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comparison scimap_plotting.xml @ 2:ef73596d678a draft default tip

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planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit c39cea5ae2ebf61b3d51d687fd9d2930c907b72d
author goeckslab
date Tue, 30 Jul 2024 18:20:43 +0000
parents 834ee9481948
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1:c42e97dc5a3a 2:ef73596d678a
36 <section name="options" title="Advanced Options" expanded="false"> 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" /> 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" /> 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" /> 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" /> 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 <param argument="matplotlib_cmap" type="select" label="Matplotlib colormap to use for y-axis categories" help="See link below for colormaps explanation">
42 <option value="Pastel1">Pastel1</option>
43 <option value="Pastel2">Pastel2</option>
44 <option value="Paired">Paired</option>
45 <option value="Accent">Accent</option>
46 <option value="Dark2">Dark2</option>
47 <option selected="true" value="Set1">Set1</option>
48 <option value="Set2">Set2</option>
49 <option value="Set3">Set3</option>
50 <option value="tab10">tab10</option>
51 <option value="tab20">tab20</option>
52 <option value="tab20b">tab20b</option>
53 <option value="tab20c">tab20c</option>
54 </param>
41 </section> 55 </section>
42 </when> 56 </when>
43 <when value="voronoi"> 57 <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" /> 58 <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" /> 59 <param argument="x_coordinate" type="text" value="X_centroid" optional="false" label="Pass the name of the column containing cell X coordinates" />
95 </tests> 109 </tests>
96 <help> 110 <help>
97 <![CDATA[ 111 <![CDATA[
98 **What it does** 112 **What it does**
99 113
100 This tool does various single cell spatial analyses with Scimap. 114 This tool creates stacked barplots or Voronoi plots from single-cell spatial data using Scimap
101 115
102 **Input** 116 For the stacked barplot tool, find colormap descriptions here: https://matplotlib.org/stable/users/explain/colors/colormaps.html
103
104 AnnData.
105
106 **Output**
107
108 Anndata with a corresponding key added.
109
110 117
111 ]]> 118 ]]>
112 </help> 119 </help>
113 <expand macro="citations" /> 120 <expand macro="citations" />
114 </tool> 121 </tool>