| Previous changeset 8:e98619de2776 (2023-11-12) Next changeset 10:db575b4c8b22 (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:
macros.xml modify_loom.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 e98619de2776 -r 0f1aaff9b22d macros.xml --- a/macros.xml Sun Nov 12 16:44:29 2023 +0000 +++ b/macros.xml Sat Sep 14 19:59:12 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 '${hd5_format.input}' - ]]> - </token> <token name="@CMD_imports@"><![CDATA[ import anndata as ad ]]> @@ -76,4 +71,11 @@ </when> </conditional> </xml> + <xml name="sanitize_query" token_validinitial="string.printable"> + <sanitizer> + <valid initial="@VALIDINITIAL@"> + <remove value="'" /> + </valid> + </sanitizer> + </xml> </macros> |
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| diff -r e98619de2776 -r 0f1aaff9b22d modify_loom.xml --- a/modify_loom.xml Sun Nov 12 16:44:29 2023 +0000 +++ b/modify_loom.xml Sat Sep 14 19:59:12 2024 +0000 |
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| b'@@ -1,62 +1,191 @@\n-<tool id="modify_loom" name="Manipulate loom object" version="@TOOL_VERSION@+galaxy1">\n- <description>Add layers, or row/column attributes to a loom file</description>\n+<tool id="modify_loom" name="Loom operations" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">\n+ <description>Manipulate, export and import loom data</description>\n <macros>\n <import>macros.xml</import>\n </macros>\n- <expand macro="requirements"/>\n+ <expand macro="requirements">\n+ <requirement type="package" version="1.26.4">numpy</requirement><!-- loompy seems to adapt to numpy 2.x. Remove this in the next update -->\n+ </expand>\n <expand macro="version_command"/>\n <command detect_errors="exit_code"><![CDATA[\n-cp \'${input}\' loom_add_out.loom &&\n-python \'$__tool_directory__/modify_loom.py\' -f \'loom_add_out.loom\'\n-#if $which_add.add_type == "cols":\n- -a cols -c \'${which_add.cols}\'\n-#else if $which_add.add_type == "cols":\n- -a rows -r \'${which_add.rows}\'\n-#else if $which_add.add_type == "layers":\n- -a layers -l \'${which_add.layers}\'\n+#if $operation.to_perform == \'manipulate\'\n+cp \'${operation.loom}\' converted.loom &&\n+python \'$__tool_directory__/modify_loom.py\' -f \'converted.loom\'\n+ #if $operation.which_add.add_type == "cols":\n+ -a cols -c \'${operation.which_add.cols}\'\n+ #else if $operation.which_add.add_type == "rows":\n+ -a rows -r \'${operation.which_add.rows}\'\n+ #else if $operation.which_add.add_type == "layers":\n+ -a layers -l \'${operation.which_add.layers}\'\n+ #end if\n+\n+#else if $operation.to_perform == \'export\'\n+mkdir ./output &&\n+mkdir ./attributes &&\n+python \'$__tool_directory__/loompy_to_tsv.py\' -f \'$operation.loom\'\n+\n+#else if $operation.to_perform == \'import\'\n+ #if $operation.from.file_type == \'ad\'\n+@CMD@\n+ #else if $operation.from.file_type == \'tab\'\n+python \'$__tool_directory__/tsv_to_loompy.py\'\n+ -c \'${operation.coldata}\'\n+ -r \'${operation.rowdata}\'\n+ -f \'${operation.mainmatrix}\'\n+ #if $operation.other_files\n+ \'${operation.other_files}\'\n+ #end if\n+ #end if\n #end if\n ]]></command>\n+ <configfiles>\n+ <configfile name="script_file"><![CDATA[\n+@CMD_imports@\n+#if $operation.to_perform == \'import\'\n+ #if $operation.from.file_type == \'ad\'\n+adata = ad.read_h5ad(\'$operation.anndata\')\n+adata.write_loom(\'converted.loom\')\n+ #end if\n+#end if\n+ ]]></configfile>\n+ </configfiles>\n <inputs>\n- <param name="input" type="data" format="loom" label="Loom file"/>\n- <conditional name="which_add">\n- <param name="add_type" type="select" label="Select data attribute to add to loom">\n- <option value="cols">Columns</option>\n- <option value="rows">Rows</option>\n- <option value="layers">Layers</option>\n+ <conditional name="operation">\n+ <param name="to_perform" type="select" label="Operation to perform on loom data">\n+ <option value="manipulate">Manipulate loom data</option>\n+ <option value="export">Export loom layers and attributes</option>\n+ <option value="import">Import loom from an anndata or tabular files</option>\n </param>\n- <when value="cols">\n- <param name="cols" type="data" format="tabular" label="Column file of same dimensions as existing file"/>\n+ <when value="manipulate">\n+ <param name="loom" type="data" format="loom" label="Loom file"/>\n+ <conditional name="which_add">\n+ <param name="add_type" type="select" label="Select data attribute to add to loom">\n+ <option value="cols">Columns</option>\n+ <option value="rows">Rows</option>\n+ <option value="layers">Layers</option>\n+ </param>\n+ <when value="cols">\n+ <param name="cols" type="data" format="'..b' <param name="cols" value="cols.tsv"/>\n+ </conditional>\n+ </conditional>\n <output name="loomout" value="addloomout1.loom" ftype="loom" compare="sim_size"/>\n </test>\n <test expect_num_outputs="1">\n- <param name="input" value="addtest.loom"/>\n- <param name="add_type" value="rows"/>\n- <param name="rows" value="rows.tsv"/>\n+ <conditional name="operation">\n+ <param name="to_perform" value="manipulate"/>\n+ <param name="loom" value="addtest.loom"/>\n+ <conditional name="which_add">\n+ <param name="add_type" value="rows"/>\n+ <param name="rows" value="rows.tsv"/>\n+ </conditional>\n+ </conditional>\n <output name="loomout" value="addloomout2.loom" ftype="loom" compare="sim_size"/>\n </test>\n <test expect_num_outputs="1">\n- <param name="input" value="addtest.loom"/>\n- <param name="add_type" value="layers"/>\n- <param name="layers" value="addlayer1.tsv"/>\n+ <conditional name="operation">\n+ <param name="to_perform" value="manipulate"/>\n+ <param name="loom" value="addtest.loom"/>\n+ <conditional name="which_add">\n+ <param name="add_type" value="layers"/>\n+ <param name="layers" value="addlayer1.tsv"/>\n+ </conditional>\n+ </conditional>\n <output name="loomout" value="addloomout3.loom" ftype="loom" compare="sim_size"/>\n </test>\n+ <test expect_num_outputs="2">\n+ <conditional name="operation">\n+ <param name="to_perform" value="export"/>\n+ <param name="loom" value="loomtest.loom"/>\n+ </conditional>\n+ <output_collection name="layer_tsvs" type="list">\n+ <element name="extralayer.tsv" value="secondlayer.tsv" ftype="tabular"/>\n+ <element name="mainmatrix.tsv" value="firstlayer.tsv" ftype="tabular"/>\n+ <element name="thirdlayer.tsv" value="finallayer.tsv" ftype="tabular"/>\n+ </output_collection>\n+ <output_collection name="attribute_tsvs" type="list">\n+ <element name="col_attr.tsv" value="cols.tsv" ftype="tabular"/>\n+ <element name="row_attr.tsv" value="rows.tsv" ftype="tabular"/>\n+ </output_collection>\n+ </test>\n+ <test expect_num_outputs="1">\n+ <conditional name="operation">\n+ <param name="to_perform" value="import"/>\n+ <conditional name="from">\n+ <param name="file_type" value="ad"/>\n+ <param name="anndata" value="krumsiek11.h5ad"/>\n+ </conditional>\n+ </conditional>\n+ <assert_stdout>\n+ <has_text_matching expression="adata.write_loom"/>\n+ </assert_stdout>\n+ <output name="loomout" value="export.krumsiek11.loom" ftype="loom" compare="sim_size"/>\n+ </test>\n+ <test expect_num_outputs="1">\n+ <conditional name="operation">\n+ <param name="to_perform" value="import"/>\n+ <conditional name="from">\n+ <param name="file_type" value="tab"/>\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+ </conditional>\n+ </conditional>\n+ <output name="loomout" value="converted.loom.test" ftype="loom" compare="sim_size"/>\n+ </test>\n </tests>\n <help><![CDATA[\n This tool allows the user to modify an existing loom data file by adding column attributes, row attributes or additional layers via tsv files.\n' |
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