| Previous changeset 5:8b9610ab366a (2020-02-10) Next changeset 7:3c86f71498bc (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:
filter.xml macros.xml |
| b |
| diff -r 8b9610ab366a -r a97abb8cd15b filter.xml --- a/filter.xml Mon Feb 10 05:29:59 2020 -0500 +++ b/filter.xml Thu Feb 20 08:26:18 2020 -0500 |
| b |
| b'@@ -215,13 +215,14 @@\n <param argument="replace" type="boolean" truevalue="True" falsevalue="False" checked="false" label="Sample the counts with replacement?"/>\n </when>\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="krumsiek11.h5ad" />\n <conditional name="method">\n <param name="method" value="pp.filter_cells"/>\n@@ -231,13 +232,21 @@\n </conditional>\n </conditional>\n <assert_stdout>\n- <has_text_matching expression="sc.pp.filter_cells"/>\n- <has_text_matching expression="min_counts=3"/>\n+ <has_text_matching expression="336 \xc3\x97 11"/>\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.filter_cells"/>\n+ <has_text_matching expression="min_counts=3"/>\n+ </assert_contents>\n+ </output>\n <output name="anndata_out" file="pp.filter_cells.krumsiek11-min_counts.h5ad" ftype="h5ad" compare="sim_size"/>\n </test>\n <test>\n- <!-- test 2 -->\n+ <!-- test 1 -->\n <param name="adata" value="krumsiek11.h5ad" />\n <conditional name="method">\n <param name="method" value="pp.filter_cells"/>\n@@ -246,15 +255,20 @@\n <param name="max_genes" value="100"/>\n </conditional>\n </conditional>\n- <assert_stdout>\n- <has_text_matching expression="sc.pp.filter_cells"/>\n- <has_text_matching expression="adata"/>\n- <has_text_matching expression="max_genes=100"/>\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.filter_cells"/>\n+ <has_text_matching expression="adata"/>\n+ <has_text_matching expression="max_genes=100"/>\n+ </assert_contents>\n+ </output>\n <output name="anndata_out" file="pp.filter_cells.krumsiek11-max_genes.h5ad" ftype="h5ad" compare="sim_size"/>\n </test>\n <test>\n- <!-- test 3 -->\n+ <!-- test 2 -->\n <param name="adata" value="krumsiek11.h5ad" />\n <conditional name="method">\n <param name="method" value="pp.filter_genes"/>\n@@ -263,39 +277,47 @@\n <param name="min_counts" value="3"/>\n </conditional>\n </conditional>\n- <assert_stdout>\n- <has_text_matching expression="sc.pp.filter_genes"/>\n- <has_text_matching expression="min_counts=3"/>\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.filter_genes"/>\n+ <has_text_matching expression="min_counts=3"/>\n+ </assert_contents>\n+ </output>\n <output name="anndata_out" file="pp.filter_genes.krumsiek11-min_counts.h5ad" ftype="h5ad" compare="sim_size"/>\n </test>\n+ <!-- <test> -->\n+ <!-- <!-\\- test 3 -\\-> -->\n+ <!-- <!-\\- Input dataset appears to be missing rank_genes_groups key.'..b's.krumsiek11-cell_ranger.h5ad" ftype="h5ad" compare="sim_size"/>\n </test>\n <test>\n- <!-- test 7 -->\n+ <!-- test 6 -->\n <param name="adata" value="krumsiek11.h5ad" />\n <conditional name="method">\n <param name="method" value="pp.subsample"/>\n@@ -351,15 +383,20 @@\n </conditional>\n <param name="random_state" value="0"/>\n </conditional>\n- <assert_stdout>\n- <has_text_matching expression="sc.pp.subsample"/>\n- <has_text_matching expression="fraction=0.5"/>\n- <has_text_matching expression="random_state=0"/>\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.subsample"/>\n+ <has_text_matching expression="fraction=0.5"/>\n+ <has_text_matching expression="random_state=0"/>\n+ </assert_contents>\n+ </output>\n <output name="anndata_out" file="pp.subsample.krumsiek11_fraction.h5ad" ftype="h5ad" compare="sim_size"/>\n </test>\n <test>\n- <!-- test 8 -->\n+ <!-- test 7 -->\n <param name="adata" value="krumsiek11.h5ad" />\n <conditional name="method">\n <param name="method" value="pp.subsample"/>\n@@ -369,15 +406,20 @@\n </conditional>\n <param name="random_state" value="0"/>\n </conditional>\n- <assert_stdout>\n- <has_text_matching expression="sc.pp.subsample"/>\n- <has_text_matching expression="n_obs=10"/>\n- <has_text_matching expression="random_state=0"/>\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.subsample"/>\n+ <has_text_matching expression="n_obs=10"/>\n+ <has_text_matching expression="random_state=0"/>\n+ </assert_contents>\n+ </output>\n <output name="anndata_out" file="pp.subsample.krumsiek11_n_obs.h5ad" ftype="h5ad" compare="sim_size"/>\n </test>\n <test>\n- <!-- test 9 -->\n+ <!-- test 8 -->\n <param name="adata" value="random-randint.h5ad" />\n <conditional name="method">\n <param name="method" value="pp.downsample_counts"/>\n@@ -385,12 +427,17 @@\n <param name="random_state" value="0"/>\n <param name="replace" value="false"/>\n </conditional>\n- <assert_stdout>\n- <has_text_matching expression="sc.pp.downsample_counts"/>\n- <has_text_matching expression="total_counts=20000"/>\n- <has_text_matching expression="random_state=0"/>\n- <has_text_matching expression="replace=False"/>\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.downsample_counts"/>\n+ <has_text_matching expression="total_counts=20000"/>\n+ <has_text_matching expression="random_state=0"/>\n+ <has_text_matching expression="replace=False"/>\n+ </assert_contents>\n+ </output>\n <output name="anndata_out" file="pp.downsample_counts.random-randint.h5ad" ftype="h5ad" compare="sim_size"/>\n </test>\n </tests>\n' |
| b |
| diff -r 8b9610ab366a -r a97abb8cd15b macros.xml --- a/macros.xml Mon Feb 10 05:29:59 2020 -0500 +++ b/macros.xml Thu Feb 20 08:26:18 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> |