Mercurial > repos > iuc > scanpy_filter
changeset 12:a03ff8633507 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 6fc3a3aa54d7ece1fd8bfffe62ad7e2b620539e0
| author | iuc |
|---|---|
| date | Fri, 17 Nov 2023 09:12:00 +0000 |
| parents | 2d02d9702d3a |
| children | 277313130da5 |
| files | filter.xml macros.xml test-data/pl.rank_genes_groups_dotplot.rank_genes_groups.krumsiek11.png |
| diffstat | 3 files changed, 74 insertions(+), 73 deletions(-) [+] |
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--- a/filter.xml Wed Nov 08 14:44:39 2023 +0000 +++ b/filter.xml Fri Nov 17 09:12:00 2023 +0000 @@ -1,4 +1,4 @@ -<tool id="scanpy_filter" name="Filter" version="@galaxy_version@" profile="@profile@"> +<tool id="scanpy_filter" name="Filter" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@profile@"> <description>with scanpy</description> <macros> <import>macros.xml</import> @@ -45,10 +45,10 @@ #else if $method.method == 'tl.filter_rank_genes_groups' sc.tl.filter_rank_genes_groups( adata, - #if str($method.key) != '' + #if $method.key key='$method.key', #end if - #if str($method.groupby) != '' + #if $method.groupby groupby='$method.groupby', #end if use_raw=$method.use_raw, @@ -62,17 +62,11 @@ adata=adata, flavor='$method.flavor.flavor', #if $method.flavor.flavor == 'seurat' - #if str($method.flavor.min_mean) != '' - min_mean=$method.flavor.min_mean, - #end if - #if str($method.flavor.max_mean) != '' - max_mean=$method.flavor.max_mean, - #end if - #if str($method.flavor.min_disp) != '' - min_disp=$method.flavor.min_disp, - #end if + min_mean=$method.flavor.min_mean, + max_mean=$method.flavor.max_mean, + min_disp=$method.flavor.min_disp, #if str($method.flavor.max_disp) != '' - max_disp=$method.flavor.max_disp, + max_disp=$method.flavor.max_disp, #end if #else if $method.flavor.flavor == 'cell_ranger' n_top_genes=$method.flavor.n_top_genes,
--- a/macros.xml Wed Nov 08 14:44:39 2023 +0000 +++ b/macros.xml Fri Nov 17 09:12:00 2023 +0000 @@ -1,10 +1,10 @@ <macros> - <token name="@version@">1.9.6</token> + <token name="@TOOL_VERSION@">1.9.6</token> + <token name="@VERSION_SUFFIX@">1</token> <token name="@profile@">22.05</token> - <token name="@galaxy_version@"><![CDATA[@version@+galaxy0]]></token> <xml name="requirements"> <requirements> - <requirement type="package" version="@version@">scanpy</requirement> + <requirement type="package" version="@TOOL_VERSION@">scanpy</requirement> <requirement type="package" version="3.0.6">loompy</requirement> <requirement type="package" version="0.10.1">leidenalg</requirement> <requirement type="package" version="0.8.1">louvain</requirement> @@ -469,13 +469,13 @@ <token name="@CMD_params_inputs@"><![CDATA[ #if $method.var_names.type == 'all' var_names=adata.var_names, -#else + #else #set $var_names = ([x.strip() for x in str($method.var_names.var_names).split(',')]) var_names=$var_names, -#end if -#if str($method.groupby) != '' + #end if + #if $method.groupby groupby='$method.groupby', -#end if + #end if num_categories=$method.num_categories, ]]></token> <xml name="params_plots"> @@ -501,15 +501,15 @@ var_group_positions=$var_group_positions, var_group_labels=$var_group_labels, #end if -#if $method.var_group_rotation - var_group_rotation=$method.var_group_rotation, -#end if -#if $method.figsize.test == 'yes' - figsize=($method.figsize.width, $method.figsize.height), -#end if -#if $method.layer != '' - layer='$method.layer', -#end if + #if str($method.var_group_rotation) != '' + var_group_rotation=$method.var_group_rotation, + #end if + #if $method.figsize.test == 'yes' + figsize=($method.figsize.width, $method.figsize.height), + #end if + #if $method.layer + layer='$method.layer', + #end if ]]></token> <xml name="matplotlib_color"> <option value="AliceBlue">AliceBlue</option> @@ -662,9 +662,8 @@ <option value="YellowGreen">YellowGreen</option> </xml> <xml name="param_matplotlib_pyplot_edgecolors"> - <param argument="edgecolors" type="select" label="Edge color of the marker" help=""> + <param argument="edgecolors" type="select" optional="true" label="Edge color of the marker" help=""> <option value="face">The edge color will always be the same as the face color</option> - <option value="none">No patch boundary will be drawn</option> <expand macro="matplotlib_color"/> </param> </xml> @@ -702,17 +701,19 @@ </section> </xml> <token name="@CMD_params_matplotlib_pyplot_scatter@"><![CDATA[ - #if $method.matplotlib_pyplot_scatter.vmin + #if str($method.matplotlib_pyplot_scatter.vmin) != '' vmin=$method.matplotlib_pyplot_scatter.vmin, #end if - #if $method.matplotlib_pyplot_scatter.vmax + #if str($method.matplotlib_pyplot_scatter.vmax) != '' vmax=$method.matplotlib_pyplot_scatter.vmax, #end if - #if $method.matplotlib_pyplot_scatter.alpha + #if str($method.matplotlib_pyplot_scatter.alpha) != '' alpha=$method.matplotlib_pyplot_scatter.alpha, #end if - linewidths=$method.matplotlib_pyplot_scatter.linewidths, - edgecolors='$method.matplotlib_pyplot_scatter.edgecolors' + lw=$method.matplotlib_pyplot_scatter.linewidths, + #if $method.matplotlib_pyplot_scatter.edgecolors + ec='$method.matplotlib_pyplot_scatter.edgecolors' + #end if ]]></token> <xml name="conditional_stripplot"> <conditional name="stripplot"> @@ -752,13 +753,7 @@ </param> </xml> <token name="@CMD_params_violin_plots@"><![CDATA[ - stripplot=$method.violin_plot.stripplot.stripplot, -#if $method.violin_plot.stripplot.stripplot == "True" - jitter=$method.violin_plot.stripplot.jitter.jitter, - #if $method.violin_plot.stripplot.jitter.jitter == "True" - size=$method.violin_plot.stripplot.jitter.size, - #end if -#end if + @CMD_conditional_stripplot@ multi_panel=$method.violin_plot.multi_panel.multi_panel, #if $method.multi_panel.violin_plot.multi_panel == "True" and str($method.violin_plot.multi_panel.width) != '' and str($method.violin_plot.multi_panel.height) != '' figsize=($method.violin_plot.multi_panel.width, $method.violin_plot.multi_panel.height) @@ -776,7 +771,7 @@ <option value="h">horizontal</option> </param> <param argument="linewidth" type="float" value="0" label="Width of the gray lines that frame the plot elements" help=""/> - <param argument="color" type="select" label="Color for all of the elements" help=""> + <param argument="color" type="select" optional="true" label="Color for all of the elements" help=""> <expand macro="matplotlib_color"/> </param> <param argument="saturation" type="float" value="0.75" min="0" max="1" label="Proportion of the original saturation to draw colors at" help=""/> @@ -788,7 +783,9 @@ orient='$method.seaborn_violinplot.orient', #end if linewidth=$method.seaborn_violinplot.linewidth, + #if $method.seaborn_violinplot.color color='$method.seaborn_violinplot.color', + #end if saturation=$method.seaborn_violinplot.saturation ]]></token> <xml name="param_color"> @@ -797,7 +794,7 @@ </param> </xml> <token name="@CMD_param_color@"><![CDATA[ -#if str($method.color) != '' +#if $method.color #set $color = ([x.strip() for x in str($method.color).split(',')]) color=$color, #end if @@ -808,7 +805,7 @@ </param> </xml> <token name="@CMD_params_groups@"><![CDATA[ -#if str($method.groups) != '' +#if $method.groups #set $groups=([x.strip() for x in str($method.groups).split(',')]) groups=$groups, #end if @@ -878,14 +875,12 @@ </param> </xml> <xml name="param_palette"> - <param argument="palette" type="select" label="Colors to use for plotting categorical annotation groups" help=""> - <option value="default">Default</option> + <param argument="palette" type="select" optional="true" label="Colors to use for plotting categorical annotation groups" help=""> <expand macro="matplotlib_pyplot_colormap"/> </param> </xml> <xml name="param_color_map"> - <param argument="color_map" type="select" label="Color map to use for continous variables" help=""> - <option value="" >Default</option> + <param argument="color_map" type="select" optional="true" label="Color map to use for continous variables" help=""> <expand macro="matplotlib_pyplot_colormap"/> </param> </xml> @@ -941,7 +936,7 @@ </param> <when value="True"> <param argument="edges_width" type="float" min="0" value="0.1" label="Width of edges"/> - <param argument="edges_color" type="select" label="Color of edges"> + <param argument="edges_color" type="select" optional="true" label="Color of edges"> <expand macro="matplotlib_color"/> </param> </when> @@ -952,7 +947,9 @@ #if str($method.edges.edges) == 'True' edges=True, edges_width=$method.edges.edges_width, + #if $method.edges.edges_color edges_color='$method.edges.edges_color', + #end if #else edges=False, #end if @@ -962,7 +959,7 @@ <param argument="arrows" type="boolean" truevalue="True" falsevalue="False" checked="false" label="Show arrows?" help="It requires to run 'tl.rna_velocity' before."/> </xml> <xml name="param_cmap"> - <param argument="cmap" type="select" label="Colors to use for plotting categorical annotation groups" help=""> + <param argument="cmap" type="select" optional="true" label="Colors to use for plotting categorical annotation groups" help=""> <expand macro="matplotlib_pyplot_colormap"/> </param> </xml> @@ -989,10 +986,10 @@ @CMD_param_legend_fontsize@ legend_fontweight='$method.plot.legend_fontweight', @CMD_param_size@ - #if str($method.plot.color_map) != '' + #if $method.plot.color_map color_map='$method.plot.color_map', #end if - #if str($method.plot.palette) != '' + #if $method.plot.palette palette='$method.plot.palette', #end if frameon=$method.plot.frameon, @@ -1062,18 +1059,18 @@ </xml> <token name="@CMD_params_pl_paga@"><![CDATA[ threshold=$method.threshold, -#if str($method.groups) != '' +#if $method.groups #set $groups=([x.strip() for x in str($method.groups).split(',')]) groups=$groups, #end if -#if str($method.color) != '' +#if $method.color #set $color=([x.strip() for x in str($method.color).split(',')]) color=$color, #end if #if $method.pos pos=np.fromfile($method.pos, dtype=dt), #end if -#if str($method.labels) != '' +#if $method.labels #set $labels=([x.strip() for x in str($method.labels).split(',')]) labels=$labels, #end if @@ -1082,7 +1079,7 @@ init_pos=np.fromfile($method.init_pos, dtype=dt), #end if random_state=$method.random_state, -#if str($method.root) != '' +#if $method.root #set $root=([int(x.strip()) for x in str($method.root).split(',')]) root=$root, #end if @@ -1098,15 +1095,17 @@ node_size_scale=$method.node_size_scale, node_size_power=$method.node_size_power, edge_width_scale=$method.edge_width_scale, -#if $method.min_edge_width +#if str($method.min_edge_width) != '' min_edge_width=$method.min_edge_width, #end if -#if $method.max_edge_width +#if str($method.max_edge_width) != '' max_edge_width=$method.max_edge_width, #end if arrowsize=$method.arrowsize, normalize_to_color=$method.normalize_to_color, + #if $method.cmap cmap='$method.cmap', + #end if #if $method.title title='$method.title', #end if @@ -1125,7 +1124,7 @@ <param argument="n_genes" type="integer" min="0" value="10" label="Number of genes to show" help=""/> </xml> <xml name="pl_dotplot"> - <param argument="color_map" type="select" label="Color palette"> + <param argument="color_map" type="select" optional="true" label="Color palette"> <expand macro="matplotlib_pyplot_colormap"/> </param> <param argument="dot_max" type="float" value="" min="0" max="1" optional="true" label="Maximum dot size" help="If none, the maximum dot size is set to the maximum fraction value found (e.g. 0.6). If given, the value should be a number between 0 and 1. All fractions larger than dot_max are clipped to this value."/> @@ -1133,7 +1132,9 @@ <expand macro="section_matplotlib_pyplot_scatter"/> </xml> <token name="@CMD_pl_dotplot@"><![CDATA[ + #if $method.color_map color_map='$method.color_map', + #end if #if str($method.dot_max) != '' dot_max=$method.dot_max, #end if @@ -1184,17 +1185,19 @@ <token name="@CMD_pl_heatmap@"><![CDATA[ swap_axes=$method.swap_axes, show_gene_labels=$method.show_gene_labels, + #if $method.matplotlib_pyplot_imshow.cmap cmap='$method.matplotlib_pyplot_imshow.cmap', + #end if #if str($method.matplotlib_pyplot_imshow.interpolation) != 'None' interpolation='$method.matplotlib_pyplot_imshow.interpolation', #end if - #if $method.matplotlib_pyplot_imshow.alpha + #if str($method.matplotlib_pyplot_imshow.alpha) != '' alpha=$method.matplotlib_pyplot_imshow.alpha, #end if - #if $method.matplotlib_pyplot_imshow.vmin + #if str($method.matplotlib_pyplot_imshow.vmin) != '' vmin=$method.matplotlib_pyplot_imshow.vmin, #end if - #if $method.matplotlib_pyplot_imshow.vmax + #if str($method.matplotlib_pyplot_imshow.vmax) != '' vmax=$method.matplotlib_pyplot_imshow.vmax, #end if origin='$method.matplotlib_pyplot_imshow.origin' @@ -1207,10 +1210,8 @@ </xml> <token name="@CMD_pl_rank_genes_groups_ext@"><![CDATA[ @CMD_params_groups@ - #if str($method.n_genes) != '' n_genes=$method.n_genes, - #end if - #if str($method.key) != '' + #if $method.key key='$method.key', #end if ]]> @@ -1218,7 +1219,7 @@ <xml name="pl_matrixplot"> <expand macro="param_swap_axes"/> <section name="matplotlib_pyplot_pcolor" title="Parameters for matplotlib.pyplot.pcolor"> - <param argument="cmap" type="select" label="Color palette"> + <param argument="cmap" type="select" optional="true" label="Color palette"> <expand macro="seaborn_color_palette_options"/> </param> <param argument="vmin" type="float" value="" optional="true" label="Minimum value to anchor the colormap" help=""/> @@ -1230,15 +1231,19 @@ </xml> <token name="@CMD_pl_matrixplot@"><![CDATA[ swap_axes=$method.swap_axes, + #if $method.matplotlib_pyplot_pcolor.cmap cmap='$method.matplotlib_pyplot_pcolor.cmap', - #if $method.matplotlib_pyplot_pcolor.vmin + #end if + #if str($method.matplotlib_pyplot_pcolor.vmin) != '' vmin=$method.matplotlib_pyplot_pcolor.vmin, #end if - #if $method.matplotlib_pyplot_pcolor.vmax + #if str($method.matplotlib_pyplot_pcolor.vmax) != '' vmax=$method.matplotlib_pyplot_pcolor.vmax, #end if - edgecolors='$method.matplotlib_pyplot_pcolor.edgecolors', - #if $method.matplotlib_pyplot_pcolor.alpha + #if $method.matplotlib_pyplot_pcolor.edgecolors + ec='$method.matplotlib_pyplot_pcolor.edgecolors', + #end if + #if str($method.matplotlib_pyplot_pcolor.alpha) != '' alpha=$method.matplotlib_pyplot_pcolor.alpha, #end if snap=$method.matplotlib_pyplot_pcolor.snap @@ -1250,7 +1255,7 @@ <expand macro="conditional_stripplot"/> <expand macro="param_scale"/> </section> - <param argument="row_palette" type="select" label="Colors to use in each of the stacked violin plots"> + <param argument="row_palette" type="select" optional="true" label="Colors to use in each of the stacked violin plots"> <option value="muted">muted</option> <expand macro="seaborn_color_palette_options"/> </param> @@ -1265,7 +1270,9 @@ swap_axes=$method.swap_axes, @CMD_conditional_stripplot@ scale='$method.violin_plot.scale', + #if $method.row_palette row_palette='$method.row_palette', + #end if #if str($method.standard_scale) != 'None' standard_scale='$method.standard_scale', #end if