| Previous changeset 5:6f2d2c7f77ee (2020-02-10) Next changeset 7:b2df381a6004 (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:
cluster_reduce_dimension.xml macros.xml |
| b |
| diff -r 6f2d2c7f77ee -r 77b91b9bdf52 cluster_reduce_dimension.xml --- a/cluster_reduce_dimension.xml Mon Feb 10 05:27:02 2020 -0500 +++ b/cluster_reduce_dimension.xml Thu Feb 20 08:23:29 2020 -0500 |
| b |
| b'@@ -276,13 +276,14 @@\n </param>\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="pp.neighbors_gauss_braycurtis.recipe_weinreb17.paul15_subsample.h5ad" />\n <conditional name="method">\n <param name="method" value="tl.louvain"/>\n@@ -295,20 +296,25 @@\n <param name="directed" value="true"/>\n <param name="use_weights" value="false"/>\n </conditional>\n- <assert_stdout>\n- <has_text_matching expression="sc.tl.louvain"/>\n- <has_text_matching expression="adata=adata"/>\n- <has_text_matching expression="flavor = \'vtraag\'"/>\n- <has_text_matching expression="resolution=1.0"/>\n- <has_text_matching expression="random_state=10"/>\n- <has_text_matching expression="key_added=\'louvain\'"/>\n- <has_text_matching expression="directed=True"/>\n- <has_text_matching expression="use_weights=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.tl.louvain"/>\n+ <has_text_matching expression="adata=adata"/>\n+ <has_text_matching expression="flavor = \'vtraag\'"/>\n+ <has_text_matching expression="resolution=1.0"/>\n+ <has_text_matching expression="random_state=10"/>\n+ <has_text_matching expression="key_added=\'louvain\'"/>\n+ <has_text_matching expression="directed=True"/>\n+ <has_text_matching expression="use_weights=False"/>\n+ </assert_contents>\n+ </output>\n <output name="anndata_out" file="tl.louvain.neighbors_gauss_braycurtis.recipe_weinreb17.paul15_subsample.h5ad" ftype="h5ad" compare="sim_size"/>\n </test>\n <test>\n- <!-- test 2 -->\n+ <!-- test 1 -->\n <param name="adata" value="pp.neighbors_gauss_braycurtis.recipe_weinreb17.paul15_subsample.h5ad" />\n <conditional name="method">\n <param name="method" value="tl.leiden"/>\n@@ -318,18 +324,23 @@\n <param name="use_weights" value="false"/>\n <param name="n_iterations" value="-1"/>\n </conditional>\n- <assert_stdout>\n- <has_text_matching expression="sc.tl.leiden"/>\n- <has_text_matching expression="resolution=1"/>\n- <has_text_matching expression="random_state=10"/>\n- <has_text_matching expression="key_added=\'leiden\'"/>\n- <has_text_matching expression="use_weights=False"/>\n- <has_text_matching expression="n_iterations=-1"/>\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.tl.leiden"/>\n+ <has_text_matching expression="resolution=1"/>\n+ <has_text_matching expression="random_state=10"/>\n+ <has_text_matching expression="key_added=\'leiden\'"/>\n+ <has_text_matching expression="use_weights=False"/>\n+ <has_text_matching expression="n_iterations=-1"/>\n+ </assert_contents>\n+ </output>\n <output name="anndata_out" file="tl.leiden.neighbors_gauss_braycurtis.recipe_we'..b' <has_text_matching expression="layout=\'fa\'"/>\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.tl.draw_graph"/>\n+ <has_text_matching expression="layout=\'fa\'"/>\n+ <has_text_matching expression="random_state=0"/>\n+ </assert_contents>\n+ </output>\n <output name="anndata_out" file="tl.draw_graph.pp.neighbors_umap_euclidean.recipe_weinreb17.paul15_subsample.h5ad" ftype="h5ad" compare="sim_size"/>\n </test>\n <test>\n- <!-- test 8 -->\n+ <!-- test 7 -->\n <param name="adata" value="pp.neighbors_gauss_braycurtis.recipe_weinreb17.paul15_subsample.h5ad"/>\n <conditional name="method">\n <param name="method" value="tl.paga"/>\n@@ -502,16 +543,21 @@\n <param name="use_rna_velocity" value="False"/>\n <param name="model" value="v1.2"/>\n </conditional>\n- <assert_stdout>\n- <has_text_matching expression="sc.tl.paga"/>\n- <has_text_matching expression="groups=\'paul15_clusters\'"/>\n- <has_text_matching expression="use_rna_velocity=False"/>\n- <has_text_matching expression="model=\'v1.2\'"/>\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.tl.paga"/>\n+ <has_text_matching expression="groups=\'paul15_clusters\'"/>\n+ <has_text_matching expression="use_rna_velocity=False"/>\n+ <has_text_matching expression="model=\'v1.2\'"/>\n+ </assert_contents>\n+ </output>\n <output name="anndata_out" file="tl.paga.neighbors_gauss_braycurtis.recipe_weinreb17.paul15_subsample.h5ad" ftype="h5ad" compare="sim_size"/>\n </test>\n <test>\n- <!-- test 9 -->\n+ <!-- test 8 -->\n <param name="adata" value="tl.diffmap.neighbors_gauss_braycurtis.recipe_weinreb17.paul15_subsample.h5ad" />\n <conditional name="method">\n <param name="method" value="tl.dpt"/>\n@@ -520,13 +566,18 @@\n <param name="min_group_size" value="0.01"/>\n <param name="allow_kendall_tau_shift" value="True"/>\n </conditional>\n- <assert_stdout>\n- <has_text_matching expression="sc.tl.dpt"/>\n- <has_text_matching expression="n_dcs=15"/>\n- <has_text_matching expression="n_branchings=1"/>\n- <has_text_matching expression="min_group_size=0.01"/>\n- <has_text_matching expression="allow_kendall_tau_shift=True"/>\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.tl.dpt"/>\n+ <has_text_matching expression="n_dcs=15"/>\n+ <has_text_matching expression="n_branchings=1"/>\n+ <has_text_matching expression="min_group_size=0.01"/>\n+ <has_text_matching expression="allow_kendall_tau_shift=True"/>\n+ </assert_contents>\n+ </output>\n <output name="anndata_out" file="tl.dpt.diffmap.neighbors_gauss_braycurtis.recipe_weinreb17.paul15_subsample.h5ad" ftype="h5ad" compare="sim_size"/>\n </test>\n </tests>\n' |
| b |
| diff -r 6f2d2c7f77ee -r 77b91b9bdf52 macros.xml --- a/macros.xml Mon Feb 10 05:27:02 2020 -0500 +++ b/macros.xml Thu Feb 20 08:23:29 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> |