| Previous changeset 5:524aa62a6066 (2020-02-10) Next changeset 7:215733a383f2 (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:
macros.xml remove_confounders.xml |
| b |
| diff -r 524aa62a6066 -r f2f6c703da06 macros.xml --- a/macros.xml Mon Feb 10 05:27:49 2020 -0500 +++ b/macros.xml Thu Feb 20 08:24:15 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> |
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| diff -r 524aa62a6066 -r f2f6c703da06 remove_confounders.xml --- a/remove_confounders.xml Mon Feb 10 05:27:49 2020 -0500 +++ b/remove_confounders.xml Thu Feb 20 08:24:15 2020 -0500 |
| [ |
| @@ -103,22 +103,28 @@ <param argument="key" type="text" value="batch" label="Key to a categorical annotation from adata.obs that will be used for batch effect removal"/> </when> </conditional> + <expand macro="inputs_common_advanced"/> </inputs> <outputs> <expand macro="anndata_outputs"/> </outputs> <tests> <test> - <!-- test 1 --> + <!-- test 0 --> <param name="adata" value="krumsiek11.h5ad" /> <conditional name="method"> <param name="method" value="pp.regress_out"/> <param name="keys" value="cell_type"/> </conditional> - <assert_stdout> - <has_text_matching expression="sc.pp.regress_out"/> - <has_text_matching expression="keys=\['cell_type'\]"/> - </assert_stdout> + <section name="advanced_common"> + <param name="show_log" value="true" /> + </section> + <output name="hidden_output"> + <assert_contents> + <has_text_matching expression="sc.pp.regress_out"/> + <has_text_matching expression="keys=\['cell_type'\]"/> + </assert_contents> + </output> <output name="anndata_out" file="pp.regress_out.krumsiek11.h5ad" ftype="h5ad" compare="sim_size"/> </test> <!--<test> @@ -135,16 +141,21 @@ <output name="anndata_out" file="pp.mnn_correct.krumsiek11.h5ad" ftype="h5ad" compare="sim_size"/> </test>--> <test> - <!-- test 2 --> + <!-- test 1 --> <param name="adata" value="blobs.h5ad" /> <conditional name="method"> <param name="method" value="pp.combat"/> <param name="key" value="blobs"/> </conditional> - <assert_stdout> - <has_text_matching expression="sc.pp.combat"/> - <has_text_matching expression="key='blobs'"/> - </assert_stdout> + <section name="advanced_common"> + <param name="show_log" value="true" /> + </section> + <output name="hidden_output"> + <assert_contents> + <has_text_matching expression="sc.pp.combat"/> + <has_text_matching expression="key='blobs'"/> + </assert_contents> + </output> <output name="anndata_out" file="pp.combat.blobs.h5ad" ftype="h5ad" compare="sim_size"/> </test> </tests> |