| Previous changeset 5:8599fd07d140 (2020-02-10) Next changeset 7:7647e5cd1b8b (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 plot.xml |
| b |
| diff -r 8599fd07d140 -r dbbe1ea8ecb1 macros.xml --- a/macros.xml Mon Feb 10 05:25:58 2020 -0500 +++ b/macros.xml Thu Feb 20 08:22:46 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 ${on_string}: Annotated data matrix"/> + <data name="hidden_output" format="txt" label="Log file" > + <filter>advanced_common['show_log']</filter> + </data> </xml> <token name="@CMD_anndata_write_outputs@"><![CDATA[ adata.write('anndata.h5ad') +with open('anndata_info.txt','w', encoding='utf-8') as ainfo: + print(adata, file=ainfo) ]]> </token> + <token name="@CMD_prettify_stdout@"><![CDATA[ | sed -r '1 s|AnnData object with (.+) = (.*)\s*|\1: \2|g' | sed "s|'||g" | sed -r 's|^\s*(.*):\s(.*)|[\1]\n- \2|g' | sed 's|, |\n- |g' + ]]></token> <xml name="svd_solver"> <param name="svd_solver" type="select" label="SVD solver to use" help=""> <option value="auto">Automatically chosen depending on the size of the problem</option> |
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| diff -r 8599fd07d140 -r dbbe1ea8ecb1 plot.xml --- a/plot.xml Mon Feb 10 05:25:58 2020 -0500 +++ b/plot.xml Thu Feb 20 08:22:46 2020 -0500 |
| [ |
| b'@@ -82,7 +82,7 @@\n log=$method.log,\n use_raw=$method.use_raw,\n @CMD_conditional_stripplot@\n- multi_panel=$method.violin_plot.multi_panel.multi_panel, \n+ multi_panel=$method.violin_plot.multi_panel.multi_panel,\n #if $method.violin_plot.multi_panel.multi_panel == "True" and str($method.violin_plot.multi_panel.width) != \'\' and str($method.violin_plot.multi_panel.height) != \'\'\n figsize=($method.violin_plot.multi_panel.width, $method.violin_plot.multi_panel.height),\n #end if\n@@ -551,7 +551,7 @@\n <param argument="palette" type="select" optional="true" label="Colors to use for the different levels of the hue variable" help="See https://seaborn.pydata.org/tutorial/color_palettes.html for more details.">\n <expand macro="seaborn_color_palette_options"/>\n </param>\n- <param argument="saturation" type="float" value="1" label="Proportion of the original saturation to draw colors at" help="Large patches often look better with slightly desaturated colors, but set this to 1 if you want the plot colors to perfectly match the input color spec."/> \n+ <param argument="saturation" type="float" value="1" label="Proportion of the original saturation to draw colors at" help="Large patches often look better with slightly desaturated colors, but set this to 1 if you want the plot colors to perfectly match the input color spec."/>\n </section>\n </when>\n <when value="pl.pca">\n@@ -641,7 +641,7 @@\n <expand macro="inputs_paga"/>\n </when>\n <when value="pl.paga_path">\n- <param argument="nodes" type="text" value="" label="A path through nodes of the abstracted graph" \n+ <param argument="nodes" type="text" value="" label="A path through nodes of the abstracted graph"\n help="Each node is represented by its indice (within .categories) for the groups that have been used to run PAGA. Comma-separated"/>\n <param argument="keys" type="text" value="" label="Keys for accessing variables" help="One or a list of comma-separated index or key from \'.var_names\' or fields of \'.obs\'"/>\n <expand macro="param_use_raw"/>\n@@ -706,6 +706,7 @@\n <expand macro="pl_stacked_violin"/>\n </when>\n </conditional>\n+ <expand macro="inputs_common_advanced"/>\n </inputs>\n <outputs>\n <data name="out_png" format="png" from_work_dir="*.png" label="${tool.name} (${method.method}) on ${on_string}">\n@@ -729,10 +730,13 @@\n <discover_datasets pattern="rank_genes_groups_(?P<designation>.*).svg" format="svg"/>\n <filter>format == \'svg\' and method[\'method\'] == \'pl.rank_genes_groups_violin\'</filter>\n </collection>\n+ <data name="hidden_output" format="txt" label="Log file" hidden="true" >\n+ <filter>advanced_common[\'show_log\']</filter>\n+ </data>\n </outputs>\n <tests>\n <test>\n- <!-- test 1: pl.scatter !-->\n+ <!-- test 0: pl.scatter !-->\n <param name="adata" value="pbmc68k_reduced.h5ad" />\n <param name="format" value="png"/>\n <conditional name="method">\n@@ -755,25 +759,30 @@\n <param name="size" value="1"/>\n </section>\n </conditional>\n- <assert_stdout>\n- <has_text_matching expression="sc.pl.scatter"/>\n- <has_text_matching expression="basis=\'umap\'" />\n- <has_text_matching expression="color=\\[\'HES4\'\\]"/>\n- <has_text_matching expression="use_raw=True"/>\n- <has_text_matching expression="sort_order=True"/>\n- <has_text_matching expression="projection=\'2d\'"/>\n- <has_text_matching expression="legend_loc=\'right margin\'"/>\n- <has_text_matching expression="leg'..b' <has_text_matching expression="cmap=\'viridis\'"/>\n+ <has_text_matching expression="edgecolors=\'face\'"/>\n+ <has_text_matching expression="snap=False"/>\n+ </assert_contents>\n+ </output>\n <output name="out_png" file="pl.rank_genes_groups_matrixplot.rank_genes_groups.krumsiek11.png" ftype="png" compare="sim_size"/>\n </test>\n <test>\n- <!-- test 25: pl.rank_genes_groups_stacked_violin !-->\n+ <!-- test 24: pl.rank_genes_groups_stacked_violin !-->\n <param name="adata" value="tl.rank_genes_groups.krumsiek11.h5ad" />\n <param name="format" value="png"/>\n <conditional name="method">\n@@ -1692,24 +1816,29 @@\n <param name="saturation" value="0.75"/>\n </section>\n </conditional>\n- <assert_stdout>\n- <has_text_matching expression="sc.pl.rank_genes_groups_stacked_violin"/>\n- <has_text_matching expression="n_genes=10"/>\n- <has_text_matching expression="log=False"/>\n- <has_text_matching expression="use_raw=False"/>\n- <has_text_matching expression="dendrogram=True"/>\n- <has_text_matching expression="swap_axes=True"/>\n- <has_text_matching expression="stripplot=True"/>\n- <has_text_matching expression="jitter=True"/>\n- <has_text_matching expression="size=1"/>\n- <has_text_matching expression="scale=\'width\'"/>\n- <has_text_matching expression="bw=\'scott\'"/>\n- <has_text_matching expression="scale=\'width\'"/>\n- <has_text_matching expression="linewidth=0.0"/>\n- <has_text_matching expression="color=\'AliceBlue\'"/>\n- <has_text_matching expression="palette=\'viridis\'"/>\n- <has_text_matching expression="saturation=0.75"/>\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.pl.rank_genes_groups_stacked_violin"/>\n+ <has_text_matching expression="n_genes=10"/>\n+ <has_text_matching expression="log=False"/>\n+ <has_text_matching expression="use_raw=False"/>\n+ <has_text_matching expression="dendrogram=True"/>\n+ <has_text_matching expression="swap_axes=True"/>\n+ <has_text_matching expression="stripplot=True"/>\n+ <has_text_matching expression="jitter=True"/>\n+ <has_text_matching expression="size=1"/>\n+ <has_text_matching expression="scale=\'width\'"/>\n+ <has_text_matching expression="bw=\'scott\'"/>\n+ <has_text_matching expression="scale=\'width\'"/>\n+ <has_text_matching expression="linewidth=0.0"/>\n+ <has_text_matching expression="color=\'AliceBlue\'"/>\n+ <has_text_matching expression="palette=\'viridis\'"/>\n+ <has_text_matching expression="saturation=0.75"/>\n+ </assert_contents>\n+ </output>\n <output name="out_png" file="pl.rank_genes_groups_stacked_violin.rank_genes_groups.krumsiek11.png" ftype="png" compare="sim_size"/>\n </test>\n </tests>\n@@ -1763,7 +1892,7 @@\n Generic: Stacked violin plots (`pl.stacked_violin`)\n ===================================================\n \n-Makes a compact image composed of individual violin plots (from `seaborn.violinplot`) \n+Makes a compact image composed of individual violin plots (from `seaborn.violinplot`)\n stacked on top of each other. Useful to visualize gene expression per cluster.\n \n More details on the `scanpy documentation\n' |