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comparison scimap_plotting.xml @ 0:834ee9481948 draft

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planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit 9fb5578191db8a559191e45156cfb95350f01aea
author goeckslab
date Mon, 10 Jun 2024 18:45:07 +0000
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1 <tool id="scimap_plotting" name="Spatial plotting functions" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
2 <description>from Scimap</description>
3 <macros>
4 <import>main_macros.xml</import>
5 </macros>
6
7 <expand macro="scimap_requirements"/>
8 <expand macro="macro_stdio" />
9 <version_command>echo "@VERSION@"</version_command>
10 <command detect_errors="aggressive">
11 <![CDATA[
12 python '$__tool_directory__/scimap_plotting.py'
13 --inputs '$inputs'
14 --anndata '$anndata'
15 --output '$output'
16
17 ]]>
18 </command>
19 <configfiles>
20 <inputs name="inputs" />
21 </configfiles>
22 <inputs>
23 <param name="anndata" type="data" format="h5ad" label="Select the input anndata" />
24 <conditional name="analyses">
25 <param name="selected_tool" type="select" label="Select a plotting function to run">
26 <option value="stacked_barplot">Stacked barplot</option>
27 <option value="voronoi">Voronoi</option>
28 </param>
29 <when value="stacked_barplot">
30 <param argument="x_axis" type="text" value="imageid" label="Categorical column in adata.obs to be plotted on the x axis" />
31 <param argument="y_axis" type="text" value="phenotype" label="Categorical column in adata.obs to be plotted on the y axis" />
32 <param name="method" type="select" label="Select the metric for plotting">
33 <option value="percent" selected="true">Percent abundance</option>
34 <option value="absolute">Absolute abundance</option>
35 </param>
36 <section name="options" title="Advanced Options" expanded="false">
37 <param argument="subset_xaxis" type="text" value="" optional="true" label="Subset x-axis prior to plotting. Type in a list of categories to include on x-axis" help="Optional. Comma delimited. Default is all categories in x-axis variable" />
38 <param argument="subset_yaxis" type="text" value="" optional="true" label="Subset y-axis prior to plotting. Type in a list of categories to include on y-axis" help="Optional. Comma delimited. Default is all categories in y-axis variable" />
39 <param argument="order_xaxis" type="text" value="" optional="true" label="Type in a list of categories to order to x-axis" help="Optional. Comma delimited. Default ordering is alphabetical" />
40 <param argument="order_yaxis" type="text" value="" optional="true" label="Type in a list of categories to order to y-axis" help="Optional. Comma delimited. Default ordering is alphabetical" />
41 </section>
42 </when>
43 <when value="voronoi">
44 <param argument="color_by" type="text" value="phenotype" optional="false" label="Pass the name of the categorical variable by which to color the voronoi diagram" />
45 <param argument="x_coordinate" type="text" value="X_centroid" optional="false" label="Pass the name of the column containing cell X coordinates" />
46 <param argument="y_coordinate" type="text" value="Y_centroid" optional="false" label="Pass the name of the column containing cell Y coordinates" />
47 <section name="options" title="Advanced Options" expanded="false">
48 <param argument="imageid" type="text" value="imageid" optional="true" label="Pass the name of the column containing image IDs" help="Only necessary if subsetting one image out of a multi-image file" />
49 <param argument="subset" type="text" value="" optional="true" label="Image ID of a single image to be subsetted for plotting" />
50 <param argument="x_lim" type="text" value="" optional="true" label="Type in a list of limits for the x-axis" help="Optional. Comma delimited: xmin,xmax" />
51 <param argument="y_lim" type="text" value="" optional="true" label="Type in a list of limits for the y-axis" help="Optional. Comma delimited: ymin,ymax" />
52 <param argument="flip_y" type="boolean" truevalue="True" falsevalue="False" label="Flip Y-axis" />
53 <param argument="voronoi_edge_color" type="text" value="black" optional="true" label="Specify a Matplotlib color for marking the edges of the voronoi cells" />
54 <param argument="voronoi_line_width" type="float" value="0.1" optional="true" label="The linewidth of the marker edges" />
55 <param argument="voronoi_alpha" type="float" value="0.5" optional="true" label="The alpha blending value for voronoi cells" help="between 0 (transparent) and 1 (opaque)" />
56 <param argument="size_max" type="float" value="" optional="true" label="The maximum size for the Voronoi cells" help="Default is Inf" />
57 <param argument="overlay_points" type="text" value="" optional="true" label="Pass the name of the column which contains categorical variable to be overlayed" help="overlays a scatter plot on top of the voronoi diagram" />
58 <param argument="overlay_points_categories" type="text" value="" optional="true" label="Subset overlay categories to plotting. Type in a list of categories to include" help="Optional. Comma delimited. Default is all categories" />
59 <param argument="overlay_drop_categories" type="text" value="" optional="true" label="Specify a list of categories to exclude from overlay plotting." help="Convenience alternative to specifying categories to keep" />
60 <param argument="overlay_point_size" type="integer" value="5" optional="true" label="Overlay point size" />
61 <param argument="overlay_point_alpha" type="float" value="1" optional="true" label="The alpha blending value for overlay points" help="between 0 (transparent) and 1 (opaque)" />
62 <param argument="plot_legend" type="boolean" checked="true" truevalue="True" falsevalue="False" label="Whether to include a legend" />
63 <param argument="legend_size" type="integer" value="6" label="Point size of legend text" />
64 </section>
65 </when>
66 </conditional>
67 </inputs>
68 <outputs>
69 <data from_work_dir="out.png" format="png" name="output" label="Scimap.pl.${analyses.selected_tool} on ${on_string}" />
70 </outputs>
71 <tests>
72 <test>
73 <param name="anndata" value="tutorial_data_pheno.h5ad" />
74 <conditional name="analyses">
75 <param name="selected_tool" value="stacked_barplot" />
76 <param name="method" value="percent" />
77 </conditional>
78 <output name="output">
79 <assert_contents>
80 <has_size value="147000" delta="10000" />
81 </assert_contents>
82 </output>
83 </test>
84 <test>
85 <param name="anndata" value="tutorial_data_pheno.h5ad" />
86 <conditional name="analyses">
87 <param name="selected_tool" value="voronoi" />
88 </conditional>
89 <output name="output">
90 <assert_contents>
91 <has_size value="510000" delta="10000" />
92 </assert_contents>
93 </output>
94 </test>
95 </tests>
96 <help>
97 <![CDATA[
98 **What it does**
99
100 This tool does various single cell spatial analyses with Scimap.
101
102 **Input**
103
104 AnnData.
105
106 **Output**
107
108 Anndata with a corresponding key added.
109
110
111 ]]>
112 </help>
113 <expand macro="citations" />
114 </tool>