manipulate.obs_names_make_unique.h5ad test-data/manipulate.rename_categories.h5ad test-data/manipulate.save_raw.h5ad test-data/manipulate.strings_to_categoricals.h5ad test-data/manipulate.transpose.h5ad test-data/manipulate.var_names_make_unique.h5ad 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 |
| diffstat | 33 files changed, 290 insertions(+), 37 deletions(-) [+] |
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--- a/macros.xml Sun Nov 12 16:42:25 2023 +0000 +++ b/macros.xml Sat Sep 14 19:58:00 2024 +0000 @@ -1,6 +1,7 @@ <macros> - <token name="@TOOL_VERSION@">0.10.3</token> + <token name="@TOOL_VERSION@">0.10.9</token> <token name="@VERSION_SUFFIX@">0</token> + <token name="@PROFILE@">21.09</token> <xml name="requirements"> <requirements> <requirement type="package" version="@TOOL_VERSION@">anndata</requirement> @@ -21,12 +22,6 @@ python '$script_file' ]]> </token> - <token name="@LOOMCMD@"><![CDATA[ -mkdir ./output && -mkdir ./attributes && -python '$__tool_directory__/loompy_to_tsv.py' -f '${hd5_format.input}' - ]]> - </token> <token name="@CMD_imports@"><![CDATA[ import anndata as ad ]]> @@ -76,4 +71,11 @@ </when> </conditional> </xml> + <xml name="sanitize_query" token_validinitial="string.printable"> + <sanitizer> + <valid initial="@VALIDINITIAL@"> + <remove value="'" /> + </valid> + </sanitizer> + </xml> </macros>
--- a/manipulate.xml Sun Nov 12 16:42:25 2023 +0000 +++ b/manipulate.xml Sat Sep 14 19:58:00 2024 +0000 @@ -1,4 +1,4 @@ -<tool id="anndata_manipulate" name="Manipulate AnnData" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@"> +<tool id="anndata_manipulate" name="Manipulate AnnData" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@"> <description>object</description> <macros> <import>macros.xml</import> @@ -50,6 +50,27 @@ key='$manipulate.key', categories=$categories) +#else if $manipulate.function == 'remove_keys' + #if $manipulate.obs_keys + #set $keys = [x.strip() for x in str($manipulate.obs_keys).split(',')] +adata.obs = adata.obs.drop(columns=$keys) + #end if + + #if $manipulate.var_keys + #set $keys = [x.strip() for x in str($manipulate.var_keys).split(',')] +adata.var = adata.vars.drop(columns=$keys) + #end if + +#else if $manipulate.function == 'flag_genes' +## adapted from anndata operations + #for $flag in $manipulate.gene_flags +k_cat = adata.var_names.str.startswith('${flag.startswith}') +if k_cat.sum() > 0: + adata.var['${flag.col_name}'] = k_cat +else: + print(f'No genes starting with {'${flag.startswith}'} found.') +#end for + #else if $manipulate.function == 'strings_to_categoricals' adata.strings_to_categoricals() @@ -71,6 +92,14 @@ adata.obs = obs #end if +#else if $manipulate.function == 'split_on_obs' +import os +res_dir = "output_split" +os.makedirs(res_dir, exist_ok=True) +for s,field_value in enumerate(adata.obs["${manipulate.key}"].unique()): + ad_s = adata[adata.obs.${manipulate.key} == field_value] + ad_s.write(f"{res_dir}/${manipulate.key}_{s}.h5ad", compression='gzip') + #else if $manipulate.function == 'filter' #if $manipulate.filter.filter == 'key' #if $manipulate.var_obs == 'var' @@ -126,7 +155,11 @@ #end if -adata.write('anndata.h5ad') +#if $manipulate.function != 'split_on_obs' +adata.write('anndata.h5ad', compression='gzip') +print(adata) +#end if + ]]></configfile> </configfiles> <inputs> @@ -137,9 +170,12 @@ <option value="obs_names_make_unique">Makes the obs index unique by appending '1', '2', etc</option> <option value="var_names_make_unique">Makes the var index unique by appending '1', '2', etc</option> <option value="rename_categories">Rename categories of annotation</option> + <option value="remove_keys">Remove keys from obs or var annotations</option> + <option value="flag_genes">Flag genes start with a pattern</option><!--adapted from EBI anndata operations tool --> <option value="strings_to_categoricals">Transform string annotations to categoricals</option> <option value="transpose">Transpose the data matrix, leaving observations and variables interchanged</option> <option value="add_annotation">Add new annotation(s) for observations or variables</option> + <option value="split_on_obs">Split the AnnData object into multiple AnnData objects based on the values of a given obs key</option><!--adapted from EBI anndata operations tool--> <option value="filter">Filter observations or variables</option> <option value="save_raw">Freeze the current state into the 'raw' attribute</option> </param> @@ -167,6 +203,26 @@ <param name="key" type="text" value="" label="Key for observations or variables annotation" help="Annotation key in obs or var"/> <param name="categories" type="text" value="" label="Comma-separated list of new categories" help="It should be the same number as the old categories"/> </when> + <when value="remove_keys"> + <param name="obs_keys" type="text" value="" optional="true" label="Keys/fields to remove from observations (obs)"> + <expand macro="sanitize_query"/> + </param> + <param name="var_keys" type="text" value="" optional="true" label="Keys/fields to remove from variables (var)"> + <expand macro="sanitize_query"/> + </param> + </when> + <when value="flag_genes"> + <repeat name="gene_flags" title="Flag genes that start with these names"> + <param name="startswith" type="text" label="Text that you expect the genes to be flagged to start with" help="For example, 'MT-' for mito genes"> + <sanitizer invalid_char=""> + <valid initial="string.ascii_letters,string.digits,string.punctuation"> + <remove value="'" /> + </valid> + </sanitizer> + </param> + <param name="col_name" type="text" label="Name of the column in var.names where this boolean flag is stored" help="For example, name this column as 'mito' for mitochondrial genes."/> + </repeat> + </when> <when value="strings_to_categoricals" ></when> <when value="transpose" ></when> <when value="add_annotation"> @@ -177,6 +233,15 @@ <param name="new_annot" type="data" format="tabular" label="Table with new annotations" help="The new table should have the same number of rows and same order than obs or var. The key names should be in the header (1st line)"/> </when> + <when value="split_on_obs"> + <param name="key" type="text" label="The obs key to split on" help="For example, if you want to split on cluster annotation, you can use the key 'louvain'. The output will be a collection of anndata objects"> + <sanitizer invalid_char=""> + <valid initial="string.ascii_letters,string.digits,string.punctuation"> + <remove value="'" /> + </valid> + </sanitizer> + </param> + </when> <when value="filter"> <param name="var_obs" type="select" label="What to filter?"> <option value="var">Variables (var)</option> @@ -237,10 +302,16 @@ </conditional> </inputs> <outputs> - <data name="anndata" format="h5ad" from_work_dir="anndata.h5ad" label="${tool.name} (${manipulate.function}) on ${on_string}"/> + <data name="anndata" format="h5ad" from_work_dir="anndata.h5ad" label="${tool.name} (${manipulate.function}) on ${on_string}"> + <filter>manipulate['function'] != 'split_on_obs'</filter> + </data> + <collection name="output_h5ad_split" type="list" label="${tool.name} (${manipulate.function}) on ${on_string} Collection"> + <discover_datasets pattern="(?P<designation>.+)\.h5" directory="output_split" format="h5ad" visible="true"/> + <filter>manipulate['function'] == 'split_on_obs'</filter> + </collection> </outputs> <tests> - <test> + <test expect_num_outputs="1"> <!-- test 1 --> <param name="input" value="import.csv.h5ad"/> <conditional name="manipulate"> @@ -256,10 +327,15 @@ <has_text_matching expression="join='inner'"/> <has_text_matching expression="index_unique='-'"/> <has_text_matching expression="batch_key='batch'"/> + <has_text_matching expression="6 × 2"/> </assert_stdout> - <output name="anndata" value="manipulate.concatenate.h5ad" ftype="h5ad" compare="sim_size"/> + <output name="anndata" ftype="h5ad"> + <assert_contents> + <has_h5_keys keys="obs/batch"/> + </assert_contents> + </output> </test> - <test> + <test expect_num_outputs="1"> <!-- test 2 --> <param name="input" value="krumsiek11.h5ad"/> <conditional name="manipulate"> @@ -268,10 +344,17 @@ </conditional> <assert_stdout> <has_text_matching expression="adata.obs_names_make_unique\(join='-'\)"/> + <has_text_matching expression="500 × 11"/> </assert_stdout> - <output name="anndata" value="manipulate.obs_names_make_unique.h5ad" ftype="h5ad" compare="sim_size"/> + <output name="anndata" ftype="h5ad"> + <assert_contents> + <has_h5_keys keys="obs/cell_type"/> + <has_h5_keys keys="uns/highlights"/> + <has_h5_keys keys="uns/iroot"/> + </assert_contents> + </output> </test> - <test> + <test expect_num_outputs="1"> <!-- test 3 --> <param name="input" value="krumsiek11.h5ad"/> <conditional name="manipulate"> @@ -280,25 +363,39 @@ </conditional> <assert_stdout> <has_text_matching expression="adata.var_names_make_unique\(join='-'\)"/> + <has_text_matching expression="500 × 11"/> </assert_stdout> - <output name="anndata" value="manipulate.var_names_make_unique.h5ad" ftype="h5ad" compare="sim_size"/> + <output name="anndata" ftype="h5ad"> + <assert_contents> + <has_h5_keys keys="obs/cell_type"/> + <has_h5_keys keys="uns/highlights"/> + <has_h5_keys keys="uns/iroot"/> + </assert_contents> + </output> </test> - <test> + <test expect_num_outputs="1"> <!-- test 4 --> <param name="input" value="krumsiek11.h5ad"/> <conditional name="manipulate"> <param name="function" value="rename_categories"/> <param name="key" value="cell_type"/> - <param name="categories" value="Ery, Mk, Mo, progenitor"/> + <param name="categories" value="ery, mk, mo, progenitor"/> </conditional> <assert_stdout> <has_text_matching expression="adata.rename_categories"/> <has_text_matching expression="key='cell_type'"/> - <has_text_matching expression="categories=\['Ery', 'Mk', 'Mo', 'progenitor'\]"/> + <has_text_matching expression="categories=\['ery', 'mk', 'mo', 'progenitor'\]"/> + <has_text_matching expression="500 × 11"/> </assert_stdout> - <output name="anndata" value="manipulate.rename_categories.h5ad" ftype="h5ad" compare="sim_size"/> + <output name="anndata" ftype="h5ad"> + <assert_contents> + <has_h5_keys keys="obs/cell_type"/> + <has_h5_keys keys="uns/highlights"/> + <has_h5_keys keys="uns/iroot"/> + </assert_contents> + </output> </test> - <test> + <test expect_num_outputs="1"> <!-- test 5 --> <param name="input" value="krumsiek11.h5ad"/> <conditional name="manipulate"> @@ -306,10 +403,17 @@ </conditional> <assert_stdout> <has_text_matching expression="adata.strings_to_categoricals"/> + <has_text_matching expression="500 × 11"/> </assert_stdout> - <output name="anndata" value="manipulate.strings_to_categoricals.h5ad" ftype="h5ad" compare="sim_size"/> + <output name="anndata" ftype="h5ad"> + <assert_contents> + <has_h5_keys keys="obs/cell_type"/> + <has_h5_keys keys="uns/highlights"/> + <has_h5_keys keys="uns/iroot"/> + </assert_contents> + </output> </test> - <test> + <test expect_num_outputs="1"> <!-- test 6 --> <param name="input" value="krumsiek11.h5ad"/> <conditional name="manipulate"> @@ -317,10 +421,17 @@ </conditional> <assert_stdout> <has_text_matching expression="adata.transpose"/> + <has_text_matching expression="11 × 500"/> </assert_stdout> - <output name="anndata" value="manipulate.transpose.h5ad" ftype="h5ad" compare="sim_size"/> + <output name="anndata" ftype="h5ad"> + <assert_contents> + <has_h5_keys keys="var/cell_type"/> + <has_h5_keys keys="uns/highlights"/> + <has_h5_keys keys="uns/iroot"/> + </assert_contents> + </output> </test> - <test> + <test expect_num_outputs="1"> <!-- test 7 --> <param name="input" value="krumsiek11.h5ad"/> <conditional name="manipulate"> @@ -328,9 +439,20 @@ <param name="var_obs" value="var"/> <param name="new_annot" value="var_add_annotation.tabular"/> </conditional> - <output name="anndata" value="manipulate.add_annotation_var.h5ad" ftype="h5ad" compare="sim_size"/> + <assert_stdout> + <has_text_matching expression="500 × 11"/> + </assert_stdout> + <output name="anndata" ftype="h5ad"> + <assert_contents> + <has_h5_keys keys="obs/cell_type"/> + <has_h5_keys keys="var/annot1"/> + <has_h5_keys keys="var/annot2"/> + <has_h5_keys keys="uns/highlights"/> + <has_h5_keys keys="uns/iroot"/> + </assert_contents> + </output> </test> - <test> + <test expect_num_outputs="1"> <!-- test 8 --> <param name="input" value="krumsiek11.h5ad"/> <conditional name="manipulate"> @@ -338,9 +460,20 @@ <param name="var_obs" value="obs"/> <param name="new_annot" value="obs_add_annotation.tabular"/> </conditional> - <output name="anndata" value="manipulate.add_annotation_obs.h5ad" ftype="h5ad" compare="sim_size"/> + <assert_stdout> + <has_text_matching expression="500 × 11"/> + </assert_stdout> + <output name="anndata" ftype="h5ad"> + <assert_contents> + <has_h5_keys keys="obs/cell_type"/> + <has_h5_keys keys="obs/annot1"/> + <has_h5_keys keys="obs/annot2"/> + <has_h5_keys keys="uns/highlights"/> + <has_h5_keys keys="uns/iroot"/> + </assert_contents> + </output> </test> - <test> + <test expect_num_outputs="1"> <!-- test 9 --> <param name="input" value="krumsiek11.h5ad"/> <conditional name="manipulate"> @@ -354,9 +487,18 @@ </conditional> </conditional> </conditional> - <output name="anndata" value="manipulate.filter_var_index.h5ad" ftype="h5ad" compare="sim_size"/> + <assert_stdout> + <has_text_matching expression="500 × 2"/> + </assert_stdout> + <output name="anndata" ftype="h5ad"> + <assert_contents> + <has_h5_keys keys="obs/cell_type"/> + <has_h5_keys keys="uns/highlights"/> + <has_h5_keys keys="uns/iroot"/> + </assert_contents> + </output> </test> - <test> + <test expect_num_outputs="1"> <!-- test 10 --> <param name="input" value="krumsiek11.h5ad"/> <conditional name="manipulate"> @@ -372,23 +514,120 @@ </conditional> </conditional> </conditional> - <output name="anndata" value="manipulate.filter_obs_key.h5ad" ftype="h5ad" compare="sim_size"/> + <assert_stdout> + <has_text_matching expression="260 × 11"/> + </assert_stdout> + <output name="anndata" ftype="h5ad"> + <assert_contents> + <has_h5_keys keys="obs/cell_type"/> + <has_h5_keys keys="uns/highlights"/> + <has_h5_keys keys="uns/iroot"/> + </assert_contents> + </output> </test> - <test> + <test expect_num_outputs="1"> <!-- test 11 --> <param name="input" value="krumsiek11.h5ad"/> <conditional name="manipulate"> <param name="function" value="save_raw"/> </conditional> - <output name="anndata" value="manipulate.save_raw.h5ad" ftype="h5ad" compare="sim_size" delta="20000" /> + <assert_stdout> + <has_text_matching expression="500 × 11"/> + </assert_stdout> + <output name="anndata" ftype="h5ad"> + <assert_contents> + <has_h5_keys keys="obs/cell_type"/> + <has_h5_keys keys="uns/highlights"/> + <has_h5_keys keys="uns/iroot"/> + </assert_contents> + </output> + </test> + <test expect_num_outputs="1"> + <!-- test 12 remove_keys --> + <param name="input" value="krumsiek11.h5ad"/> + <conditional name="manipulate"> + <param name="function" value="remove_keys"/> + <param name="obs_keys" value="cell_type"/> + </conditional> + <assert_stdout> + <has_text_matching expression="500 × 11"/> + </assert_stdout> + <output name="anndata" ftype="h5ad"> + <assert_contents> + <has_h5_keys keys="uns/highlights"/> + <has_h5_keys keys="uns/iroot"/> + </assert_contents> + </output> + </test> + <test expect_num_outputs="1"> + <!-- test 13 flag_genes --> + <param name="input" value="krumsiek11.h5ad"/> + <conditional name="manipulate"> + <param name="function" value="flag_genes"/> + <repeat name="gene_flags"> + <param name="startswith" value="Gata"/> + <param name="col_name" value="Gata_TF"/> + </repeat> + <repeat name="gene_flags"> + <param name="startswith" value="Gf"/> + <param name="col_name" value="GF"/> + </repeat> + </conditional> + <assert_stdout> + <has_text_matching expression="500 × 11"/> + </assert_stdout> + <output name="anndata" ftype="h5ad"> + <assert_contents> + <has_h5_keys keys="var/Gata_TF"/> + <has_h5_keys keys="var/GF"/> + </assert_contents> + </output> + </test> + <test expect_num_outputs="1"> + <!-- test 14 split_on_obs --> + <param name="input" value="krumsiek11.h5ad"/> + <conditional name="manipulate"> + <param name="function" value="split_on_obs"/> + <param name="key" value="cell_type"/> + </conditional> + <output_collection name="output_h5ad_split" type="list"> + <element name="cell_type_0"> + <assert_contents> + <has_h5_keys keys="obs/cell_type"/> + <has_h5_keys keys="uns/highlights"/> + <has_h5_keys keys="uns/iroot"/> + </assert_contents> + </element> + <element name="cell_type_1"> + <assert_contents> + <has_h5_keys keys="obs/cell_type"/> + <has_h5_keys keys="uns/highlights"/> + <has_h5_keys keys="uns/iroot"/> + </assert_contents> + </element> + <element name="cell_type_2"> + <assert_contents> + <has_h5_keys keys="obs/cell_type"/> + <has_h5_keys keys="uns/highlights"/> + <has_h5_keys keys="uns/iroot"/> + </assert_contents> + </element> + <element name="cell_type_3"> + <assert_contents> + <has_h5_keys keys="obs/cell_type"/> + <has_h5_keys keys="uns/highlights"/> + <has_h5_keys keys="uns/iroot"/> + </assert_contents> + </element> + </output_collection> </test> </tests> <help><![CDATA[ **What it does** -This tool takes a AnnData dataset, manipulates it and returns it. +This tool takes a AnnData dataset, manipulates it and returns it. -The possible manipulations are: +The possible manipulations are: - Concatenate along the observations axis (`concatenate method <https://anndata.readthedocs.io/en/latest/generated/anndata.AnnData.concatenate.html>`__) @@ -408,6 +647,14 @@ Besides calling `self.obs[key].cat.categories = categories` - similar for `var` - this also renames categories in unstructured annotation that uses the categorical annotation `key` +- Remove keys from obs or var annotations + + Helps in cleaning up andata with many annotations. For example, helps in removing qc metrics calculated during the preprocesing or already existing cluster annotations. + +- Flag genes start with a pattern + + Useful for flagging the mitochoncdrial or ribosomal protein genes + - Transform string annotations to categoricals (`strings_to_categoricals method <https://anndata.readthedocs.io/en/latest/generated/anndata.AnnData.strings_to_categoricals.html>`__) Only affects string annotations that lead to less categories than the total number of observations. @@ -416,7 +663,11 @@ Data matrix is transposed, observations and variables are interchanged. -- Add annotation for variables or observations +- Add annotation for variables or + +- Split the AnnData object into multiple AnnData objects based on the values of a given obs key + + 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. - Filter data variables or observations, by index or key
Binary file test-data/pp.neighbors_umap_euclidean.recipe_weinreb17.paul15_subsample.h5ad has changed