anndata_manipulate: manipulate.xml comparison

comparison manipulate.xml @ 15:d1e49c3c0aa2 draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 4f6d044223f374ba44a4d46ad77559ca781e6db7

author	iuc
date	Sat, 11 Jan 2025 21:10:19 +0000
parents	c4209ea387d4
children

comparison

equal deleted inserted replaced

-:c4209ea387d4
+:d1e49c3c0aa2
 #if str($manipulate.index_unique) != ''
 index_unique='$manipulate.index_unique',
 #else
 index_unique=None,
 #end if
+#if str($manipulate.uns_merge) != 'None'
+uns_merge='$manipulate.uns_merge',
+#else
+uns_merge=None,
+#end if
 batch_key='$manipulate.batch_key')
 #else if $manipulate.function == 'var_names_make_unique'
 adata.var_names_make_unique(join='$manipulate.join')
 #else if $manipulate.function == 'obs_names_make_unique'
 adata.obs_names_make_unique(join='$manipulate.join')
 #else if $manipulate.function == 'rename_categories'
 #set $categories = [x.strip() for x in str($manipulate.categories).split(',')]
+#if $manipulate.update_key.new_key == 'no':
 adata.rename_categories(
 key='$manipulate.key',
 categories=$categories)
+#else
+if '$manipulate.key' in adata.obs:
+print("changing key in obs")
+adata.obs['$manipulate.key_name'] = adata.obs['$manipulate.key']
+adata.rename_categories(
+key='$manipulate.key_name',
+categories=$categories)
+elif '$manipulate.key' in adata.var:
+print("changing key in var")
+adata.var['$manipulate.key_name'] = adata.var['$manipulate.key']
+adata.rename_categories(
+key='$manipulate.key_name',
+categories=$categories)
+else:
+print("chanigng key in uns")
+adata.uns['$manipulate.key_name'] = adata.uns['$manipulate.key']
+adata.rename_categories(
+key='$manipulate.key_name',
+categories=$categories)
+#end if
 #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
 #else if $manipulate.function == 'flag_genes'
 ## adapted from anndata operations
 #for $flag in $manipulate.gene_flags
+#if str($flag.col_in) != '':
+k_cat = adata.var['${flag.col_in}'].str.startswith('${flag.startswith}')
+#else:
 k_cat = adata.var_names.str.startswith('${flag.startswith}')
+#end if
 if k_cat.sum() > 0:
-adata.var['${flag.col_name}'] = k_cat
+adata.var['${flag.col_out}'] = k_cat
 else:
 print(f'No genes starting with {'${flag.startswith}'} found.')
 #end for
+#else if $manipulate.function == 'rename_obs':
+adata.obs['${to_obs}'] = adata.obs['${from_obs}']
+#if not $keep_original:
+del adata.obs['${from_obs}']
+#end if
+#else if $manipulate.function == 'rename_var':
+adata.var['${to_var}'] = adata.var['${from_var}']
+#if not $keep_original:
+del adata.var['${from_var}']
+#end if
 #else if $manipulate.function == 'strings_to_categoricals'
 adata.strings_to_categoricals()
 #else if $manipulate.function == 'transpose'
 os.makedirs(res_dir, exist_ok=True)
 for s,field_value in enumerate(adata.obs["${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'
+#else if $manipulate.function == 'copy_obs'
-#if $manipulate.filter.filter == 'key'
+source_adata = ad.read_h5ad('$source_adata')
-#if $manipulate.var_obs == 'var'
+#for $key in $manipulate.keys
-filtered = adata.var['$manipulate.filter.key']
+if '$key.source_key' in source_adata.obs:
-#else if $manipulate.var_obs == 'obs'
+#if str($key.target_key) == '':
-filtered = adata.obs['$manipulate.filter.key']
+adata.obs['$key.source_key'] = source_adata.obs['$key.source_key']
+#else
+adata.obs['$key.target_key'] = source_adata.obs['$key.source_key']
 #end if
+else:
-#if $manipulate.filter.filter_key.type == 'number'
+print(f"Obs column {'{$key.source_key}'} not found in source AnnData.")
-#if $manipulate.filter.filter_key.filter == 'equal'
+#end for
-filtered = filtered == $manipulate.filter.filter_key.value
-#else if $manipulate.filter.filter_key.filter == 'equal'
+#else if $manipulate.function == 'copy_uns'
-filtered = filtered != $manipulate.filter.filter_key.value
+source_adata = ad.read_h5ad('$source_adata')
-#else if $manipulate.filter.filter_key.filter == 'less'
+#for $key in $manipulate.keys
-filtered = filtered < $manipulate.filter.filter_key.value
+if '$key.source_key' in source_adata.uns:
-#else if $manipulate.filter.filter_key.filter == 'less_or_equal'
+#if str($key.target_key) == '':
-filtered = filtered <= $manipulate.filter.filter_key.value
+adata.uns['$key.source_key'] = source_adata.uns['$key.source_key']
-#else if $manipulate.filter.filter_key.filter == 'greater'
+#else
-filtered = filtered > $manipulate.filter.filter_key.value
+adata.uns['$key.target_key'] = source_adata.uns['$key.source_key']
-#else if $manipulate.filter.filter_key.filter == 'greater_or_equal'
-filtered = filtered >= $manipulate.filter.filter_key.value
-#end if
-#else if $manipulate.filter.filter_key.type == 'text'
-#if $manipulate.filter.filter_key.filter == 'equal'
-filtered = filtered == '$manipulate.filter.filter_key.value'
-#else
-filtered = filtered != '$manipulate.filter.filter_key.value'
-#end if
-#else if $manipulate.filter.filter_key.type == 'boolean'
-filtered = filtered == $manipulate.filter.filter_key.value
 #end if
+else:
-#else if $manipulate.filter.filter == 'index'
+print(f"Uns key {'{$key.source_key}'} not found in source AnnData.")
-#if str($manipulate.filter.index.format) == 'file'
+#end for
-with open('$manipulate.filter.index.file', 'r') as filter_f:
-filters = [str(x.strip()) for x in filter_f.readlines()]
+#else if $manipulate.function == 'copy_embed'
-filtered = filters
+source_adata = ad.read_h5ad('$source_adata')
+#for $key in $manipulate.keys
+if '$key.source_key' in source_adata.obsm:
+#if $key.target_key is None
+adata.obsm['$key.source_key'] = source_adata.obsm['$key.source_key']
 #else
-#set $filters = [str(x.strip()) for x in $manipulate.filter.index.text.split(',')]
+adata.obsm['$key.target_key'] = source_adata.obsm['$key.source_key']
-filtered = $filters
 #end if
-#end if
+else:
-print(filtered)
+print(f"Embedding key {'{$key.source_key}'} not found in source AnnData.")
+#end for
-#if $manipulate.var_obs == 'var'
-adata = adata[:,filtered]
+#else if $manipulate.function == 'copy_layers'
-#else if $manipulate.var_obs == 'obs'
+source_adata = ad.read_h5ad('$source_adata')
-adata = adata[filtered, :]
+#for $key in $manipulate.keys
+if '$key.source_key' in source_adata.layers:
+#if $key.target_key is None
+adata.layers['$key.source_key'] = source_adata.layers['$key.source_key']
+#else
+adata.layers['$key.target_key'] = source_adata.layers['$key.source_key']
+#end if
+else:
+print(f"Layer {'{$key.source_key}'} not found in source AnnData.")
+#end for
+#else if $manipulate.function == 'copy_X'
+source_adata = ad.read_h5ad('$source_adata')
+#if $target_key is None
+adata.X = source_adata.X
+#else
+adata.layers['$target_key'] = source_adata.X
 #end if
 #else if $manipulate.function == 'save_raw'
 adata.raw = adata
 <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="rename_obs">Rename fileds in AnnData observations</option><!--adapted from EBI anndata operations tool -->
+<option value="rename_var">Rename fileds in AnnData variables</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="copy_obs">Copy observation keys from a different anndata object</option>
+<option value="copy_uns">Copy uns keys from a different anndata object</option>
+<option value="copy_embed">Copy embeddings from a different anndata object</option>
+<option value="copy_layers">Copy layers from a different anndata object</option>
+<option value="copy_X">Copy data matrix (.X) from a different anndata object</option>
 <option value="save_raw">Freeze the current state into the 'raw' attribute</option>
 </param>
 <when value="concatenate">
 <param name="other_adatas" type="data" format="h5ad" multiple="true" label="Annotated data matrix to add"/>
 <param name="join" type="select" label="Join method">
 <option value="inner">Intersection of variables</option>
 <option value="outer">Union of variables</option>
 </param>
 <param name="batch_key" type="text" value="batch" label="Key to add the batch annotation to obs"/>
+<param name="uns_merge" type="select" label="Strategy to use for merging entries of uns" help="These strategies are applied recusivley.">
+<option value="None" selected="true">The default. The concatenated object will just have an empty dict for uns</option>
+<option value="same">Only entries which have the same value in all AnnData objects are kept</option>
+<option value="unique">Only entries which have one unique value in all AnnData objects are kept</option>
+<option value="first">The first non-missing value is used</option>
+<option value="only">A value is included if only one of the AnnData objects has a value at this path</option>
+</param>
 <param name="index_unique" type="select" label="Separator to join the existing index names with the batch category" help="Leave it empty to keep existing indices">
 <option value="-">-</option>
 <option value="_">_</option>
 <option value=" "> </option>
 <option value="/">/</option>
 <expand macro="param_join"/>
 </when>
 <when value="rename_categories">
 <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"/>
+<conditional name="update_key">
+<param name="new_key" type="select" label="Add categories to a new key?" help="If Yes, a new key will be created with the new categories, otherwise the old key will be updated">
+<option value="yes">Yes</option>
+<option value="no" selected="true">No</option>
+</param>
+<when value="yes">
+<param name="key_name" type="text" value="" optional="false" label="Key name">
+<expand macro="sanitize_query"/>
+</param>
+</when>
+<when value="no"></when>
+</conditional>
 </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>
 <valid initial="string.ascii_letters,string.digits,string.punctuation">
 <remove value="&apos;" />
 </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."/>
+<param name="col_in" value='' optional="true" type="text" label="Column in .var to use" help="By default it uses the var_names (normally gene symbols)">
-</repeat>
+<expand macro="sanitize_query"/>
+</param>
+<param name="col_out" 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.">
+<expand macro="sanitize_query"/>
+</param>
+</repeat>
+</when>
+<when value="rename_obs">
+<param name="from_obs" type="text" label="Name of the observations field that you want to change">
+<expand macro="sanitize_query"/>
+</param>
+<param name="to_obs" type="text" label="New name of the field in the observations">
+<expand macro="sanitize_query"/>
+</param>
+<param name="keep_original" type="boolean" checked="false" label="Keep original" help="If activated, it will also keep the original column"/>
+</when>
+<when value="rename_var">
+<param name="from_var" type="text" label="Name of the variables field that you want to change">
+<expand macro="sanitize_query"/>
+</param>
+<param name="to_var" type="text" label="New name of the filed in the variables">
+<expand macro="sanitize_query"/>
+</param>
+<param name="keep_original" type="boolean" checked="false" label="Keep original" help="If activated, it will also keep the original column"/>
 </when>
 <when value="strings_to_categoricals" ></when>
 <when value="transpose" ></when>
 <when value="add_annotation">
 <param name="var_obs" type="select" label="What to annotate?">
 <option value="var">Variables (var)</option>
 <option value="obs">Observations (obs)</option>
 </param>
 <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)"/>
+help="The new table should have the same number of rows and the same order as 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="&apos;" />
 </valid>
 </sanitizer>
 </param>
 </when>
-<when value="filter">
-<param name="var_obs" type="select" label="What to filter?">
-<option value="var">Variables (var)</option>
-<option value="obs">Observations (obs)</option>
-</param>
-<conditional name="filter">
-<param name="filter" type="select" label="Type of filtering?">
-<option value="key">By key (column) values</option>
-<option value="index">By index (row)</option>
-</param>
-<when value="key">
-<param name="key" type="text" value="n_genes" label="Key to filter"/>
-<conditional name="filter_key">
-<param name="type" type="select" label="Type of value to filter">
-<option value="number">Number</option>
-<option value="text">Text</option>
-<option value="boolean">Boolean</option>
-</param>
-<when value="number">
-<param name="filter" type="select" label="Filter">
-<option value="equal">equal to</option>
-<option value="not_equal">not equal to</option>
-<option value="less">less than</option>
-<option value="less_or_equal">less than or equal to</option>
-<option value="greater">greater than</option>
-<option value="greater_or_equal">greater than or equal to</option>
-</param>
-<param name="value" type="float" value="2500" label="Value"/>
-</when>
-<when value="text">
-<param name="filter" type="select" label="Filter">
-<option value="equal">equal to</option>
-<option value="not_equal">not equal to</option></param>
-<param name="value" type="text" value="2500" label="Value"/>
-</when>
-<when value="boolean">
-<param name="value" type="boolean" truevalue="True" falsevalue="False" checked="true" label="Value to keep"/>
-</when>
-</conditional>
-</when>
-<when value="index">
-<conditional name="index">
-<param name="format" type="select" label="Format for the filter by index">
-<option value="file">File</option>
-<option value="text" selected="true">Text</option>
-</param>
-<when value="text">
-<param name="text" type="text" value="" label="List of index to keep" help="Indexes separated by a comma"/>
-</when>
-<when value="file">
-<param name="file" type="data" format="txt" label="File with the list of index to keep" help="One index per line"/>
-</when>
-</conditional>
-</when>
-</conditional>
-</when>
 <when value="save_raw"></when>
+<when value="copy_obs">
+<param name="source_adata" type="data" format="h5ad" label="Source anndata object" help="Ideally the source AnnData object should contain the same set of genes and cells."/>
+<repeat name="keys" title="Keys from obs to copy" min="1">
+<param name="source_key" type="text" optional="true" label="Column to be copied from the source anndata" help="louvain, batch, etc. Provide one key at a time.">
+<expand macro="sanitize_query"/>
+</param>
+<param name="target_key" type="text" optional="true" label="Target column name" help="Warning! Provide a new key name to avoid rewriting. Leave empty to copy to the same key.">
+<expand macro="sanitize_query"/>
+</param>
+</repeat>
+</when>
+<when value="copy_uns">
+<param name="source_adata" type="data" format="h5ad" label="Source anndata object" help="Ideally the source AnnData object should contain the same set of genes and cells."/>
+<repeat name="keys" title="Keys from uns to copy" min="1">
+<param name="source_key" type="text" optional="true" label="Uns key to be copied from the source anndata" help="hvg, neighbors, etc. Provide one key at a time.">
+<expand macro="sanitize_query"/>
+</param>
+<param name="target_key" type="text" optional="true" label="Target key name" help="Warning! Provide a new key name to avoid rewriting. Leave empty to copy to the same key.">
+<expand macro="sanitize_query"/>
+</param>
+</repeat>
+</when>
+<when value="copy_embed">
+<param name="source_adata" type="data" format="h5ad" label="Source anndata object" help="Ideally the source AnnData object should contain the same set of genes and cells."/>
+<repeat name="keys" title="Keys from embeddings to copy" min="1">
+<param name="source_key" type="text" label="Key to be copied from the source anndata" help="tSNE, UMAP, etc. Provide one key at a time.">
+<expand macro="sanitize_query"/>
+</param>
+<param name="target_key" type="text" optional="true" label="Target key name" help="Warning! Provide a new key name to avoid rewriting. Leave empty to copy to the same key.">
+<expand macro="sanitize_query"/>
+</param>
+</repeat>
+</when>
+<when value="copy_layers">
+<param name="source_adata" type="data" format="h5ad" label="Source anndata object" help="Ideally the source AnnData object should contain the same set of genes and cells."/>
+<repeat name="keys" title="Layers to copy" min="1">
+<param name="source_key" type="text" label="Layer to be copied from the source anndata">
+<expand macro="sanitize_query"/>
+</param>
+<param name="target_key" type="text" optional="true" label="Target layer name" help="Warning! give a new key name to avoid rewriting. Leave empty to copy to the same key.">
+<expand macro="sanitize_query"/>
+</param>
+</repeat>
+</when>
+<when value="copy_X">
+<param name="source_adata" type="data" format="h5ad" label="Source anndata object" help="Ideally the source AnnData object should contain the same set of genes and cells."/>
+<param name="target_key" type="text" optional="true" label="Give a target layer name or leave empty to overwrite .X" help="Warning! give a new key name to avoid rewriting. Leave empty to copy to the .X of the current anndata">
+<expand macro="sanitize_query"/>
+</param>
+</when>
 </conditional>
 </inputs>
 <outputs>
 <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>
 <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"/>
+<conditional name="update_key">
+<param name="new_key" value="no"/>
+</conditional>
 </conditional>
 <assert_stdout>
 <has_text_matching expression="adata.rename_categories"/>
 <has_text_matching expression="key='cell_type'"/>
 <has_text_matching expression="categories=\['ery', 'mk', 'mo', 'progenitor'\]"/>
 </test>
 <test expect_num_outputs="1">
 <!-- test 9 -->
 <param name="input" value="krumsiek11.h5ad"/>
 <conditional name="manipulate">
-<param name="function" value="filter"/>
+<param name="function" value="save_raw"/>
-<param name="var_obs" value="var"/>
+</conditional>
-<conditional name="filter">
+<assert_stdout>
-<param name="filter" value="index"/>
+<has_text_matching expression="500 × 11"/>
-<conditional name="index">
-<param name="format" value="text"/>
-<param name="text" value="Gata2,EKLF"/>
-</conditional>
-</conditional>
-</conditional>
-<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 expect_num_outputs="1">
-<!-- test 10 -->
+<!-- test 10 remove_keys -->
-<param name="input" value="krumsiek11.h5ad"/>
-<conditional name="manipulate">
-<param name="function" value="filter"/>
-<param name="var_obs" value="obs"/>
-<conditional name="filter">
-<param name="filter" value="key"/>
-<param name="key" value="cell_type"/>
-<conditional name="filter_key">
-<param name="type" value="text"/>
-<param name="filter" value="equal"/>
-<param name="value" value="progenitor"/>
-</conditional>
-</conditional>
-</conditional>
-<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 expect_num_outputs="1">
-<!-- test 11 -->
-<param name="input" value="krumsiek11.h5ad"/>
-<conditional name="manipulate">
-<param name="function" value="save_raw"/>
-</conditional>
-<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>
 <has_h5_keys keys="uns/iroot"/>
 </assert_contents>
 </output>
 </test>
 <test expect_num_outputs="1">
-<!-- test 13 flag_genes -->
+<!-- test 11 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"/>
+<param name="col_out" value="Gata_TF"/>
 </repeat>
 <repeat name="gene_flags">
 <param name="startswith" value="Gf"/>
-<param name="col_name" value="GF"/>
+<param name="col_out" value="GF"/>
 </repeat>
 </conditional>
 <assert_stdout>
 <has_text_matching expression="500 × 11"/>
 </assert_stdout>
 <has_h5_keys keys="var/GF"/>
 </assert_contents>
 </output>
 </test>
 <test expect_num_outputs="1">
-<!-- test 14 split_on_obs -->
+<!-- test 12 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>
 <has_h5_keys keys="uns/iroot"/>
 </assert_contents>
 </element>
 </output_collection>
 </test>
+<test expect_num_outputs="1">
+<!-- test 13 rename categories with new key -->
+<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"/>
+<conditional name="update_key">
+<param name="new_key" value="yes"/>
+<param name="key_name" value="new_cell_type"/>
+</conditional>
+</conditional>
+<assert_stdout>
+<has_text_matching expression="adata.rename_categories"/>
+<has_text_matching expression="key='new_cell_type'"/>
+<has_text_matching expression="categories=\['ery', 'mk', 'mo', 'progenitor'\]"/>
+<has_text_matching expression="changing key in obs"/>
+<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/new_cell_type"/>
+<has_h5_keys keys="uns/highlights"/>
+<has_h5_keys keys="uns/iroot"/>
+</assert_contents>
+</output>
+</test>
+<test expect_num_outputs="1">
+<!-- test 14 flag_genes with a key -->
+<param name="input" value="flag_new_key.h5ad"/>
+<conditional name="manipulate">
+<param name="function" value="flag_genes"/>
+<repeat name="gene_flags">
+<param name="startswith" value="ENSG"/>
+<param name="col_in" value="gene_ids"/>
+<param name="col_out" value="ensembl"/>
+</repeat>
+</conditional>
+<assert_stdout>
+<has_text_matching expression="199 × 199"/>
+</assert_stdout>
+<output name="anndata" ftype="h5ad">
+<assert_contents>
+<has_h5_keys keys="var/ensembl"/>
+</assert_contents>
+</output>
+</test>
+<test expect_num_outputs="1">
+<!-- test 15 copy_obs -->
+<param name="input" value="krumsiek11.h5ad"/>
+<conditional name="manipulate">
+<param name="function" value="copy_obs"/>
+<param name="source_adata" value="krumsiek11.h5ad"/>
+<repeat name="keys">
+<param name="source_key" value="cell_type"/>
+<param name="target_key" value="new_cell_type"/>
+</repeat>
+</conditional>
+<assert_stdout>
+<has_text_matching expression="adata.obs\['new_cell_type'\] = source_adata.obs\['cell_type'\]"/>
+<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/new_cell_type"/>
+<has_h5_keys keys="uns/highlights"/>
+<has_h5_keys keys="uns/iroot"/>
+</assert_contents>
+</output>
+</test>
+<test expect_num_outputs="1">
+<!-- test 16 copy_uns -->
+<param name="input" value="krumsiek11.h5ad"/>
+<conditional name="manipulate">
+<param name="function" value="copy_uns"/>
+<param name="source_adata" value="krumsiek11.h5ad"/>
+<repeat name="keys">
+<param name="source_key" value="iroot"/>
+<param name="target_key" value="new_iroot"/>
+</repeat>
+</conditional>
+<assert_stdout>
+<has_text_matching expression="adata.uns\['new_iroot'\] = source_adata.uns\['iroot'\]"/>
+<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"/>
+<has_h5_keys keys="uns/new_iroot"/>
+</assert_contents>
+</output>
+</test>
+<test expect_num_outputs="1">
+<!-- test 17 copy_embed -->
+<param name="input" value="tl.umap.h5ad"/>
+<conditional name="manipulate">
+<param name="function" value="copy_embed"/>
+<param name="source_adata" value="tl.umap.h5ad"/>
+<repeat name="keys">
+<param name="source_key" value="X_pca"/>
+<param name="target_key" value="new_X_pca"/>
+</repeat>
+</conditional>
+<assert_stdout>
+<has_text_matching expression="adata.obsm\['new_X_pca'\] = source_adata.obsm\['X_pca'\]"/>
+<has_text_matching expression="100 × 800"/>
+</assert_stdout>
+<output name="anndata" ftype="h5ad">
+<assert_contents>
+<has_h5_keys keys="obs/paul15_clusters"/>
+<has_h5_keys keys="uns/neighbors"/>
+<has_h5_keys keys="uns/iroot"/>
+<has_h5_keys keys="obsm/X_pca"/>
+<has_h5_keys keys="obsm/new_X_pca"/>
+<has_h5_keys keys="obsm/X_umap"/>
+<has_h5_keys keys="layers/count"/>
+<has_h5_keys keys="obsp/connectivities"/>
+<has_h5_keys keys="obsp/distances"/>
+</assert_contents>
+</output>
+</test>
+<test expect_num_outputs="1">
+<!-- test 18 copy_layers -->
+<param name="input" value="tl.umap.h5ad"/>
+<conditional name="manipulate">
+<param name="function" value="copy_layers"/>
+<param name="source_adata" value="tl.umap.h5ad"/>
+<repeat name="keys">
+<param name="source_key" value="count"/>
+<param name="target_key" value="new_count"/>
+</repeat>
+</conditional>
+<assert_stdout>
+<has_text_matching expression="adata.layers\['new_count'\] = source_adata.layers\['count'\]"/>
+<has_text_matching expression="100 × 800"/>
+</assert_stdout>
+<output name="anndata" ftype="h5ad">
+<assert_contents>
+<has_h5_keys keys="obs/paul15_clusters"/>
+<has_h5_keys keys="uns/neighbors"/>
+<has_h5_keys keys="uns/iroot"/>
+<has_h5_keys keys="obsm/X_pca"/>
+<has_h5_keys keys="obsm/X_umap"/>
+<has_h5_keys keys="layers/count"/>
+<has_h5_keys keys="layers/new_count"/>
+<has_h5_keys keys="obsp/connectivities"/>
+<has_h5_keys keys="obsp/distances"/>
+</assert_contents>
+</output>
+</test>
+<test expect_num_outputs="1">
+<!-- test 19 copy_X -->
+<param name="input" value="tl.umap.h5ad"/>
+<conditional name="manipulate">
+<param name="function" value="copy_X"/>
+<param name="source_adata" value="tl.umap.h5ad"/>
+<param name="target_key" value="new_X"/>
+</conditional>
+<assert_stdout>
+<has_text_matching expression="adata.layers\['new_X'\] = source_adata.X"/>
+<has_text_matching expression="100 × 800"/>
+</assert_stdout>
+<output name="anndata" ftype="h5ad">
+<assert_contents>
+<has_h5_keys keys="obs/paul15_clusters"/>
+<has_h5_keys keys="uns/neighbors"/>
+<has_h5_keys keys="uns/iroot"/>
+<has_h5_keys keys="obsm/X_pca"/>
+<has_h5_keys keys="obsm/X_umap"/>
+<has_h5_keys keys="layers/count"/>
+<has_h5_keys keys="layers/new_X"/>
+<has_h5_keys keys="obsp/connectivities"/>
+<has_h5_keys keys="obsp/distances"/>
+</assert_contents>
+</output>
+</test>
+<test expect_num_outputs="1">
+<!-- test 20 save_raw -->
+<param name="input" value="tl.umap.h5ad"/>
+<conditional name="manipulate">
+<param name="function" value="save_raw"/>
+</conditional>
+<assert_stdout>
+<has_text_matching expression="adata.raw = adata"/>
+<has_text_matching expression="100 × 800"/>
+</assert_stdout>
+<output name="anndata" ftype="h5ad">
+<assert_contents>
+<has_h5_keys keys="obs/paul15_clusters"/>
+<has_h5_keys keys="uns/neighbors"/>
+<has_h5_keys keys="uns/iroot"/>
+<has_h5_keys keys="obsm/X_pca"/>
+<has_h5_keys keys="obsm/X_umap"/>
+<has_h5_keys keys="layers/count"/>
+<has_h5_keys keys="obsp/connectivities"/>
+<has_h5_keys keys="obsp/distances"/>
+</assert_contents>
+</output>
+</test>
+<test expect_num_outputs="1">
+<!-- test 21 rename_obs -->
+<param name="input" value="krumsiek11.h5ad"/>
+<conditional name="manipulate">
+<param name="function" value="rename_obs"/>
+<param name="from_obs" value="cell_type"/>
+<param name="to_obs" value="new_cell_type"/>
+<param name="keep_original" value="false"/>
+</conditional>
+<assert_stdout>
+<has_text_matching expression="adata.obs\['new_cell_type'\] = adata.obs\['cell_type'\]"/>
+<has_text_matching expression="del adata.obs\['cell_type'\]"/>
+<has_text_matching expression="500 × 11"/>
+</assert_stdout>
+<output name="anndata" ftype="h5ad">
+<assert_contents>
+<has_h5_keys keys="obs/new_cell_type"/>
+<has_h5_keys keys="uns/highlights"/>
+<has_h5_keys keys="uns/iroot"/>
+</assert_contents>
+</output>
+</test>
+<test expect_num_outputs="1">
+<!-- test 22 rename_var -->
+<param name="input" value="flag_new_key.h5ad"/>
+<conditional name="manipulate">
+<param name="function" value="rename_var"/>
+<param name="from_var" value="gene_ids"/>
+<param name="to_var" value="new_id"/>
+<param name="keep_original" value="false"/>
+</conditional>
+<assert_stdout>
+<has_text_matching expression="adata.var\['new_id'\] = adata.var\['gene_ids'\]"/>
+<has_text_matching expression="del adata.var\['gene_ids'\]"/>
+<has_text_matching expression="199 × 199"/>
+</assert_stdout>
+<output name="anndata" ftype="h5ad">
+<assert_contents>
+<has_h5_keys keys="var/feature_types"/>
+<has_h5_keys keys="var/test"/>
+<has_h5_keys keys="var/new_id"/>
+</assert_contents>
+</output>
+</test>
 </tests>
 <help><![CDATA[
 **What it does**
-This tool takes a AnnData dataset, manipulates it and returns it.
+This tool takes an AnnData dataset, manipulates it and returns it.
 The possible manipulations are:
 - Concatenate along the observations axis (`concatenate method <https://anndata.readthedocs.io/en/latest/generated/anndata.AnnData.concatenate.html>`__)
 If you use `join='outer'` this fills 0s for sparse data when variables are absent in a batch. Use this with care. Dense data is filled with `NaN`
 - 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>`__)
-The first occurance of a non-unique value is ignored.
+The first occurrence of a non-unique value is ignored.
 - 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>`__)
-The first occurance of a non-unique value is ignored.
+The first occurrence of a non-unique value is ignored.
 - 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>`__)
 Besides calling `self.obs[key].cat.categories = categories` - similar for `var` - this also renames categories in unstructured annotation that uses the categorical annotation `key`
 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
+Useful for flagging the mitochondrial 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.
 - 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.
+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.
 - Filter data variables or observations, by index or key
 - Freeze the current state into the 'raw' attribute

Mercurial > repos > iuc > anndata_manipulate

comparison manipulate.xml @ 15:d1e49c3c0aa2 draft default tip