| Previous changeset 11:6bd82ed14acd (2023-11-08) Next changeset 13:5c3ebe2adc77 (2024-03-14) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 6fc3a3aa54d7ece1fd8bfffe62ad7e2b620539e0 |
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modified:
inspect.xml macros.xml test-data/pl.rank_genes_groups_dotplot.rank_genes_groups.krumsiek11.png |
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| diff -r 6bd82ed14acd -r 3081ff5c84a3 inspect.xml --- a/inspect.xml Wed Nov 08 14:48:14 2023 +0000 +++ b/inspect.xml Fri Nov 17 09:15:15 2023 +0000 |
| [ |
| @@ -1,4 +1,4 @@ -<tool id="scanpy_inspect" name="Inspect and manipulate" version="@galaxy_version@" profile="@profile@"> +<tool id="scanpy_inspect" name="Inspect and manipulate" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@profile@"> <description> with scanpy</description> <macros> <import>macros.xml</import> @@ -66,11 +66,11 @@ adata=adata, expr_type='$method.expr_type', var_type='$method.var_type', - #if str($method.qc_vars) != '' + #if $method.qc_vars #set $qc_vars = [str(x.strip()) for x in str($method.qc_vars).split(',')] qc_vars=$qc_vars, #end if - #if str($method.percent_top) != '' + #if $method.percent_top #set $percent_top = [int(x.strip()) for x in str($method.percent_top).split(',')] percent_top=$method.percent_top, #end if @@ -125,7 +125,7 @@ #if str($method.n_pcs) != '' n_pcs=$method.n_pcs, #end if - #if str($method.use_rep) != '' + #if $method.use_rep use_rep='$method.use_rep', #end if knn=$method.knn, @@ -138,7 +138,7 @@ sc.tl.rank_genes_groups( adata=adata, groupby='$method.groupby', - #if str($method.groups) != '' + #if $method.groups #set $group=[x.strip() for x in str($method.groups).split(',')] groups=$group, #end if @@ -176,13 +176,13 @@ #if $method.tl_rank_genes_groups_method.solver.intercept_scaling.fit_intercept == 'True' intercept_scaling=$method.tl_rank_genes_groups_method.solver.intercept_scaling.intercept_scaling, #end if - #if $method.tl_rank_genes_groups_method.solver.random_state + #if str($method.tl_rank_genes_groups_method.solver.random_state) != '' random_state=$method.tl_rank_genes_groups_method.solver.random_state, #end if #else if $method.tl_rank_genes_groups_method.solver.solver == 'sag' penalty='l2', fit_intercept=$method.tl_rank_genes_groups_method.solver.fit_intercept, - #if $method.tl_rank_genes_groups_method.solver.random_state + #if str($method.tl_rank_genes_groups_method.solver.random_state) != '' random_state=$method.tl_rank_genes_groups_method.solver.random_state, #end if max_iter=$method.tl_rank_genes_groups_method.solver.max_iter, @@ -213,7 +213,7 @@ sc.tl.marker_gene_overlap( adata, reference_markers, - #if str($method.key) != '' + #if $method.key key='$method.key', #end if method='$method.overlap.method', @@ -226,7 +226,7 @@ #if str($method.adj_pval_threshold) != '' adj_pval_threshold=$method.adj_pval_threshold, #end if - #if str($method.key_added) != '' + #if $method.key_added key_added='$method.key_added', #end if inplace=True) @@ -240,7 +240,7 @@ sc.pp.scale( adata, zero_center=$method.zero_center, - #if $method.max_value + #if str($method.max_value) != '' max_value=$method.max_value, #end if copy=False) @@ -368,9 +368,9 @@ <param argument="n_genes" type="integer" min="0" value="100" label="The number of genes that appear in the returned tables" help=""/> <conditional name="tl_rank_genes_groups_method"> <param argument="method" type="select" label="Method"> - <option value="t-test">t-test</option> + <option value="t-test" selected="true">t-test</option> <option value="wilcoxon">Wilcoxon-Rank-Sum</option> - <option value="t-test_overestim_var" selected="true">t-test with overestimate of variance of each group</option> + <option value="t-test_overestim_var">t-test with overestimate of variance of each group</option> <option value="logreg">Logistic regression</option> </param> <when value="t-test"> |
| b |
| diff -r 6bd82ed14acd -r 3081ff5c84a3 macros.xml --- a/macros.xml Wed Nov 08 14:48:14 2023 +0000 +++ b/macros.xml Fri Nov 17 09:15:15 2023 +0000 |
| [ |
| b'@@ -1,10 +1,10 @@\n <macros>\n- <token name="@version@">1.9.6</token>\n+ <token name="@TOOL_VERSION@">1.9.6</token>\n+ <token name="@VERSION_SUFFIX@">1</token>\n <token name="@profile@">22.05</token>\n- <token name="@galaxy_version@"><![CDATA[@version@+galaxy0]]></token>\n <xml name="requirements">\n <requirements>\n- <requirement type="package" version="@version@">scanpy</requirement>\n+ <requirement type="package" version="@TOOL_VERSION@">scanpy</requirement>\n <requirement type="package" version="3.0.6">loompy</requirement>\n <requirement type="package" version="0.10.1">leidenalg</requirement>\n <requirement type="package" version="0.8.1">louvain</requirement>\n@@ -469,13 +469,13 @@\n <token name="@CMD_params_inputs@"><![CDATA[\n #if $method.var_names.type == \'all\'\n var_names=adata.var_names,\n-#else\n+ #else\n #set $var_names = ([x.strip() for x in str($method.var_names.var_names).split(\',\')])\n var_names=$var_names,\n-#end if\n-#if str($method.groupby) != \'\'\n+ #end if\n+ #if $method.groupby\n groupby=\'$method.groupby\',\n-#end if\n+ #end if\n num_categories=$method.num_categories,\n ]]></token>\n <xml name="params_plots">\n@@ -501,15 +501,15 @@\n var_group_positions=$var_group_positions,\n var_group_labels=$var_group_labels,\n #end if\n-#if $method.var_group_rotation\n- var_group_rotation=$method.var_group_rotation,\n-#end if\n-#if $method.figsize.test == \'yes\'\n- figsize=($method.figsize.width, $method.figsize.height),\n-#end if\n-#if $method.layer != \'\'\n- layer=\'$method.layer\',\n-#end if\n+ #if str($method.var_group_rotation) != \'\'\n+ var_group_rotation=$method.var_group_rotation,\n+ #end if\n+ #if $method.figsize.test == \'yes\'\n+ figsize=($method.figsize.width, $method.figsize.height),\n+ #end if\n+ #if $method.layer\n+ layer=\'$method.layer\',\n+ #end if\n ]]></token>\n <xml name="matplotlib_color">\n <option value="AliceBlue">AliceBlue</option>\n@@ -662,9 +662,8 @@\n <option value="YellowGreen">YellowGreen</option>\n </xml>\n <xml name="param_matplotlib_pyplot_edgecolors">\n- <param argument="edgecolors" type="select" label="Edge color of the marker" help="">\n+ <param argument="edgecolors" type="select" optional="true" label="Edge color of the marker" help="">\n <option value="face">The edge color will always be the same as the face color</option>\n- <option value="none">No patch boundary will be drawn</option>\n <expand macro="matplotlib_color"/>\n </param>\n </xml>\n@@ -702,17 +701,19 @@\n </section>\n </xml>\n <token name="@CMD_params_matplotlib_pyplot_scatter@"><![CDATA[\n- #if $method.matplotlib_pyplot_scatter.vmin\n+ #if str($method.matplotlib_pyplot_scatter.vmin) != \'\'\n vmin=$method.matplotlib_pyplot_scatter.vmin,\n #end if\n- #if $method.matplotlib_pyplot_scatter.vmax\n+ #if str($method.matplotlib_pyplot_scatter.vmax) != \'\'\n vmax=$method.matplotlib_pyplot_scatter.vmax,\n #end if\n- #if $method.matplotlib_pyplot_scatter.alpha\n+ #if str($method.matplotlib_pyplot_scatter.alpha) != \'\'\n alpha=$method.matplotlib_pyplot_scatter.alpha,\n #end if\n- linewidths=$method.matplotlib_pyplot_scatter.linewidths,\n- edgecolors=\'$method.matplotlib_pyplot_scatter.edgecolors\'\n+ lw=$method.matplotlib_pyplot_scatter.linewidths,\n+ #if $method.matplotlib_pyplot_scatter.edgecolors\n+ ec=\'$method.matplotlib_pyplot_scatter.edgecolors\'\n+ #end if\n ]]></token>\n <xml name="conditional_stripplot">\n <conditional name="stripplot">\n@@ -752,13 +753,7 @@\n </param>\n </xml>\n <token name="@CMD_params_violin_plots@"><![CDATA[\n- stripplot=$method.violin_plot.stripplot.stripplot,\n-#if $method.violin_plot.stripplot.stripplot == "True"\n- jitter=$method.violin_plot.stripplot.jitter.jitter,\n- #if $method.violin_plot.stripplot.jitter.jitt'..b' All fractions larger than dot_max are clipped to this value."/>\n@@ -1133,7 +1132,9 @@\n <expand macro="section_matplotlib_pyplot_scatter"/>\n </xml>\n <token name="@CMD_pl_dotplot@"><![CDATA[\n+ #if $method.color_map\n color_map=\'$method.color_map\',\n+ #end if\n #if str($method.dot_max) != \'\'\n dot_max=$method.dot_max,\n #end if\n@@ -1184,17 +1185,19 @@\n <token name="@CMD_pl_heatmap@"><![CDATA[\n swap_axes=$method.swap_axes,\n show_gene_labels=$method.show_gene_labels,\n+ #if $method.matplotlib_pyplot_imshow.cmap\n cmap=\'$method.matplotlib_pyplot_imshow.cmap\',\n+ #end if\n #if str($method.matplotlib_pyplot_imshow.interpolation) != \'None\'\n interpolation=\'$method.matplotlib_pyplot_imshow.interpolation\',\n #end if\n- #if $method.matplotlib_pyplot_imshow.alpha\n+ #if str($method.matplotlib_pyplot_imshow.alpha) != \'\'\n alpha=$method.matplotlib_pyplot_imshow.alpha,\n #end if\n- #if $method.matplotlib_pyplot_imshow.vmin\n+ #if str($method.matplotlib_pyplot_imshow.vmin) != \'\'\n vmin=$method.matplotlib_pyplot_imshow.vmin,\n #end if\n- #if $method.matplotlib_pyplot_imshow.vmax\n+ #if str($method.matplotlib_pyplot_imshow.vmax) != \'\'\n vmax=$method.matplotlib_pyplot_imshow.vmax,\n #end if\n origin=\'$method.matplotlib_pyplot_imshow.origin\'\n@@ -1207,10 +1210,8 @@\n </xml>\n <token name="@CMD_pl_rank_genes_groups_ext@"><![CDATA[\n @CMD_params_groups@\n- #if str($method.n_genes) != \'\'\n n_genes=$method.n_genes,\n- #end if\n- #if str($method.key) != \'\'\n+ #if $method.key\n key=\'$method.key\',\n #end if\n ]]>\n@@ -1218,7 +1219,7 @@\n <xml name="pl_matrixplot">\n <expand macro="param_swap_axes"/>\n <section name="matplotlib_pyplot_pcolor" title="Parameters for matplotlib.pyplot.pcolor">\n- <param argument="cmap" type="select" label="Color palette">\n+ <param argument="cmap" type="select" optional="true" label="Color palette">\n <expand macro="seaborn_color_palette_options"/>\n </param>\n <param argument="vmin" type="float" value="" optional="true" label="Minimum value to anchor the colormap" help=""/>\n@@ -1230,15 +1231,19 @@\n </xml>\n <token name="@CMD_pl_matrixplot@"><