Mercurial > repos > iuc > episcanpy_preprocess
changeset 1:29f5f25b9935 draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit bb79cb8cad3bc1433bff7caf9d7b45e7993dd470
| author | iuc |
|---|---|
| date | Sat, 22 Apr 2023 12:13:44 +0000 |
| parents | 8ba672d0d8aa |
| children | |
| files | macros.xml preprocess.xml test-data/chrY.h5ad test-data/chrY_norm_peaks.h5ad test-data/chrY_with_transcript_annotation.h5ad |
| diffstat | 5 files changed, 84 insertions(+), 6 deletions(-) [+] |
line wrap: on
line diff
--- a/macros.xml Tue Apr 18 13:18:50 2023 +0000 +++ b/macros.xml Sat Apr 22 12:13:44 2023 +0000 @@ -1,6 +1,6 @@ <macros> <token name="@TOOL_VERSION@">0.3.2</token> - <token name="@VERSION_SUFFIX@">0</token> + <token name="@VERSION_SUFFIX@">1</token> <token name="@PROFILE@">21.01</token> <xml name="requirements"> <requirements>
--- a/preprocess.xml Tue Apr 18 13:18:50 2023 +0000 +++ b/preprocess.xml Sat Apr 22 12:13:44 2023 +0000 @@ -102,6 +102,16 @@ save='plot.png' ) +#else if $method.method == 'tl.find_genes' +esc.tl.find_genes( + adata, + gtf_file='$method.find_genes_gtf_file', + key_added='$method.find_genes_key_added', + upstream=$method.find_genes_upstream, + feature_type='$method.find_genes_feature_type', + annotation='$method.find_genes_annotation', + raw=$method.find_genes_raw) + #end if @CMD_anndata_write_outputs@ ]]></configfile> @@ -119,6 +129,7 @@ <option value="pp.select_var_feature">Select the most variable features, 'pp.select_var_feature'</option> <option value="pp.cal_var">Show distribution plots of cells sharing features and variability score 'pp.cal_var'</option> <option value="pp.variability_features">Computes variability score to rank the most variable features across all cells, using 'pp.variability_features'</option> + <option value="tl.find_genes">Embedding: Find genes and add annotations, using 'pp.find_genes'</option> </param> <when value="pp.binarize" /> <when value="pp.filter_cells"> @@ -186,13 +197,57 @@ <option value="log10">Log10</option> </param> </when> + <when value="tl.find_genes"> + <param name="find_genes_gtf_file" type="data" format="gtf" label="Annotation GTF file" help="(gtf_file)"/> + <param name="find_genes_key_added" value="transcript_annotation" type="text" label="Key added" help="(key_added)"> + <sanitizer invalid_char=""> + <valid initial="string.letters,string.digits"> + <add value="_" /> + <add value="-" /> + <add value="." /> + <add value=" " /> + <add value="," /> + </valid> + </sanitizer> + <validator type="regex">[0-9a-zA-Z_., -]+</validator> + </param> + <param name="find_genes_upstream" value="2000" min="0" type="integer" label="Upstream" help="(upstream)"/> + <param name="find_genes_feature_type" value="transcript" type="text" label="Feature type" help="(feature_type)"> + <sanitizer invalid_char=""> + <valid initial="string.letters,string.digits"> + <add value="_" /> + <add value="-" /> + <add value="." /> + <add value=" " /> + <add value="," /> + </valid> + </sanitizer> + <validator type="regex">[0-9a-zA-Z_., -]+</validator> + </param> + <param name="find_genes_annotation" value="HAVANA" type="text" label="Annotation" help="(annotation)"> + <sanitizer invalid_char=""> + <valid initial="string.letters,string.digits"> + <add value="_" /> + <add value="-" /> + <add value="." /> + <add value=" " /> + <add value="," /> + </valid> + </sanitizer> + <validator type="regex">[0-9a-zA-Z_., -]+</validator> + </param> + <param name="find_genes_raw" type="select" label="Raw?" help="(raw)"> + <option value="True">True</option> + <option value="False" selected="true">False</option> + </param> + </when> </conditional> <expand macro="inputs_common_advanced"/> </inputs> <outputs> <expand macro="anndata_outputs"/> - <data name="out_png" format="png" from_work_dir="plot.png" label="${tool.name} (${method.method}) on ${on_string}"> - <filter>method['method'] != 'pp.binarize' and method['method'] != 'pp.filter_cells' and method['method'] != 'pp.filter_features' and method['method'] != 'nb_feat_log' and method['method'] != 'select_var_feature'</filter> + <data name="out_png" format="png" from_work_dir="plot.png" label="${tool.name} (${method.method}) plot on ${on_string}"> + <filter>method['method'] != 'pp.binarize' and method['method'] != 'pp.filter_cells' and method['method'] != 'pp.filter_features' and method['method'] != 'nb_feat_log' and method['method'] != 'pp.select_var_feature' and method['method'] !='tl.find_genes'</filter> </data> </outputs> <tests> @@ -263,7 +318,7 @@ <has_text_matching expression="nb_features"/> </assert_stdout> </test> - <test expect_num_outputs="3"> + <test expect_num_outputs="2"> <!-- pp.select_var_feature --> <param name="adata" value="krumsiek11.h5ad" /> <conditional name="method"> @@ -372,6 +427,27 @@ <output name="anndata_out" file="krumsiek11.pp.variability_features.h5ad" ftype="h5ad" compare="sim_size"/> <output name="out_png" file="krumsiek11.pp.variability_features.png" ftype="png" compare="sim_size"/> </test> + <test expect_num_outputs="2"> + <!-- tl.find_genes --> + <param name="adata" value="chrY.h5ad" /> + <conditional name="method"> + <param name="method" value="tl.find_genes"/> + <param name="find_genes_gtf_file" value="chrY.gtf"/> + <param name="find_genes_key_added" value="transcript_annotation"/> + <param name="find_genes_upstream" value="2000"/> + <param name="find_genes_feature_type" value="transcript"/> + <param name="find_genes_annotation" value="HAVANA"/> + <param name="find_genes_raw" value="False"/> + </conditional> + <section name="advanced_common"> + <param name="show_log" value="true" /> + </section> + <output name="anndata_out" file="chrY_with_transcript_annotation.h5ad" ftype="h5ad" compare="sim_size"> + <assert_contents> + <has_h5_keys keys="var" /> + </assert_contents> + </output> + </test> </tests> <help><![CDATA[ @@ -426,7 +502,6 @@ Distribution of cells sharing features and variability score (`pp.cal_var`) ============================================================================= - Show distribution plots of cells sharing features and variability score. More details on the `episcanpy documentation @@ -434,8 +509,11 @@ Compute a variability score to rank the most variable features across all cells (`pp.variability_features`) ============================================================================================================ +This function computes a variability score to rank the most variable features across all cells. Then it selects the most variable features according to either a specified number of features (nb_features) or a minimum variance score (min_score). -This function computes a variability score to rank the most variable features across all cells. Then it selects the most variable features according to either a specified number of features (nb_features) or a minimum variance score (min_score). +Find and add gene annotations (`tl.find_genes`) +======================================================================================== +This function adds a gene annotation to an AnnData (h5ad) file from annotations file (.annotation.gtf). More details on the `episcanpy documentation <https://colomemaria.github.io/episcanpy_doc/api/episcanpy.api.pp.variability_features.html>`__