Mercurial > repos > iuc > modify_loom
changeset 9:0f1aaff9b22d 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 19:59:12 +0000 |
| parents | e98619de2776 |
| children | |
| files | 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/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, 171 insertions(+), 40 deletions(-) [+] |
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--- a/macros.xml Sun Nov 12 16:44:29 2023 +0000 +++ b/macros.xml Sat Sep 14 19:59:12 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 '${hd5_format.input}' - ]]> - </token> <token name="@CMD_imports@"><![CDATA[ import anndata as ad ]]> @@ -76,4 +71,11 @@ </when> </conditional> </xml> + <xml name="sanitize_query" token_validinitial="string.printable"> + <sanitizer> + <valid initial="@VALIDINITIAL@"> + <remove value="'" /> + </valid> + </sanitizer> + </xml> </macros>
--- a/modify_loom.xml Sun Nov 12 16:44:29 2023 +0000 +++ b/modify_loom.xml Sat Sep 14 19:59:12 2024 +0000 @@ -1,62 +1,191 @@ -<tool id="modify_loom" name="Manipulate loom object" version="@TOOL_VERSION@+galaxy1"> - <description>Add layers, or row/column attributes to a loom file</description> +<tool id="modify_loom" name="Loom operations" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@"> + <description>Manipulate, export and import loom data</description> <macros> <import>macros.xml</import> </macros> - <expand macro="requirements"/> + <expand macro="requirements"> + <requirement type="package" version="1.26.4">numpy</requirement><!-- loompy seems to adapt to numpy 2.x. Remove this in the next update --> + </expand> <expand macro="version_command"/> <command detect_errors="exit_code"><![CDATA[ -cp '${input}' loom_add_out.loom && -python '$__tool_directory__/modify_loom.py' -f 'loom_add_out.loom' -#if $which_add.add_type == "cols": - -a cols -c '${which_add.cols}' -#else if $which_add.add_type == "cols": - -a rows -r '${which_add.rows}' -#else if $which_add.add_type == "layers": - -a layers -l '${which_add.layers}' +#if $operation.to_perform == 'manipulate' +cp '${operation.loom}' converted.loom && +python '$__tool_directory__/modify_loom.py' -f 'converted.loom' + #if $operation.which_add.add_type == "cols": + -a cols -c '${operation.which_add.cols}' + #else if $operation.which_add.add_type == "rows": + -a rows -r '${operation.which_add.rows}' + #else if $operation.which_add.add_type == "layers": + -a layers -l '${operation.which_add.layers}' + #end if + +#else if $operation.to_perform == 'export' +mkdir ./output && +mkdir ./attributes && +python '$__tool_directory__/loompy_to_tsv.py' -f '$operation.loom' + +#else if $operation.to_perform == 'import' + #if $operation.from.file_type == 'ad' +@CMD@ + #else if $operation.from.file_type == 'tab' +python '$__tool_directory__/tsv_to_loompy.py' + -c '${operation.coldata}' + -r '${operation.rowdata}' + -f '${operation.mainmatrix}' + #if $operation.other_files + '${operation.other_files}' + #end if + #end if #end if ]]></command> + <configfiles> + <configfile name="script_file"><![CDATA[ +@CMD_imports@ +#if $operation.to_perform == 'import' + #if $operation.from.file_type == 'ad' +adata = ad.read_h5ad('$operation.anndata') +adata.write_loom('converted.loom') + #end if +#end if + ]]></configfile> + </configfiles> <inputs> - <param name="input" type="data" format="loom" label="Loom file"/> - <conditional name="which_add"> - <param name="add_type" type="select" label="Select data attribute to add to loom"> - <option value="cols">Columns</option> - <option value="rows">Rows</option> - <option value="layers">Layers</option> + <conditional name="operation"> + <param name="to_perform" type="select" label="Operation to perform on loom data"> + <option value="manipulate">Manipulate loom data</option> + <option value="export">Export loom layers and attributes</option> + <option value="import">Import loom from an anndata or tabular files</option> </param> - <when value="cols"> - <param name="cols" type="data" format="tabular" label="Column file of same dimensions as existing file"/> + <when value="manipulate"> + <param name="loom" type="data" format="loom" label="Loom file"/> + <conditional name="which_add"> + <param name="add_type" type="select" label="Select data attribute to add to loom"> + <option value="cols">Columns</option> + <option value="rows">Rows</option> + <option value="layers">Layers</option> + </param> + <when value="cols"> + <param name="cols" type="data" format="tabular" label="Column file of same dimensions as existing file"/> + </when> + <when value="rows"> + <param name="rows" type="data" format="tabular" label="Row file of same dimensions as existing file"/> + </when> + <when value="layers"> + <param name="layers" type="data" multiple="true" format="tabular" label="Layer file(s) of same dimensions as existing file"/> + </when> + </conditional> </when> - <when value="rows"> - <param name="rows" type="data" format="tabular" label="Row file of same dimensions as existing file"/> + <when value="export"> + <param name="loom" type="data" format="loom" label="Loom file"/> </when> - <when value="layers"> - <param name="layers" type="data" multiple="true" format="tabular" label="Layer file(s) of same dimensions as existing file"/> + <when value="import"> + <conditional name="from"> + <param name="file_type" type="select" label="Create loom file from"> + <option value="ad">an anndata object</option> + <option value="tab">from tabular files of matrix and row and column attributes</option> + </param> + <when value="ad"> + <param name="anndata" type="data" format="h5ad" label="Anndata file"/> + </when> + <when value="tab"> + <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> + </conditional> + </when> </conditional> </inputs> <outputs> - <data name="loomout" format="loom" from_work_dir='loom_add_out.loom' label="Expanded loom file from '${on_string}'"/> + <data name="loomout" format="loom" from_work_dir='converted.loom' label="${tool.name} (${operation.to_perform}) on ${on_string} Loom file"> + <filter>operation['to_perform'] == 'manipulate' or operation['to_perform'] == 'import'</filter> + </data> + <collection name="layer_tsvs" type="list" label="Layer matrices" > + <filter>operation['to_perform'] == 'export'</filter> + <discover_datasets pattern="__designation__" format="tabular" directory="output" visible="false" /> + </collection> + <collection name="attribute_tsvs" type="list" label="Attribute matrices" > + <filter>operation['to_perform'] == 'export'</filter> + <discover_datasets pattern="__designation__" format="tabular" directory="attributes" visible="false" /> + </collection> </outputs> <tests> <test expect_num_outputs="1"> - <param name="input" value="addtest.loom"/> - <param name="add_type" value="cols"/> - <param name="cols" value="cols.tsv"/> + <conditional name="operation"> + <param name="to_perform" value="manipulate"/> + <param name="loom" value="addtest.loom"/> + <conditional name="which_add"> + <param name="add_type" value="cols"/> + <param name="cols" value="cols.tsv"/> + </conditional> + </conditional> <output name="loomout" value="addloomout1.loom" ftype="loom" compare="sim_size"/> </test> <test expect_num_outputs="1"> - <param name="input" value="addtest.loom"/> - <param name="add_type" value="rows"/> - <param name="rows" value="rows.tsv"/> + <conditional name="operation"> + <param name="to_perform" value="manipulate"/> + <param name="loom" value="addtest.loom"/> + <conditional name="which_add"> + <param name="add_type" value="rows"/> + <param name="rows" value="rows.tsv"/> + </conditional> + </conditional> <output name="loomout" value="addloomout2.loom" ftype="loom" compare="sim_size"/> </test> <test expect_num_outputs="1"> - <param name="input" value="addtest.loom"/> - <param name="add_type" value="layers"/> - <param name="layers" value="addlayer1.tsv"/> + <conditional name="operation"> + <param name="to_perform" value="manipulate"/> + <param name="loom" value="addtest.loom"/> + <conditional name="which_add"> + <param name="add_type" value="layers"/> + <param name="layers" value="addlayer1.tsv"/> + </conditional> + </conditional> <output name="loomout" value="addloomout3.loom" ftype="loom" compare="sim_size"/> </test> + <test expect_num_outputs="2"> + <conditional name="operation"> + <param name="to_perform" value="export"/> + <param name="loom" value="loomtest.loom"/> + </conditional> + <output_collection name="layer_tsvs" type="list"> + <element name="extralayer.tsv" value="secondlayer.tsv" ftype="tabular"/> + <element name="mainmatrix.tsv" value="firstlayer.tsv" ftype="tabular"/> + <element name="thirdlayer.tsv" value="finallayer.tsv" ftype="tabular"/> + </output_collection> + <output_collection name="attribute_tsvs" type="list"> + <element name="col_attr.tsv" value="cols.tsv" ftype="tabular"/> + <element name="row_attr.tsv" value="rows.tsv" ftype="tabular"/> + </output_collection> + </test> + <test expect_num_outputs="1"> + <conditional name="operation"> + <param name="to_perform" value="import"/> + <conditional name="from"> + <param name="file_type" value="ad"/> + <param name="anndata" value="krumsiek11.h5ad"/> + </conditional> + </conditional> + <assert_stdout> + <has_text_matching expression="adata.write_loom"/> + </assert_stdout> + <output name="loomout" value="export.krumsiek11.loom" ftype="loom" compare="sim_size"/> + </test> + <test expect_num_outputs="1"> + <conditional name="operation"> + <param name="to_perform" value="import"/> + <conditional name="from"> + <param name="file_type" value="tab"/> + <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"/> + </conditional> + </conditional> + <output name="loomout" value="converted.loom.test" ftype="loom" compare="sim_size"/> + </test> </tests> <help><![CDATA[ This tool allows the user to modify an existing loom data file by adding column attributes, row attributes or additional layers via tsv files.
Binary file test-data/pp.neighbors_umap_euclidean.recipe_weinreb17.paul15_subsample.h5ad has changed