Mercurial > repos > goeckslab > squidpy

comparison main_macros.xml @ 0:be0e7952e229 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/squidpy commit ee16860018eba110ff845d62b18396db22abd91e
author goeckslab
date Mon, 29 Aug 2022 23:20:54 +0000
parents
children bad34051dc8a
comparison
equal deleted inserted replaced
-1:000000000000 0:be0e7952e229
1 <macros>
2 <token name="@TOOL_VERSION@">1.1.2</token>
3 <token name="@PROFILE@">20.01</token>
4 <token name="@VERSION_SUFFIX@">0</token>
5
6 <xml name="macro_stdio">
7 <stdio>
8 <exit_code range="1:" level="fatal" description="Error occurred. Please check Tool Standard Error" />
9 </stdio>
10 </xml>
11
12 <xml name="squidpy_requirements">
13 <requirements>
14 <container type="docker">quay.io/goeckslab/squidpy:@TOOL_VERSION@</container>
15 </requirements>
16 </xml>
17
18 <xml name="citations">
19 <citations>
20 <citation type="doi">10.1038/s41592-021-01358-2</citation>
21 </citations>
22 </xml>
23
24 <xml name="squidpy_spatial_options">
25 <section name="options" title="Advanced Graph Options" expanded="false">
26 <yield/>
27 <!-- <param argument="copy" type="hidden" value="false" help="If True, return the result, otherwise save it to the adata object." /> -->
28 </section>
29 </xml>
30
31 <xml name="squidpy_plotting_options">
32 <section name="plotting_options" title="Plotting Options" expanded="false">
33 <yield />
34 <!-- <param argument="legend_kwargs" type="text" value="" optional="true" label="Keyword arguments for matplotlib.pyplot.legend()" /> -->
35 <param argument="figsize" type="text" value="" optional="true" label="Size of the figure in inches" help="Optional. e.g.: (12, 12)." />
36 <param argument="dpi" type="integer" value="" optional="true" label="Dots per inch" help="Optional" />
37 </section>
38 </xml>
39
40 <xml name="squidpy_plotting_option_palette">
41 <param argument="palette" type="text" value="" optional="true" label="Categorical colormap for the clusters" help="Comma delimited for multiple. If None, use anndata.AnnData.uns ['{cluster_key}_colors'], if available." />
42 </xml>
43
44 <xml name="squidpy_plotting_options_more">
45 <expand macro="squidpy_plotting_options">
46 <yield />
47 <param argument="annotate" type="boolean" checked="false" label="Whether to annotate the cells of the heatmap?" />
48 <param argument="method" type="select" label="The linkage method to be used for dendrogram/clustering" help="see scipy.cluster.hierarchy.linkage().">
49 <option value="none" selected="true">None</option>
50 <option value="single">single</option>
51 <option value="complete">complete</option>
52 <option value="average">average</option>
53 <option value="weighted">weighted</option>
54 <option value="centroid">centroid</option>
55 <option value="median">median</option>
56 <option value="ward">ward</option>
57 </param>
58 <param argument="title" type="text" value="" optional="true" label="The title of the plot" help="Optional." />
59 <param argument="cmap" type="text" value="viridis" label="Continuous colormap to use" help="Refer to `matplotlib.pyplot.cmap`." />
60 <!-- <param argument="cbar_kwargs" type="text" value="" label="Keyword arguments for matplotlib.figure.Figure.colorbar()" /> -->
61 <expand macro="squidpy_plotting_option_palette" />
62 </expand>
63 </xml>
64 </macros>