Mercurial > repos > iuc > anndata_import
changeset 12:404cbf857547 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
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--- a/import.xml Wed Jun 22 07:17:15 2022 +0000 +++ b/import.xml Sat Sep 14 19:56:19 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="1.7.0">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"> @@ -226,10 +200,12 @@ <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> + <test expect_num_outputs="1"> <conditional name="in"> <param name="adata_format" value="mtx"/> <param name="matrix" value="matrix_10x_v1.2.0.mtx"/> @@ -242,9 +218,16 @@ <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> + <test expect_num_outputs="1"> <conditional name="in"> <param name="adata_format" value="mtx"/> <param name="matrix" value="matrix_10x_v3.0.0.mtx"/> @@ -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"/> - </test>!--> + <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 Wed Jun 22 07:17:15 2022 +0000 +++ b/macros.xml Sat Sep 14 19:56:19 2024 +0000 @@ -1,10 +1,11 @@ <macros> - <token name="@TOOL_VERSION@">0.7.5</token> - <token name="@VERSION_SUFFIX@">1</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> - <requirement type="package" version="2.0.17">loompy</requirement> + <requirement type="package" version="3.0.6">loompy</requirement> <yield /> </requirements> </xml> @@ -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/test-data/export.krumsiek11.X.tabular Wed Jun 22 07:17:15 2022 +0000 +++ b/test-data/export.krumsiek11.X.tabular Sat Sep 14 19:56:19 2024 +0000 @@ -498,143 +498,3 @@ 0.1857 0.0587 -0.0003 0.0087 0.0084 0.0221 0.9613 0.2272 0.1058 0.0298 0.276 0.177 0.0645 0.0011 0.009 0.006 0.0222 0.9653 0.2208 0.1063 0.0291 0.2785 0.1664 0.0673 0.002 0.0078 0.0094 0.0278 0.9689 0.2125 0.1041 0.0294 0.2794 -0.159 0.0738 0.0015 0.0092 0.0068 0.0289 0.97 0.2054 0.1042 0.0299 0.2807 -0.1509 0.0722 0.002 0.0078 0.0038 0.0353 0.9718 0.2007 0.0995 0.0284 0.2862 -0.1492 0.0714 0.0025 0.014 0.0066 0.0381 0.972 0.1993 0.0989 0.0286 0.2911 -0.1445 0.0706 0.0049 0.0148 0.0107 0.0411 0.9767 0.1999 0.0957 0.0306 0.293 -0.1402 0.073 0.0063 0.0143 0.0122 0.0407 0.9761 0.2024 0.0999 0.0315 0.2912 -0.1389 0.0725 0.0069 0.0163 0.014 0.0406 0.9781 0.206 0.0972 0.0301 0.2917 -0.1364 0.0761 0.0068 0.013 0.0147 0.0441 0.975 0.2033 0.0948 0.0285 0.2932 -0.1363 0.0786 0.0082 0.0151 0.0153 0.0463 0.9812 0.2048 0.0921 0.0291 0.2963 -0.1339 0.0796 0.0069 0.0145 0.0171 0.0539 0.984 0.2069 0.0884 0.031 0.2958 -0.1305 0.0847 0.0085 0.0156 0.015 0.0565 0.9853 0.2108 0.0883 0.0348 0.2913 -0.1276 0.0846 0.0087 0.0156 0.0124 0.0569 0.9906 0.2103 0.0888 0.0282 0.2906 -0.1238 0.0827 0.008 0.0176 0.0158 0.0603 0.9893 0.213 0.0886 0.0267 0.2899 -0.121 0.077 0.01 0.0174 0.0171 0.0605 0.9918 0.2194 0.0885 0.029 0.2966 -0.1187 0.0773 0.0107 0.0185 0.0164 0.0598 0.9913 0.2219 0.0878 0.0299 0.2996 -0.1158 0.0758 0.0095 0.0171 0.014 0.0573 0.9951 0.2252 0.0877 0.0324 0.3007 -0.1131 0.0785 0.0121 0.0212 0.0153 0.0587 0.9946 0.2275 0.0886 0.0303 0.3019 -0.1122 0.0777 0.0109 0.0218 0.0127 0.0596 0.9941 0.2355 0.0893 0.0283 0.3032 -0.1072 0.0748 0.0119 0.023 0.0139 0.0585 0.9989 0.241 0.091 0.0281 0.3086 -0.1028 0.0746 0.0094 0.0226 0.0179 0.06 1.0018 0.2489 0.0894 0.028 0.3093 -0.099 0.0747 0.0085 0.0216 0.0202 0.0572 1.0025 0.2566 0.0881 0.0277 0.3119 -0.0972 0.072 0.0094 0.0201 0.0221 0.0575 1.0 0.2602 0.0866 0.0225 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--- a/test-data/export.krumsiek11.obs.tabular Wed Jun 22 07:17:15 2022 +0000 +++ b/test-data/export.krumsiek11.obs.tabular Sat Sep 14 19:56:19 2024 +0000 @@ -1,4 +1,4 @@ -index cell_type + cell_type 0 progenitor 1 progenitor 2 progenitor @@ -499,143 +499,3 @@ 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 -65 progenitor -66 progenitor -67 progenitor -68 progenitor -69 progenitor -70 progenitor -71 progenitor -72 progenitor -73 progenitor -74 progenitor -75 progenitor -76 progenitor -77 progenitor -78 progenitor -79 progenitor -80 Neu -81 Neu -82 Neu -83 Neu -84 Neu -85 Neu -86 Neu -87 Neu -88 Neu -89 Neu -90 Neu -91 Neu -92 Neu -93 Neu -94 Neu -95 Neu -96 Neu -97 Neu -98 Neu -99 Neu -100 Neu -101 Neu -102 Neu -103 Neu -104 Neu -105 Neu -106 Neu -107 Neu -108 Neu -109 Neu -110 Neu -111 Neu -112 Neu -113 Neu -114 Neu -115 Neu -116 Neu -117 Neu -118 Neu -119 Neu -120 Neu -121 Neu -122 Neu -123 Neu -124 Neu -125 Neu -126 Neu -127 Neu -128 Neu -129 Neu -130 Neu -131 Neu -132 Neu -133 Neu -134 Neu -135 Neu -136 Neu -137 Neu -138 Neu -139 Neu -140 Neu -141 Neu -142 Neu -143 Neu -144 Neu -145 Neu -146 Neu -147 Neu -148 Neu -149 Neu -150 Neu -151 Neu -152 Neu -153 Neu -154 Neu -155 Neu -156 Neu -157 Neu -158 Neu -159 Neu
--- a/test-data/export.krumsiek11.obsm.tabular Wed Jun 22 07:17:15 2022 +0000 +++ b/test-data/export.krumsiek11.obsm.tabular Sat Sep 14 19:56:19 2024 +0000 @@ -499,143 +499,3 @@ - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
--- a/test-data/export.krumsiek11.var.tabular Wed Jun 22 07:17:15 2022 +0000 +++ b/test-data/export.krumsiek11.var.tabular Sat Sep 14 19:56:19 2024 +0000 @@ -1,4 +1,4 @@ -index +"" Gata2 Gata1 Fog1
--- a/test-data/inspect.X.tabular Wed Jun 22 07:17:15 2022 +0000 +++ b/test-data/inspect.X.tabular Sat Sep 14 19:56:19 2024 +0000 @@ -1,4 +1,4 @@ -index Gata2 Gata1 Fog1 EKLF Fli1 SCL Cebpa Pu.1 cJun EgrNab Gfi1 + Gata2 Gata1 Fog1 EKLF Fli1 SCL Cebpa Pu.1 cJun EgrNab Gfi1 0 0.8032 -0.0005 -1e-04 0.0003 0.0013 0.0011 0.7997 0.8017 0.0006 0.0009 0.0002 1 0.7239 0.0016 -0.0003 -0.001 0.0011 0.0022 0.8195 0.7256 0.0784 0.0077 0.0941 2 0.6578 0.0013 -0.001 -0.0027 0.0025 0.0011 0.8358 0.6624 0.1105 0.0239 0.1497 @@ -499,143 +499,3 @@ 17 0.1857 0.0587 -0.0003 0.0087 0.0084 0.0221 0.9613 0.2272 0.1058 0.0298 0.276 18 0.177 0.0645 0.0011 0.009 0.006 0.0222 0.9653 0.2208 0.1063 0.0291 0.2785 19 0.1664 0.0673 0.002 0.0078 0.0094 0.0278 0.9689 0.2125 0.1041 0.0294 0.2794 -20 0.159 0.0738 0.0015 0.0092 0.0068 0.0289 0.97 0.2054 0.1042 0.0299 0.2807 -21 0.1509 0.0722 0.002 0.0078 0.0038 0.0353 0.9718 0.2007 0.0995 0.0284 0.2862 -22 0.1492 0.0714 0.0025 0.014 0.0066 0.0381 0.972 0.1993 0.0989 0.0286 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--- a/test-data/inspect.general.txt Wed Jun 22 07:17:15 2022 +0000 +++ b/test-data/inspect.general.txt Sat Sep 14 19:56:19 2024 +0000 @@ -1,3 +1,3 @@ -AnnData object with n_obs × n_vars = 640 × 11 +AnnData object with n_obs × n_vars = 500 × 11 obs: 'cell_type' - uns: 'cell_type_colors', 'highlights', 'iroot' + uns: 'highlights', 'iroot'
--- a/test-data/inspect.obs.tabular Wed Jun 22 07:17:15 2022 +0000 +++ b/test-data/inspect.obs.tabular Sat Sep 14 19:56:19 2024 +0000 @@ -1,4 +1,4 @@ -index cell_type + cell_type 0 progenitor 1 progenitor 2 progenitor @@ -499,143 +499,3 @@ 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 -65 progenitor -66 progenitor -67 progenitor -68 progenitor -69 progenitor -70 progenitor -71 progenitor -72 progenitor -73 progenitor -74 progenitor -75 progenitor -76 progenitor -77 progenitor -78 progenitor -79 progenitor -80 Neu -81 Neu -82 Neu -83 Neu -84 Neu -85 Neu -86 Neu -87 Neu -88 Neu -89 Neu -90 Neu -91 Neu -92 Neu -93 Neu -94 Neu -95 Neu -96 Neu -97 Neu -98 Neu -99 Neu -100 Neu -101 Neu -102 Neu -103 Neu -104 Neu -105 Neu -106 Neu -107 Neu -108 Neu -109 Neu -110 Neu -111 Neu -112 Neu -113 Neu -114 Neu -115 Neu -116 Neu -117 Neu -118 Neu -119 Neu -120 Neu -121 Neu -122 Neu -123 Neu -124 Neu -125 Neu -126 Neu -127 Neu -128 Neu -129 Neu -130 Neu -131 Neu -132 Neu -133 Neu -134 Neu -135 Neu -136 Neu -137 Neu -138 Neu -139 Neu -140 Neu -141 Neu -142 Neu -143 Neu -144 Neu -145 Neu -146 Neu -147 Neu -148 Neu -149 Neu -150 Neu -151 Neu -152 Neu -153 Neu -154 Neu -155 Neu -156 Neu -157 Neu -158 Neu -159 Neu
--- a/test-data/inspect.var.tabular Wed Jun 22 07:17:15 2022 +0000 +++ b/test-data/inspect.var.tabular Sat Sep 14 19:56:19 2024 +0000 @@ -1,4 +1,4 @@ -index +"" Gata2 Gata1 Fog1
--- a/test-data/obs_add_annotation.tabular Wed Jun 22 07:17:15 2022 +0000 +++ b/test-data/obs_add_annotation.tabular Sat Sep 14 19:56:19 2024 +0000 @@ -499,143 +499,3 @@ 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 -65 progenitor -66 progenitor -67 progenitor -68 progenitor -69 progenitor -70 progenitor -71 progenitor -72 progenitor -73 progenitor -74 progenitor -75 progenitor -76 progenitor -77 progenitor -78 progenitor -79 progenitor -80 Neu -81 Neu -82 Neu -83 Neu -84 Neu -85 Neu -86 Neu -87 Neu -88 Neu -89 Neu -90 Neu -91 Neu -92 Neu -93 Neu -94 Neu -95 Neu -96 Neu -97 Neu -98 Neu -99 Neu -100 Neu -101 Neu -102 Neu -103 Neu -104 Neu -105 Neu -106 Neu -107 Neu -108 Neu -109 Neu -110 Neu -111 Neu -112 Neu -113 Neu -114 Neu -115 Neu -116 Neu -117 Neu -118 Neu -119 Neu -120 Neu -121 Neu -122 Neu -123 Neu -124 Neu -125 Neu -126 Neu -127 Neu -128 Neu -129 Neu -130 Neu -131 Neu -132 Neu -133 Neu -134 Neu -135 Neu -136 Neu -137 Neu -138 Neu -139 Neu -140 Neu -141 Neu -142 Neu -143 Neu -144 Neu -145 Neu -146 Neu -147 Neu -148 Neu -149 Neu -150 Neu -151 Neu -152 Neu -153 Neu -154 Neu -155 Neu -156 Neu -157 Neu -158 Neu -159 Neu
Binary file test-data/pp.neighbors_umap_euclidean.recipe_weinreb17.paul15_subsample.h5ad has changed