| Previous changeset 12:93dd15e13e6a (2023-11-12) Next changeset 14:6f143dfe902a (2024-11-08) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa |
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modified:
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/krumsiek11.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 |
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removed:
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/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 |
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| diff -r 93dd15e13e6a -r d330b3082107 import.xml --- a/import.xml Sun Nov 12 16:42:57 2023 +0000 +++ b/import.xml Sat Sep 14 19:58:24 2024 +0000 |
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| b'@@ -1,9 +1,9 @@\n-<tool id="anndata_import" name="Import Anndata and loom" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.09">\n- <description>from different format</description>\n+<tool id="anndata_import" name="Import Anndata" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">\n+ <description>from different formats</description>\n <macros>\n <import>macros.xml</import>\n <xml name="params_10x">\n- <param name="barcodes" type="data" format="tabular,txt" label="Barcodes"/>\n+ <param name="barcodes" type="data" format="tabular,txt" label="Barcodes (whitelist) file with one barcode per line"/>\n <param name="var_names" type="select" label="Variables index">\n <option value="gene_symbols">gene_symbols</option>\n <option value="gene_ids">gene_ids</option>\n@@ -13,164 +13,132 @@\n </xml>\n </macros>\n <expand macro="requirements">\n- <requirement type="package" version="1.9.6">scanpy</requirement>\n+ <requirement type="package" version="1.10.2">scanpy</requirement>\n </expand>\n <expand macro="version_command"/>\n <command detect_errors="exit_code"><![CDATA[\n-#if $hd5_format.filetype == \'anndata\'\n- #if $hd5_format.in.adata_format == \'mtx\'\n- mkdir mtx\n- #if $hd5_format.in.tenx.use == \'legacy_10x\'\n- && cp \'$hd5_format.in.matrix\' \'mtx/matrix.mtx\'\n- && cp \'$hd5_format.in.tenx.genes\' \'mtx/genes.tsv\'\n- && cp \'$hd5_format.in.tenx.barcodes\' \'mtx/barcodes.tsv\'\n- #else if $hd5_format.in.tenx.use == \'v3_10x\'\n- && cp \'$hd5_format.in.matrix\' \'mtx/matrix.mtx\'\n- && gzip \'mtx/matrix.mtx\'\n- && cp \'$hd5_format.in.tenx.features\' \'mtx/features.tsv\'\n- && gzip \'mtx/features.tsv\'\n- && cp \'$hd5_format.in.tenx.barcodes\' \'mtx/barcodes.tsv\'\n- && gzip \'mtx/barcodes.tsv\'\n- #end if\n- &&\n- #else if $hd5_format.in.adata_format == \'umi_tools\'\n- ## avoid gzipping in the inputdir\n- gzip -c \'$hd5_format.in.input\' > umi_tools_input.gz\n- &&\n+#if $in.adata_format == \'mtx\'\n+ mkdir mtx\n+ #if $in.tenx.use == \'legacy_10x\'\n+ && cp \'$in.matrix\' \'mtx/matrix.mtx\'\n+ && cp \'$in.tenx.genes\' \'mtx/genes.tsv\'\n+ && cp \'$in.tenx.barcodes\' \'mtx/barcodes.tsv\'\n+ #else if $in.tenx.use == \'v3_10x\'\n+ && cp \'$in.matrix\' \'mtx/matrix.mtx\'\n+ && gzip \'mtx/matrix.mtx\'\n+ && cp \'$in.tenx.features\' \'mtx/features.tsv\'\n+ && gzip \'mtx/features.tsv\'\n+ && cp \'$in.tenx.barcodes\' \'mtx/barcodes.tsv\'\n+ && gzip \'mtx/barcodes.tsv\'\n #end if\n-\n- @CMD@\n-\n- #if $hd5_format.in.adata_format == \'mtx\'\n- && rm -rf mtx\n- #end if\n+ &&\n+#else if $in.adata_format == \'umi_tools\'\n+ ## avoid gzipping in the inputdir\n+ gzip -c \'$in.input\' > umi_tools_input.gz\n+ &&\n+#end if\n \n-#else:\n- python \'$__tool_directory__/tsv_to_loompy.py\'\n- -c \'${hd5_format.coldata}\'\n- -r \'${hd5_format.rowdata}\'\n- -f \'${hd5_format.mainmatrix}\'\n- #if $hd5_format.other_files:\n- \'${hd5_format.other_files}\'\n- #end if\n-#end if\n+@CMD@\n ]]></command>\n <configfiles>\n <configfile name="script_file"><![CDATA[\n @CMD_imports@\n-#if $hd5_format.filetype == \'anndata\'\n- #if $hd5_format.in.adata_format == \'loom\'\n+#if $in.adata_format == \'loom\'\n adata = ad.read_loom(\n- \'$hd5_format.in.input\',\n- sparse=$hd5_format.in.sparse,\n- cleanup=$hd5_format.in.cleanup,\n- X_name=\'$hd5_format.in.x_name\',\n- obs_names=\'$hd5_format.in.obs_names\',\n- var_names=\'$hd5_format.in.var_names\')\n+ \'$in.input\',\n+ sparse=$in.sparse,\n+ cleanup=$in.cleanup,\n+ X_name=\'$in.x_name\',\n+ obs_names=\'$in.obs_names\',\n+ var_names=\'$in.var_names\')\n \n- #else if $hd5_format.in.adata_format == \'tabular\'\n- #set delimiter=$hd5_format.in.input.metadata.delimiter\n- #if $delimiter != \',\'\n- '..b't>\n- <output name="anndata" value="import.tsv.h5ad" ftype="h5ad" compare="sim_size"/>\n </test>\n <test expect_num_outputs="1">\n <conditional name="in">\n@@ -226,8 +200,10 @@\n <conditional name="tenx">\n <param name="use" value="no"/>\n </conditional>\n- </conditional>\n- <output name="anndata" value="import.mtx.no_10x.h5ad" ftype="h5ad" compare="sim_size"/>\n+ </conditional>\n+ <assert_stdout>\n+ <has_text_matching expression="343 \xc3\x97 12"/>\n+ </assert_stdout>\n </test>\n <test expect_num_outputs="1">\n <conditional name="in">\n@@ -242,7 +218,14 @@\n <param name="gex_only" value="true"/>\n </conditional>\n </conditional>\n- <output name="anndata" value="import.mtx.legacy_10x.h5ad" ftype="h5ad" compare="sim_size"/>\n+ <assert_stdout>\n+ <has_text_matching expression="12 \xc3\x97 343"/>\n+ </assert_stdout>\n+ <output name="anndata" ftype="h5ad">\n+ <assert_contents>\n+ <has_h5_keys keys="var/gene_ids"/>\n+ </assert_contents>\n+ </output>\n </test>\n <test expect_num_outputs="1">\n <conditional name="in">\n@@ -257,31 +240,29 @@\n <param name="gex_only" value="true"/>\n </conditional>\n </conditional>\n- <output name="anndata" value="import.mtx.v3_10x.h5ad" ftype="h5ad" compare="sim_size"/>\n+ <assert_stdout>\n+ <has_text_matching expression="1107 \xc3\x97 507"/>\n+ </assert_stdout>\n+ <output name="anndata" ftype="h5ad">\n+ <assert_contents>\n+ <has_h5_keys keys="var/gene_ids"/>\n+ <has_h5_keys keys="var/feature_types"/>\n+ </assert_contents>\n+ </output>\n </test>\n <test expect_num_outputs="1">\n- <param name="filetype" value="anndata"/>\n <conditional name="in">\n <param name="adata_format" value="umi_tools"/>\n <param name="input" value="umi_tools.tsv"/>\n </conditional>\n- <output name="anndata" value="import.umi_tools.h5ad" ftype="h5ad" compare="sim_size"/>\n- </test>\n- <test expect_num_outputs="1">\n- <param name="filetype" value="loom"/>\n- <param name="mainmatrix" value="firstlayer.tsv"/>\n- <param name="other_files" value="secondlayer.tsv"/>\n- <param name="coldata" value="cols.tsv"/>\n- <param name="rowdata" value="rows.tsv"/>\n- <output name="loomdata" value="converted.loom.test" ftype="loom" compare="sim_size"/>\n+ <assert_stdout>\n+ <has_text_matching expression="2 \xc3\x97 13"/>\n+ </assert_stdout>\n </test>\n <test expect_num_outputs="1"><!-- 10x h5 test -->\n- <conditional name="hd5_format">\n- <param name="filetype" value="anndata"/>\n- <conditional name="in">\n- <param name="adata_format" value="10x_h5"/>\n- <param name="input" value="dropletutils_input.h5"/>\n- </conditional>\n+ <conditional name="in">\n+ <param name="adata_format" value="10x_h5"/>\n+ <param name="input" value="dropletutils_input.h5"/>\n </conditional>\n <output name="anndata">\n <assert_contents>\n@@ -296,7 +277,7 @@\n \n **What it does**\n \n-This tool creates an AnnData or loom dataset from several input types:\n+This tool creates an AnnData from several input types:\n \n - Loom (`read_loom method <https://anndata.readthedocs.io/en/latest/generated/anndata.read_loom.html>`__)\n - Tabular (`read_csv method <https://anndata.readthedocs.io/en/latest/generated/anndata.read_csv.html>`__)\n' |
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| diff -r 93dd15e13e6a -r d330b3082107 macros.xml --- a/macros.xml Sun Nov 12 16:42:57 2023 +0000 +++ b/macros.xml Sat Sep 14 19:58:24 2024 +0000 |
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| @@ -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> |
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