| Previous changeset 5:08192eebb47d (2020-02-10) Next changeset 7:6c145a6868cc (2020-05-20) |
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Commit message:
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" |
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modified:
inspect.xml macros.xml |
| b |
| diff -r 08192eebb47d -r 5e9171dc8244 inspect.xml --- a/inspect.xml Mon Feb 10 05:29:16 2020 -0500 +++ b/inspect.xml Thu Feb 20 08:25:37 2020 -0500 |
| [ |
| b'@@ -461,13 +461,14 @@\n </when>\n <when value="pp.sqrt"/>\n </conditional>\n+ <expand macro="inputs_common_advanced"/>\n </inputs>\n <outputs>\n <expand macro="anndata_outputs"/>\n </outputs>\n <tests>\n <test>\n- <!-- test 1 -->\n+ <!-- test 0 -->\n <param name="adata" value="sparce_csr_matrix.h5ad" />\n <conditional name="method">\n <param name="method" value="pp.calculate_qc_metrics"/>\n@@ -476,16 +477,21 @@\n <param name="qc_vars" value="mito,negative"/>\n <param name="percent_top" value=""/>\n </conditional>\n- <assert_stdout>\n- <has_text_matching expression="sc.pp.calculate_qc_metrics" />\n- <has_text_matching expression="expr_type=\'counts\'" />\n- <has_text_matching expression="var_type=\'genes\'" />\n- <has_text_matching expression="qc_vars=\\[\'mito\', \'negative\'\\]" />\n- </assert_stdout>\n+ <section name="advanced_common">\n+ <param name="show_log" value="true" />\n+ </section>\n+ <output name="hidden_output">\n+ <assert_contents>\n+ <has_text_matching expression="sc.pp.calculate_qc_metrics" />\n+ <has_text_matching expression="expr_type=\'counts\'" />\n+ <has_text_matching expression="var_type=\'genes\'" />\n+ <has_text_matching expression="qc_vars=\\[\'mito\', \'negative\'\\]" />\n+ </assert_contents>\n+ </output>\n <output name="anndata_out" file="pp.calculate_qc_metrics.sparce_csr_matrix.h5ad" ftype="h5ad" compare="sim_size"/>\n </test>\n <test>\n- <!-- test 2 -->\n+ <!-- test 1 -->\n <param name="adata" value="pp.recipe_weinreb17.paul15_subsample.h5ad" />\n <conditional name="method">\n <param name="method" value="pp.neighbors"/>\n@@ -495,14 +501,19 @@\n <param name="pp_neighbors_method" value="umap"/>\n <param name="metric" value="euclidean"/>\n </conditional>\n- <assert_stdout>\n- <has_text_matching expression="sc.pp.neighbors"/>\n- <has_text_matching expression="n_neighbors=15"/>\n- <has_text_matching expression="knn=True"/>\n- <has_text_matching expression="random_state=0"/>\n- <has_text_matching expression="method=\'umap\'"/>\n- <has_text_matching expression="metric=\'euclidean\'"/>\n- </assert_stdout>\n+ <section name="advanced_common">\n+ <param name="show_log" value="true" />\n+ </section>\n+ <output name="hidden_output">\n+ <assert_contents>\n+ <has_text_matching expression="sc.pp.neighbors"/>\n+ <has_text_matching expression="n_neighbors=15"/>\n+ <has_text_matching expression="knn=True"/>\n+ <has_text_matching expression="random_state=0"/>\n+ <has_text_matching expression="method=\'umap\'"/>\n+ <has_text_matching expression="metric=\'euclidean\'"/>\n+ </assert_contents>\n+ </output>\n <output name="anndata_out" file="pp.neighbors_umap_euclidean.recipe_weinreb17.paul15_subsample.h5ad" ftype="h5ad" compare="sim_size">\n <assert_contents>\n <has_h5_keys keys="X, obs, obsm, uns, var" />\n@@ -510,7 +521,7 @@\n </output>\n </test>\n <test>\n- <!-- test 3 -->\n+ <!-- test 2 -->\n <param name="adata" value="pp.recipe_weinreb17.paul15_subsample.h5ad" />\n <conditional name="method">\n <param name="method" value="pp.neighbors"/>\n@@ -519,18 +530,23 @@\n <param name="pp_neighbors_method" value="gauss"/>\n '..b'_contents>\n+ <has_text_matching expression="sc.pp.log1p"/>\n+ </assert_contents>\n+ </output>\n <output name="anndata_out" file="pp.log1p.krumsiek11.h5ad" ftype="h5ad" compare="sim_size"/>\n </test>\n <test>\n+ <!-- test 9 -->\n+ <param name="adata" value="krumsiek11.h5ad" />\n+ <conditional name="method">\n+ <param name="method" value="pp.scale"/>\n+ <param name="zero_center" value="true"/>\n+ </conditional>\n+ <section name="advanced_common">\n+ <param name="show_log" value="true" />\n+ </section>\n+ <output name="hidden_output">\n+ <assert_contents>\n+ <has_text_matching expression="sc.pp.scale"/>\n+ <has_text_matching expression="zero_center=True"/>\n+ </assert_contents>\n+ </output>\n+ <output name="anndata_out" file="pp.scale.krumsiek11.h5ad" ftype="h5ad" compare="sim_size"/>\n+ </test>\n+ <test>\n <!-- test 10 -->\n <param name="adata" value="krumsiek11.h5ad" />\n <conditional name="method">\n <param name="method" value="pp.scale"/>\n <param name="zero_center" value="true"/>\n+ <param name="max_value" value="10"/>\n </conditional>\n- <assert_stdout>\n- <has_text_matching expression="sc.pp.scale"/>\n- <has_text_matching expression="zero_center=True"/>\n- </assert_stdout>\n- <output name="anndata_out" file="pp.scale.krumsiek11.h5ad" ftype="h5ad" compare="sim_size"/>\n+ <section name="advanced_common">\n+ <param name="show_log" value="true" />\n+ </section>\n+ <output name="hidden_output">\n+ <assert_contents>\n+ <has_text_matching expression="sc.pp.scale"/>\n+ <has_text_matching expression="zero_center=True"/>\n+ <has_text_matching expression="max_value=10.0"/>\n+ </assert_contents>\n+ </output>\n+ <output name="anndata_out" file="pp.scale_max_value.krumsiek11.h5ad" ftype="h5ad" compare="sim_size"/>\n </test>\n <test>\n <!-- test 11 -->\n <param name="adata" value="krumsiek11.h5ad" />\n <conditional name="method">\n- <param name="method" value="pp.scale"/>\n- <param name="zero_center" value="true"/>\n- <param name="max_value" value="10"/>\n- </conditional>\n- <assert_stdout>\n- <has_text_matching expression="sc.pp.scale"/>\n- <has_text_matching expression="zero_center=True"/>\n- <has_text_matching expression="max_value=10.0"/>\n- </assert_stdout>\n- <output name="anndata_out" file="pp.scale_max_value.krumsiek11.h5ad" ftype="h5ad" compare="sim_size"/>\n- </test>\n- <test>\n- <!-- test 12 -->\n- <param name="adata" value="krumsiek11.h5ad" />\n- <conditional name="method">\n <param name="method" value="pp.sqrt"/>\n </conditional>\n- <assert_stdout>\n- <has_text_matching expression="sc.pp.sqrt"/>\n- </assert_stdout>\n+ <section name="advanced_common">\n+ <param name="show_log" value="true" />\n+ </section>\n+ <output name="hidden_output">\n+ <assert_contents>\n+ <has_text_matching expression="sc.pp.sqrt"/>\n+ </assert_contents>\n+ </output>\n <output name="anndata_out" file="pp.sqrt.krumsiek11.h5ad" ftype="h5ad" compare="sim_size"/>\n </test>\n </tests>\n@@ -889,4 +950,4 @@\n `X = sqrt(X)`\n ]]></help>\n <expand macro="citations"/>\n-</tool>\n\\ No newline at end of file\n+</tool>\n' |
| b |
| diff -r 08192eebb47d -r 5e9171dc8244 macros.xml --- a/macros.xml Mon Feb 10 05:29:16 2020 -0500 +++ b/macros.xml Thu Feb 20 08:25:37 2020 -0500 |
| [ |
| @@ -21,12 +21,17 @@ </xml> <token name="@CMD@"><![CDATA[ cp '$adata' 'anndata.h5ad' && -cat '$script_file' && -python '$script_file' && -ls . +cat '$script_file' > '$hidden_output' && +python '$script_file' >> '$hidden_output' && +ls . >> '$hidden_output' && +touch 'anndata_info.txt' && +cat 'anndata_info.txt' @CMD_prettify_stdout@ ]]> </token> <token name="@CMD_imports@"><![CDATA[ +import sys +sys.stderr = open('$hidden_output', 'a') + import scanpy as sc import pandas as pd import numpy as np @@ -39,13 +44,25 @@ adata = sc.read('anndata.h5ad') ]]> </token> + <xml name="inputs_common_advanced"> + <section name="advanced_common" title="Advanced Options" expanded="false"> + <param name="show_log" type="boolean" checked="false" label="Output Log?" /> + </section> + </xml> <xml name="anndata_outputs"> <data name="anndata_out" format="h5ad" from_work_dir="anndata.h5ad" label="${tool.name} (${method.method}) on ${on_string}: Annotated data matrix"/> + <data name="hidden_output" format="txt" label="Log file" > + <filter>advanced_common['show_log']</filter> + </data> </xml> <token name="@CMD_anndata_write_outputs@"><![CDATA[ adata.write('anndata.h5ad') +with open('anndata_info.txt','w', encoding='utf-8') as ainfo: + print(adata, file=ainfo) ]]> </token> + <token name="@CMD_prettify_stdout@"><![CDATA[ | sed -r '1 s|AnnData object with (.+) = (.*)\s*|\1: \2|g' | sed "s|'||g" | sed -r 's|^\s*(.*):\s(.*)|[\1]\n- \2|g' | sed 's|, |\n- |g' + ]]></token> <xml name="svd_solver"> <param name="svd_solver" type="select" label="SVD solver to use" help=""> <option value="auto">Automatically chosen depending on the size of the problem</option> |