| Previous changeset 19:40812a65a78b (2024-10-03) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 55ba4cd74d5d8f7baff164b1864c36759d1c7fd9 |
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modified:
macros.xml plot.xml |
| b |
| diff -r 40812a65a78b -r 62acdd96d4a0 macros.xml --- a/macros.xml Thu Oct 03 22:44:36 2024 +0000 +++ b/macros.xml Fri Oct 18 10:37:11 2024 +0000 |
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| @@ -1,6 +1,6 @@ <macros> <token name="@TOOL_VERSION@">1.10.2</token> - <token name="@VERSION_SUFFIX@">1</token> + <token name="@VERSION_SUFFIX@">2</token> <token name="@PROFILE@">21.09</token> <xml name="requirements"> <requirements> @@ -1289,8 +1289,8 @@ ]]> </token> - <xml name="param_gene_symbols"> - <param argument="gene_symbols" type="text" value="" optional="true" label="Key for field in '.var' that stores gene symbols" help="By default 'var_names' refer to the index column of the '.var' DataFrame"> + <xml name="param_gene_symbols" token_label="Key for field in '.var' that stores gene symbols" token_help="By default 'var_names' refer to the index column of the '.var' DataFrame"> + <param argument="gene_symbols" type="text" value="" optional="true" label="@LABEL@" help="@HELP@"> <expand macro="sanitize_query"/> </param> </xml> |
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| diff -r 40812a65a78b -r 62acdd96d4a0 plot.xml --- a/plot.xml Thu Oct 03 22:44:36 2024 +0000 +++ b/plot.xml Fri Oct 18 10:37:11 2024 +0000 |
| b |
| @@ -223,6 +223,7 @@ sc.pl.pca( @CMD_PARAM_PLOT_INPUTS@ @CMD_PARAM_COLOR@ + @CMD_PARAM_GENE_SYMBOLS@ use_raw=$method.use_raw, sort_order=$method.sort_order, @CMD_PARAM_GROUPS@ @@ -282,6 +283,7 @@ sc.pl.umap( @CMD_PARAM_PLOT_INPUTS@ @CMD_PARAM_COLOR@ + @CMD_PARAM_GENE_SYMBOLS@ use_raw=$method.use_raw, @CMD_PL_EDGES@ arrows=$method.arrows, @@ -297,6 +299,7 @@ sc.pl.diffmap( @CMD_PARAM_PLOT_INPUTS@ @CMD_PARAM_COLOR@ + @CMD_PARAM_GENE_SYMBOLS@ use_raw=$method.use_raw, sort_order=$method.sort_order, @CMD_PARAM_GROUPS@ @@ -741,6 +744,7 @@ </when> <when value="pl.pca"> <expand macro="param_color"/> + <expand macro="param_gene_symbols"/> <expand macro="param_use_raw"/> <expand macro="param_sort_order"/> <expand macro="param_groups"/> @@ -784,6 +788,7 @@ </when> <when value="pl.umap"> <expand macro="param_color"/> + <expand macro="param_gene_symbols"/> <expand macro="param_use_raw"/> <expand macro="pl_edges"/> <expand macro="param_arrows"/> @@ -796,6 +801,7 @@ </when> <when value="pl.diffmap"> <expand macro="param_color"/> + <expand macro="param_gene_symbols"/> <expand macro="param_use_raw"/> <expand macro="param_sort_order"/> <expand macro="param_groups"/> @@ -1602,6 +1608,7 @@ <conditional name="method"> <param name="method" value="pl.pca"/> <param name="color" value="CD3D,CD79A"/> + <param name="gene_symbols" value="symbol"/> <section name="plot"> <repeat name="components"> <param name="axis1" value="1"/> @@ -1637,6 +1644,7 @@ <has_text_matching expression="ncols=2"/> <has_text_matching expression="wspace=0.1"/> <has_text_matching expression="hspace=0.25"/> + <has_text_matching expression="gene_symbols='symbol'"/> </assert_contents> </output> <output name="out_pdf" file="pl.pca.pbmc68k_reduced.CD3D_CD79A_components_2d.pdf" ftype="pdf" compare="sim_size"/> @@ -1758,6 +1766,7 @@ <conditional name="method"> <param name="method" value="pl.umap"/> <param name="color" value="paul15_clusters"/> + <param name="gene_symbols" value="symbol"/> <conditional name="edges"> <param name="edges" value="True"/> </conditional> @@ -1788,7 +1797,7 @@ <has_text_matching expression="ncols=4"/> <has_text_matching expression="wspace=0.1"/> <has_text_matching expression="hspace=0.25"/> - + <has_text_matching expression="gene_symbols='symbol'"/> </assert_contents> </output> <output name="out_png" file="pl.umap.neighbors_umap_euclidean.recipe_weinreb17.paul15_subsample.png" ftype="png" compare="image_diff"/> @@ -1801,6 +1810,7 @@ <conditional name="method"> <param name="method" value="pl.diffmap"/> <param name="color" value="paul15_clusters"/> + <param name="gene_symbols" value="symbol"/> <section name="plot"> <param name="legend_fontsize" value="1"/> <param name="legend_fontweight" value="normal"/> @@ -1825,7 +1835,7 @@ <has_text_matching expression="ncols=4"/> <has_text_matching expression="wspace=0.1"/> <has_text_matching expression="hspace=0.25"/> - + <has_text_matching expression="gene_symbols='symbol'"/> </assert_contents> </output> <output name="out_png" file="pl.diffmap.neighbors_gauss_braycurtis.recipe_weinreb17.paul15_subsample.png" ftype="png" compare="image_diff"/> |