| Previous changeset 11:c9cb76cf8d6c (2023-11-08) Next changeset 13:7b9fafe32c86 (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:
macros.xml normalize.xml test-data/pl.rank_genes_groups_dotplot.rank_genes_groups.krumsiek11.png |
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| diff -r c9cb76cf8d6c -r 94c19fb1281c macros.xml --- a/macros.xml Wed Nov 08 14:49:18 2023 +0000 +++ b/macros.xml Fri Nov 17 09:16:03 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@"><![CDATA[\n swap_axes=$method.swap_axes,\n+ #if $method.matplotlib_pyplot_pcolor.cmap\n cmap=\'$method.matplotlib_pyplot_pcolor.cmap\',\n- #if $method.matplotlib_pyplot_pcolor.vmin\n+ #end if\n+ #if str($method.matplotlib_pyplot_pcolor.vmin) != \'\'\n vmin=$method.matplotlib_pyplot_pcolor.vmin,\n #end if\n- #if $method.matplotlib_pyplot_pcolor.vmax\n+ #if str($method.matplotlib_pyplot_pcolor.vmax) != \'\'\n vmax=$method.matplotlib_pyplot_pcolor.vmax,\n #end if\n- edgecolors=\'$method.matplotlib_pyplot_pcolor.edgecolors\',\n- #if $method.matplotlib_pyplot_pcolor.alpha\n+ #if $method.matplotlib_pyplot_pcolor.edgecolors\n+ ec=\'$method.matplotlib_pyplot_pcolor.edgecolors\',\n+ #end if\n+ #if str($method.matplotlib_pyplot_pcolor.alpha) != \'\'\n alpha=$method.matplotlib_pyplot_pcolor.alpha,\n #end if\n snap=$method.matplotlib_pyplot_pcolor.snap\n@@ -1250,7 +1255,7 @@\n <expand macro="conditional_stripplot"/>\n <expand macro="param_scale"/>\n </section>\n- <param argument="row_palette" type="select" label="Colors to use in each of the stacked violin plots">\n+ <param argument="row_palette" type="select" optional="true" label="Colors to use in each of the stacked violin plots">\n <option value="muted">muted</option>\n <expand macro="seaborn_color_palette_options"/>\n </param>\n@@ -1265,7 +1270,9 @@\n swap_axes=$method.swap_axes,\n @CMD_conditional_stripplot@\n scale=\'$method.violin_plot.scale\',\n+ #if $method.row_palette\n row_palette=\'$method.row_palette\',\n+ #end if\n #if str($method.standard_scale) != \'None\'\n standard_scale=\'$method.standard_scale\',\n #end if\n' |
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| diff -r c9cb76cf8d6c -r 94c19fb1281c normalize.xml --- a/normalize.xml Wed Nov 08 14:49:18 2023 +0000 +++ b/normalize.xml Fri Nov 17 09:16:03 2023 +0000 |
| [ |
| @@ -1,4 +1,4 @@ -<tool id="scanpy_normalize" name="Normalize" version="@galaxy_version@" profile="@profile@"> +<tool id="scanpy_normalize" name="Normalize" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@profile@"> <description>with scanpy</description> <macros> <import>macros.xml</import> @@ -17,17 +17,17 @@ #if $method.method == "pp.normalize_total" sc.pp.normalize_total( adata, - #if str($method.target_sum)!= '' + #if str($method.target_sum) != '' target_sum=$method.target_sum, #end if exclude_highly_expressed=$method.exclude_highly_expressed.exclude_highly_expressed, #if $method.exclude_highly_expressed.exclude_highly_expressed == "True" max_fraction=$method.exclude_highly_expressed.max_fraction, #end if - #if str($method.key_added) != '' + #if $method.key_added key_added='$method.key_added', #end if - #if str($method.layers) != '' + #if $method.layers #if str($method.layers) != 'all' layers[str(x.strip()) for x in str($method.layers).split(',')], #else |
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| diff -r c9cb76cf8d6c -r 94c19fb1281c test-data/pl.rank_genes_groups_dotplot.rank_genes_groups.krumsiek11.png |
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| Binary file test-data/pl.rank_genes_groups_dotplot.rank_genes_groups.krumsiek11.png has changed |
