Mercurial > repos > iuc > anndata_import
changeset 13:d330b3082107 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 19:58:24 +0000 |
| parents | 93dd15e13e6a |
| children | |
| files | import.xml macros.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, 139 insertions(+), 156 deletions(-) [+] |
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--- a/import.xml Sun Nov 12 16:42:57 2023 +0000 +++ b/import.xml Sat Sep 14 19:58:24 2024 +0000 @@ -1,9 +1,9 @@ -<tool id="anndata_import" name="Import Anndata and loom" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.09"> - <description>from different format</description> +<tool id="anndata_import" name="Import Anndata" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@"> + <description>from different formats</description> <macros> <import>macros.xml</import> <xml name="params_10x"> - <param name="barcodes" type="data" format="tabular,txt" label="Barcodes"/> + <param name="barcodes" type="data" format="tabular,txt" label="Barcodes (whitelist) file with one barcode per line"/> <param name="var_names" type="select" label="Variables index"> <option value="gene_symbols">gene_symbols</option> <option value="gene_ids">gene_ids</option> @@ -13,164 +13,132 @@ </xml> </macros> <expand macro="requirements"> - <requirement type="package" version="1.9.6">scanpy</requirement> + <requirement type="package" version="1.10.2">scanpy</requirement> </expand> <expand macro="version_command"/> <command detect_errors="exit_code"><![CDATA[ -#if $hd5_format.filetype == 'anndata' - #if $hd5_format.in.adata_format == 'mtx' - mkdir mtx - #if $hd5_format.in.tenx.use == 'legacy_10x' - && cp '$hd5_format.in.matrix' 'mtx/matrix.mtx' - && cp '$hd5_format.in.tenx.genes' 'mtx/genes.tsv' - && cp '$hd5_format.in.tenx.barcodes' 'mtx/barcodes.tsv' - #else if $hd5_format.in.tenx.use == 'v3_10x' - && cp '$hd5_format.in.matrix' 'mtx/matrix.mtx' - && gzip 'mtx/matrix.mtx' - && cp '$hd5_format.in.tenx.features' 'mtx/features.tsv' - && gzip 'mtx/features.tsv' - && cp '$hd5_format.in.tenx.barcodes' 'mtx/barcodes.tsv' - && gzip 'mtx/barcodes.tsv' - #end if - && - #else if $hd5_format.in.adata_format == 'umi_tools' - ## avoid gzipping in the inputdir - gzip -c '$hd5_format.in.input' > umi_tools_input.gz - && +#if $in.adata_format == 'mtx' + mkdir mtx + #if $in.tenx.use == 'legacy_10x' + && cp '$in.matrix' 'mtx/matrix.mtx' + && cp '$in.tenx.genes' 'mtx/genes.tsv' + && cp '$in.tenx.barcodes' 'mtx/barcodes.tsv' + #else if $in.tenx.use == 'v3_10x' + && cp '$in.matrix' 'mtx/matrix.mtx' + && gzip 'mtx/matrix.mtx' + && cp '$in.tenx.features' 'mtx/features.tsv' + && gzip 'mtx/features.tsv' + && cp '$in.tenx.barcodes' 'mtx/barcodes.tsv' + && gzip 'mtx/barcodes.tsv' #end if - - @CMD@ - - #if $hd5_format.in.adata_format == 'mtx' - && rm -rf mtx - #end if + && +#else if $in.adata_format == 'umi_tools' + ## avoid gzipping in the inputdir + gzip -c '$in.input' > umi_tools_input.gz + && +#end if -#else: - python '$__tool_directory__/tsv_to_loompy.py' - -c '${hd5_format.coldata}' - -r '${hd5_format.rowdata}' - -f '${hd5_format.mainmatrix}' - #if $hd5_format.other_files: - '${hd5_format.other_files}' - #end if -#end if +@CMD@ ]]></command> <configfiles> <configfile name="script_file"><![CDATA[ @CMD_imports@ -#if $hd5_format.filetype == 'anndata' - #if $hd5_format.in.adata_format == 'loom' +#if $in.adata_format == 'loom' adata = ad.read_loom( - '$hd5_format.in.input', - sparse=$hd5_format.in.sparse, - cleanup=$hd5_format.in.cleanup, - X_name='$hd5_format.in.x_name', - obs_names='$hd5_format.in.obs_names', - var_names='$hd5_format.in.var_names') + '$in.input', + sparse=$in.sparse, + cleanup=$in.cleanup, + X_name='$in.x_name', + obs_names='$in.obs_names', + var_names='$in.var_names') - #else if $hd5_format.in.adata_format == 'tabular' - #set delimiter=$hd5_format.in.input.metadata.delimiter - #if $delimiter != ',' - #set delimiter='\\t' - #end if +#else if $in.adata_format == 'tabular' + #set delimiter=$in.input.metadata.delimiter + #if $delimiter != ',' + #set delimiter='\\t' + #end if adata = ad.read_csv( - '$hd5_format.in.input', + '$in.input', delimiter='$delimiter', - first_column_names=$hd5_format.in.first_column_names) + first_column_names=$in.first_column_names) +## convert into sparse matrix. Dense matrix needs large disk space and higher access times +from scipy.sparse import csr_matrix +adata.X = csr_matrix(adata.X) - #else if $hd5_format.in.adata_format == '10x_h5' +#else if $in.adata_format == '10x_h5' import scanpy as sc -adata = sc.read_10x_h5('$hd5_format.in.input') +adata = sc.read_10x_h5('$in.input') - #else if $hd5_format.in.adata_format == 'mtx' - #if $hd5_format.in.tenx.use == 'no' -adata = ad.read_mtx(filename='$hd5_format.in.matrix') - #else +#else if $in.adata_format == 'mtx' + #if $in.tenx.use == 'no' +adata = ad.read_mtx(filename='$in.matrix') + #else import scanpy as sc adata = sc.read_10x_mtx( 'mtx', - var_names='$hd5_format.in.tenx.var_names', - make_unique=$hd5_format.in.tenx.make_unique, + var_names='$in.tenx.var_names', + make_unique=$in.tenx.make_unique, cache=False, - gex_only=$hd5_format.in.tenx.gex_only) - #end if + gex_only=$in.tenx.gex_only) + #end if - #else if $hd5_format.in.adata_format == 'umi_tools' +#else if $in.adata_format == 'umi_tools' adata = ad.read_umi_tools('umi_tools_input.gz') - #end if -adata.write('anndata.h5ad') #end if +adata.write('anndata.h5ad', compression='gzip') +print(adata) ]]></configfile> </configfiles> <inputs> - <conditional name="hd5_format"> - <param name="filetype" type="select" label="hd5 format to be created"> - <option value="anndata" selected="true">Anndata file</option> - <option value="loom">Loom file</option> + <conditional name="in"> + <param name="adata_format" type="select" label="Create annadata from"> + <option value="loom">Loom data</option> + <option value="tabular">Tabular, CSV, TSV</option> + <option value="10x_h5">H5 format from Cell ranger or not</option> + <option value="mtx">Matrix Market (mtx), from Cell ranger or not</option> + <option value="umi_tools">UMI tools count matrix</option> </param> - <when value="anndata"> - <conditional name="in"> - <param name="adata_format" type="select" label="Format for the annotated data matrix"> - <option value="loom">Loom</option> - <option value="tabular">Tabular, CSV, TSV</option> - <option value="10x_h5">H5 format from Cell ranger or not</option> - <option value="mtx">Matrix Market (mtx), from Cell ranger or not</option> - <option value="umi_tools">UMI tools</option> + <when value="loom"> + <param name="input" type="data" format="loom" label="Annotated data matrix"/> + <param name="sparse" type="boolean" truevalue="True" falsevalue="False" checked="true" label="Is the data matrix to read sparse?"/> + <param name="cleanup" type="boolean" truevalue="True" falsevalue="False" checked="false" label="Cleanup?"/> + <param name="x_name" type="text" value="spliced" label="X_name"/> + <param name="obs_names" type="text" value="CellID" label="obs_names"/> + <param name="var_names" type="text" value="Gene" label="var_names"/> + </when> + <when value="tabular"> + <param name="input" type="data" format="tabular,csv,tsv" label="Annotated data matrix"/> + <param name="first_column_names" type="boolean" truevalue="True" falsevalue="False" checked="true" label="Does the first column store the row names?"/> + </when> + <when value="10x_h5" > + <param name="input" type="data" format="h5" label="Data matrix"/> + </when> + <when value="mtx"> + <param name="matrix" type="data" format="mtx" label="Matrix in Matrix Market format"/> + <conditional name="tenx"> + <param name="use" type="select" label="Use 10x Genomics formatted mtx"> + <option value="no">No</option> + <option value="legacy_10x">Output from Cell Ranger v2 or earlier versions</option> + <option value="v3_10x">Output from Cell Ranger v3 or later versions</option> </param> - <when value="loom"> - <param name="input" type="data" format="loom" label="Annotated data matrix"/> - <param name="sparse" type="boolean" truevalue="True" falsevalue="False" checked="true" label="Is the data matrix to read sparse?"/> - <param name="cleanup" type="boolean" truevalue="True" falsevalue="False" checked="false" label="Cleanup?"/> - <param name="x_name" type="text" value="spliced" label="X_name"/> - <param name="obs_names" type="text" value="CellID" label="obs_names"/> - <param name="var_names" type="text" value="Gene" label="var_names"/> + <when value="no"/> + <when value="legacy_10x"> + <param name="genes" type="data" format="tabular" label="2-column genes file with gene id and gene name"/> + <expand macro="params_10x"/> </when> - <when value="tabular"> - <param name="input" type="data" format="tabular,csv,tsv" label="Annotated data matrix"/> - <param name="first_column_names" type="boolean" truevalue="True" falsevalue="False" checked="true" label="Does the first column store the row names?"/> - </when> - <when value="10x_h5" > - <param name="input" type="data" format="h5" label="Data matrix"/> - </when> - <when value="mtx"> - <param name="matrix" type="data" format="mtx" label="Matrix"/> - <conditional name="tenx"> - <param name="use" type="select" label="Use 10x Genomics formatted mtx"> - <option value="no">No</option> - <option value="legacy_10x">Output from Cell Ranger v2 or earlier versions</option> - <option value="v3_10x">Output from Cell Ranger v3 or later versions</option> - </param> - <when value="no"/> - <when value="legacy_10x"> - <param name="genes" type="data" format="tabular" label="Genes"/> - <expand macro="params_10x"/> - </when> - <when value="v3_10x"> - <param name="features" type="data" format="tabular" label="Features"/> - <expand macro="params_10x"/> - </when> - </conditional> - </when> - <when value="umi_tools"> - <param name="input" type="data" format="tabular" label="condensed count matrix from UMI tools"/> + <when value="v3_10x"> + <param name="features" type="data" format="tabular" label="3-column features file with feature id, feature name and feature type" help="For scRNA-seq, features are genes. The 3rd column typically contains the word 'Gene Expression'"/> + <expand macro="params_10x"/> </when> </conditional> </when> - <when value="loom"> - <param name="mainmatrix" type="data" format="tabular" label="File for main layer of loom file." help="All subsequent tsv must be the same dimensions as this file. When converted back to tsv using hd5 export, this will be labeled as 'mainmatrix.tsv'"/> - <param name="other_files" type="data" format="tabular" multiple="true" optional="true" label="Add layers" help="Adds layers of same dimension to the loom file. When converted to tsv using hd5 export, these layers will retain their names."/> - <param name="coldata" type="data" format="tabular" label="Tsv of column data." help="First row is column attributes, subsequent are values."/> - <param name="rowdata" type="data" format="tabular" label="Tsv of row data." help="First row is row attributes, subsequent are values."/> + <when value="umi_tools"> + <param name="input" type="data" format="tabular" label="condensed count matrix from UMI tools"/> </when> </conditional> </inputs> <outputs> - <data name="anndata" format="h5ad" from_work_dir="anndata.h5ad" label="Anndata import on ${on_string}"> - <filter>hd5_format['filetype'] == 'anndata'</filter> - </data> - <data name="loomdata" format="loom" from_work_dir="converted.loom" label="Loom import on ${on_string}"> - <filter>hd5_format['filetype'] == 'loom'</filter> - </data> + <data name="anndata" format="h5ad" from_work_dir="anndata.h5ad" label="Anndata import on ${on_string}"/> </outputs> <tests> <test expect_num_outputs="1"> @@ -191,7 +159,13 @@ <has_text_matching expression="obs_names='CellID'"/> <has_text_matching expression="var_names='Gene'"/> </assert_stdout> - <output name="anndata" value="import.loom.krumsiek11.h5ad" ftype="h5ad" compare="sim_size"/> + <output name="anndata" ftype="h5ad"> + <assert_contents> + <has_h5_keys keys="obs/cell_type"/> + <has_h5_keys keys="obs/obs_names"/> + <has_h5_keys keys="var/var_names"/> + </assert_contents> + </output> </test> <test expect_num_outputs="1"> <conditional name="in"> @@ -203,8 +177,8 @@ <has_text_matching expression="ad.read_csv"/> <has_text_matching expression="delimiter=','"/> <has_text_matching expression="first_column_names=True"/> + <has_text_matching expression="3 × 2"/> </assert_stdout> - <output name="anndata" value="import.csv.h5ad" ftype="h5ad" compare="sim_size"/> </test> <test expect_num_outputs="1"> <conditional name="in"> @@ -216,8 +190,8 @@ <has_text_matching expression="ad.read_csv"/> <has_text_matching expression="delimiter='\\t'"/> <has_text_matching expression="first_column_names=True"/> + <has_text_matching expression="3 × 2"/> </assert_stdout> - <output name="anndata" value="import.tsv.h5ad" ftype="h5ad" compare="sim_size"/> </test> <test expect_num_outputs="1"> <conditional name="in"> @@ -226,8 +200,10 @@ <conditional name="tenx"> <param name="use" value="no"/> </conditional> - </conditional> - <output name="anndata" value="import.mtx.no_10x.h5ad" ftype="h5ad" compare="sim_size"/> + </conditional> + <assert_stdout> + <has_text_matching expression="343 × 12"/> + </assert_stdout> </test> <test expect_num_outputs="1"> <conditional name="in"> @@ -242,7 +218,14 @@ <param name="gex_only" value="true"/> </conditional> </conditional> - <output name="anndata" value="import.mtx.legacy_10x.h5ad" ftype="h5ad" compare="sim_size"/> + <assert_stdout> + <has_text_matching expression="12 × 343"/> + </assert_stdout> + <output name="anndata" ftype="h5ad"> + <assert_contents> + <has_h5_keys keys="var/gene_ids"/> + </assert_contents> + </output> </test> <test expect_num_outputs="1"> <conditional name="in"> @@ -257,31 +240,29 @@ <param name="gex_only" value="true"/> </conditional> </conditional> - <output name="anndata" value="import.mtx.v3_10x.h5ad" ftype="h5ad" compare="sim_size"/> + <assert_stdout> + <has_text_matching expression="1107 × 507"/> + </assert_stdout> + <output name="anndata" ftype="h5ad"> + <assert_contents> + <has_h5_keys keys="var/gene_ids"/> + <has_h5_keys keys="var/feature_types"/> + </assert_contents> + </output> </test> <test expect_num_outputs="1"> - <param name="filetype" value="anndata"/> <conditional name="in"> <param name="adata_format" value="umi_tools"/> <param name="input" value="umi_tools.tsv"/> </conditional> - <output name="anndata" value="import.umi_tools.h5ad" ftype="h5ad" compare="sim_size"/> - </test> - <test expect_num_outputs="1"> - <param name="filetype" value="loom"/> - <param name="mainmatrix" value="firstlayer.tsv"/> - <param name="other_files" value="secondlayer.tsv"/> - <param name="coldata" value="cols.tsv"/> - <param name="rowdata" value="rows.tsv"/> - <output name="loomdata" value="converted.loom.test" ftype="loom" compare="sim_size"/> + <assert_stdout> + <has_text_matching expression="2 × 13"/> + </assert_stdout> </test> <test expect_num_outputs="1"><!-- 10x h5 test --> - <conditional name="hd5_format"> - <param name="filetype" value="anndata"/> - <conditional name="in"> - <param name="adata_format" value="10x_h5"/> - <param name="input" value="dropletutils_input.h5"/> - </conditional> + <conditional name="in"> + <param name="adata_format" value="10x_h5"/> + <param name="input" value="dropletutils_input.h5"/> </conditional> <output name="anndata"> <assert_contents> @@ -296,7 +277,7 @@ **What it does** -This tool creates an AnnData or loom dataset from several input types: +This tool creates an AnnData from several input types: - Loom (`read_loom method <https://anndata.readthedocs.io/en/latest/generated/anndata.read_loom.html>`__) - Tabular (`read_csv method <https://anndata.readthedocs.io/en/latest/generated/anndata.read_csv.html>`__)
--- a/macros.xml Sun Nov 12 16:42:57 2023 +0000 +++ b/macros.xml Sat Sep 14 19:58:24 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>
Binary file test-data/pp.neighbors_umap_euclidean.recipe_weinreb17.paul15_subsample.h5ad has changed