| Previous changeset 11:edec35114f72 (2023-11-08) Next changeset 13:6f83f8fd381f (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:
cluster_reduce_dimension.xml macros.xml test-data/pl.rank_genes_groups_dotplot.rank_genes_groups.krumsiek11.png |
| b |
| diff -r edec35114f72 -r 6acb08931836 cluster_reduce_dimension.xml --- a/cluster_reduce_dimension.xml Wed Nov 08 14:46:29 2023 +0000 +++ b/cluster_reduce_dimension.xml Fri Nov 17 09:13:40 2023 +0000 |
| [ |
| @@ -1,4 +1,4 @@ -<tool id="scanpy_cluster_reduce_dimension" name="Cluster, infer trajectories and embed" version="@galaxy_version@" profile="@profile@"> +<tool id="scanpy_cluster_reduce_dimension" name="Cluster, infer trajectories and embed" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@profile@"> <description>with scanpy</description> <macros> <import>macros.xml</import> @@ -110,7 +110,7 @@ #else if $method.method == 'tl.tsne' sc.tl.tsne( adata=adata, - #if $method.n_pcs + #if str($method.n_pcs) != '' n_pcs=$method.n_pcs, #end if perplexity=$method.perplexity, @@ -126,7 +126,7 @@ min_dist=$method.min_dist, spread=$method.spread, n_components=$method.n_components, - #if $method.maxiter + #if str($method.maxiter) != '' maxiter=$method.maxiter, #end if alpha=$method.alpha, @@ -137,7 +137,6 @@ copy=False) #else if $method.method == 'tl.draw_graph' - #if str($method.adjacency) != 'None' from scipy import io adjacency = io.mmread('$method.adjacency') @@ -146,18 +145,18 @@ sc.tl.draw_graph( adata=adata, layout='$method.layout', -#if str($method.root) != '' +#if $method.root #set $root=([int(x.strip()) for x in str($method.root).split(',')]) root=$root, #end if random_state=$method.random_state, - #if str($method.init_pos) != '' + #if $method.init_pos init_pos='$method.init_pos', #end if #if str($method.adjacency) != 'None' adjacency=adjacency, #end if - #if str($method.key_ext) != '' + #if $method.key_ext key_ext='$method.key_ext', #end if copy=False) @@ -183,10 +182,10 @@ sc.tl.embedding_density( adata=adata, basis='$method.basis', -#if str($method.groupby) != '' +#if $method.groupby groupby='$method.groupby', #end if -#if str($method.key_added) != '' +#if $method.key_added key_added='$method.key_added', #end if ) |
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| diff -r edec35114f72 -r 6acb08931836 macros.xml --- a/macros.xml Wed Nov 08 14:46:29 2023 +0000 +++ b/macros.xml Fri Nov 17 09:13:40 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@"><