Mercurial > repos > goeckslab > squidpy_scatter
annotate squidpy_scatter.xml @ 1:b84c324b58bd draft default tip
planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/squidpy commit ed118f79326f83eff1315f735b4e0e1a45a5e02c
author | goeckslab |
---|---|
date | Thu, 31 Oct 2024 17:55:17 +0000 (7 weeks ago) |
parents | 6fe0d4f464f4 |
children |
rev | line source |
---|---|
0
6fe0d4f464f4
planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/squidpy commit 721eaced787aa3b04d96ad91f6b4540f26b23949
goeckslab
parents:
diff
changeset
|
1 <tool id="squidpy_scatter" name="Create spatial scatterplot" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@"> |
6fe0d4f464f4
planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/squidpy commit 721eaced787aa3b04d96ad91f6b4540f26b23949
goeckslab
parents:
diff
changeset
|
2 <description>with Squidpy</description> |
6fe0d4f464f4
planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/squidpy commit 721eaced787aa3b04d96ad91f6b4540f26b23949
goeckslab
parents:
diff
changeset
|
3 <macros> |
6fe0d4f464f4
planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/squidpy commit 721eaced787aa3b04d96ad91f6b4540f26b23949
goeckslab
parents:
diff
changeset
|
4 <import>main_macros.xml</import> |
6fe0d4f464f4
planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/squidpy commit 721eaced787aa3b04d96ad91f6b4540f26b23949
goeckslab
parents:
diff
changeset
|
5 </macros> |
6fe0d4f464f4
planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/squidpy commit 721eaced787aa3b04d96ad91f6b4540f26b23949
goeckslab
parents:
diff
changeset
|
6 <edam_operations> |
6fe0d4f464f4
planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/squidpy commit 721eaced787aa3b04d96ad91f6b4540f26b23949
goeckslab
parents:
diff
changeset
|
7 <edam_operation>operation_3443</edam_operation> |
6fe0d4f464f4
planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/squidpy commit 721eaced787aa3b04d96ad91f6b4540f26b23949
goeckslab
parents:
diff
changeset
|
8 </edam_operations> |
6fe0d4f464f4
planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/squidpy commit 721eaced787aa3b04d96ad91f6b4540f26b23949
goeckslab
parents:
diff
changeset
|
9 <expand macro="squidpy_requirements"/> |
6fe0d4f464f4
planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/squidpy commit 721eaced787aa3b04d96ad91f6b4540f26b23949
goeckslab
parents:
diff
changeset
|
10 <expand macro="macro_stdio" /> |
6fe0d4f464f4
planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/squidpy commit 721eaced787aa3b04d96ad91f6b4540f26b23949
goeckslab
parents:
diff
changeset
|
11 <version_command>echo "@TOOL_VERSION@"</version_command> |
6fe0d4f464f4
planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/squidpy commit 721eaced787aa3b04d96ad91f6b4540f26b23949
goeckslab
parents:
diff
changeset
|
12 <command detect_errors="aggressive"> |
6fe0d4f464f4
planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/squidpy commit 721eaced787aa3b04d96ad91f6b4540f26b23949
goeckslab
parents:
diff
changeset
|
13 <![CDATA[ |
6fe0d4f464f4
planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/squidpy commit 721eaced787aa3b04d96ad91f6b4540f26b23949
goeckslab
parents:
diff
changeset
|
14 export TQDM_DISABLE=True && |
6fe0d4f464f4
planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/squidpy commit 721eaced787aa3b04d96ad91f6b4540f26b23949
goeckslab
parents:
diff
changeset
|
15 python '$__tool_directory__/squidpy_scatter.py' |
6fe0d4f464f4
planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/squidpy commit 721eaced787aa3b04d96ad91f6b4540f26b23949
goeckslab
parents:
diff
changeset
|
16 --inputs '$inputs' |
6fe0d4f464f4
planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/squidpy commit 721eaced787aa3b04d96ad91f6b4540f26b23949
goeckslab
parents:
diff
changeset
|
17 --output_plot image.png |
6fe0d4f464f4
planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/squidpy commit 721eaced787aa3b04d96ad91f6b4540f26b23949
goeckslab
parents:
diff
changeset
|
18 ]]> |
6fe0d4f464f4
planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/squidpy commit 721eaced787aa3b04d96ad91f6b4540f26b23949
goeckslab
parents:
diff
changeset
|
19 </command> |
6fe0d4f464f4
planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/squidpy commit 721eaced787aa3b04d96ad91f6b4540f26b23949
goeckslab
parents:
diff
changeset
|
20 <configfiles> |
6fe0d4f464f4
planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/squidpy commit 721eaced787aa3b04d96ad91f6b4540f26b23949
goeckslab
parents:
diff
changeset
|
21 <inputs name="inputs" data_style="paths"/> |
6fe0d4f464f4
planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/squidpy commit 721eaced787aa3b04d96ad91f6b4540f26b23949
goeckslab
parents:
diff
changeset
|
22 </configfiles> |
6fe0d4f464f4
planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/squidpy commit 721eaced787aa3b04d96ad91f6b4540f26b23949
goeckslab
parents:
diff
changeset
|
23 <inputs> |
6fe0d4f464f4
planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/squidpy commit 721eaced787aa3b04d96ad91f6b4540f26b23949
goeckslab
parents:
diff
changeset
|
24 <param name="anndata" type="data" format="h5ad" label="Select the input anndata" /> |
6fe0d4f464f4
planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/squidpy commit 721eaced787aa3b04d96ad91f6b4540f26b23949
goeckslab
parents:
diff
changeset
|
25 <param name="x_coord" type="text" value="X_centroid" label="Key for X spatial coordinate in adata.obs" /> |
6fe0d4f464f4
planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/squidpy commit 721eaced787aa3b04d96ad91f6b4540f26b23949
goeckslab
parents:
diff
changeset
|
26 <param name="y_coord" type="text" value="Y_centroid" label="Key for Y spatial coordinate in adata.obs" /> |
6fe0d4f464f4
planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/squidpy commit 721eaced787aa3b04d96ad91f6b4540f26b23949
goeckslab
parents:
diff
changeset
|
27 <param argument="color" type="text" value="phenotype" label="Key for annotations in adata.obs or variables/genes" /> |
6fe0d4f464f4
planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/squidpy commit 721eaced787aa3b04d96ad91f6b4540f26b23949
goeckslab
parents:
diff
changeset
|
28 <section name="plot_opts" title="Advanced Plot Options" expanded="false"> |
6fe0d4f464f4
planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/squidpy commit 721eaced787aa3b04d96ad91f6b4540f26b23949
goeckslab
parents:
diff
changeset
|
29 <param argument="groups" type="text" optional="true" label="For discrete annotation in color, select which values to plot" /> |
6fe0d4f464f4
planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/squidpy commit 721eaced787aa3b04d96ad91f6b4540f26b23949
goeckslab
parents:
diff
changeset
|
30 <param argument="use_raw" type="boolean" checked="false" label="Use adata.raw.X instead of adata.X" /> |
6fe0d4f464f4
planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/squidpy commit 721eaced787aa3b04d96ad91f6b4540f26b23949
goeckslab
parents:
diff
changeset
|
31 <param argument="crop_coord" type="text" optional="true" label="Coordinates to crop scatterplot by" help="x1,y1,x2,y2" /> |
6fe0d4f464f4
planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/squidpy commit 721eaced787aa3b04d96ad91f6b4540f26b23949
goeckslab
parents:
diff
changeset
|
32 </section> |
6fe0d4f464f4
planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/squidpy commit 721eaced787aa3b04d96ad91f6b4540f26b23949
goeckslab
parents:
diff
changeset
|
33 <section name="legend_opts" title="Legend Options" expanded="false"> |
6fe0d4f464f4
planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/squidpy commit 721eaced787aa3b04d96ad91f6b4540f26b23949
goeckslab
parents:
diff
changeset
|
34 <param argument="legend_loc" type="text" value="right margin" optional="true" label="Location of the legend" /> |
6fe0d4f464f4
planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/squidpy commit 721eaced787aa3b04d96ad91f6b4540f26b23949
goeckslab
parents:
diff
changeset
|
35 <param argument="legend_fontsize" type="integer" value="8" optional="true" label="Font size for the legend" /> |
6fe0d4f464f4
planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/squidpy commit 721eaced787aa3b04d96ad91f6b4540f26b23949
goeckslab
parents:
diff
changeset
|
36 <param argument="legend_fontweight" type="text" value="bold" optional="true" label="Font weight for the legend" /> |
6fe0d4f464f4
planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/squidpy commit 721eaced787aa3b04d96ad91f6b4540f26b23949
goeckslab
parents:
diff
changeset
|
37 <param argument="legend_fontoutline" type="integer" value="" optional="true" label="Font outline for the legend" /> |
6fe0d4f464f4
planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/squidpy commit 721eaced787aa3b04d96ad91f6b4540f26b23949
goeckslab
parents:
diff
changeset
|
38 <param argument="legend_na" type="boolean" checked="true" label="Show NA values in the legend" /> |
6fe0d4f464f4
planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/squidpy commit 721eaced787aa3b04d96ad91f6b4540f26b23949
goeckslab
parents:
diff
changeset
|
39 </section> |
6fe0d4f464f4
planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/squidpy commit 721eaced787aa3b04d96ad91f6b4540f26b23949
goeckslab
parents:
diff
changeset
|
40 <section name="aesthetic_opts" title="Figure Aesthetic Options" expanded="false"> |
6fe0d4f464f4
planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/squidpy commit 721eaced787aa3b04d96ad91f6b4540f26b23949
goeckslab
parents:
diff
changeset
|
41 <param argument="size" type="integer" value="3" label="Size of the scatter point/shape" /> |
6fe0d4f464f4
planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/squidpy commit 721eaced787aa3b04d96ad91f6b4540f26b23949
goeckslab
parents:
diff
changeset
|
42 <param argument="alpha" type="float" min="0.01" max="1.0" value="1.0" label="Alpha value for scatter point/shape" /> |
6fe0d4f464f4
planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/squidpy commit 721eaced787aa3b04d96ad91f6b4540f26b23949
goeckslab
parents:
diff
changeset
|
43 <param argument="cmap" type="text" value="viridis" optional="true" label="Matplotlib colormap for continuous annotations" help="Refer to `matplotlib.pyplot.cmap`." /> |
6fe0d4f464f4
planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/squidpy commit 721eaced787aa3b04d96ad91f6b4540f26b23949
goeckslab
parents:
diff
changeset
|
44 <param argument="colorbar" type="boolean" checked="true" label="Show the colorbar" /> |
6fe0d4f464f4
planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/squidpy commit 721eaced787aa3b04d96ad91f6b4540f26b23949
goeckslab
parents:
diff
changeset
|
45 <param argument="scalebar_dx" type="float" min="0.01" max="1.0" value="" optional="true" label="Size of one pixel in units specified by scalebar_units" /> |
6fe0d4f464f4
planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/squidpy commit 721eaced787aa3b04d96ad91f6b4540f26b23949
goeckslab
parents:
diff
changeset
|
46 <param argument="scalebar_units" type="text" value="" optional="true" label="Units for scalebar" /> |
6fe0d4f464f4
planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/squidpy commit 721eaced787aa3b04d96ad91f6b4540f26b23949
goeckslab
parents:
diff
changeset
|
47 <param argument="title" type="text" optional="true" label="Figure title" /> |
6fe0d4f464f4
planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/squidpy commit 721eaced787aa3b04d96ad91f6b4540f26b23949
goeckslab
parents:
diff
changeset
|
48 <param argument="figsize" type="text" value="" optional="true" label="Size of the figure in inches" help="width,height"/> |
6fe0d4f464f4
planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/squidpy commit 721eaced787aa3b04d96ad91f6b4540f26b23949
goeckslab
parents:
diff
changeset
|
49 <param argument="dpi" type="integer" value="300" optional="true" label="Dots per inch" /> |
6fe0d4f464f4
planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/squidpy commit 721eaced787aa3b04d96ad91f6b4540f26b23949
goeckslab
parents:
diff
changeset
|
50 </section> |
6fe0d4f464f4
planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/squidpy commit 721eaced787aa3b04d96ad91f6b4540f26b23949
goeckslab
parents:
diff
changeset
|
51 </inputs> |
6fe0d4f464f4
planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/squidpy commit 721eaced787aa3b04d96ad91f6b4540f26b23949
goeckslab
parents:
diff
changeset
|
52 <outputs> |
6fe0d4f464f4
planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/squidpy commit 721eaced787aa3b04d96ad91f6b4540f26b23949
goeckslab
parents:
diff
changeset
|
53 <data from_work_dir="figures/image.png" format="png" name="output_plot" label="Squidpy spatial scatterplot on ${on_string}" /> |
6fe0d4f464f4
planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/squidpy commit 721eaced787aa3b04d96ad91f6b4540f26b23949
goeckslab
parents:
diff
changeset
|
54 </outputs> |
6fe0d4f464f4
planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/squidpy commit 721eaced787aa3b04d96ad91f6b4540f26b23949
goeckslab
parents:
diff
changeset
|
55 <tests> |
6fe0d4f464f4
planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/squidpy commit 721eaced787aa3b04d96ad91f6b4540f26b23949
goeckslab
parents:
diff
changeset
|
56 <test> |
6fe0d4f464f4
planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/squidpy commit 721eaced787aa3b04d96ad91f6b4540f26b23949
goeckslab
parents:
diff
changeset
|
57 <param name="anndata" value="imc_sn.h5ad" ftype="h5ad" /> |
6fe0d4f464f4
planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/squidpy commit 721eaced787aa3b04d96ad91f6b4540f26b23949
goeckslab
parents:
diff
changeset
|
58 <param name="color" value="cell type" /> |
6fe0d4f464f4
planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/squidpy commit 721eaced787aa3b04d96ad91f6b4540f26b23949
goeckslab
parents:
diff
changeset
|
59 <output name="output_plot" file="scatter_image.png" compare="sim_size" delta="2000" /> |
6fe0d4f464f4
planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/squidpy commit 721eaced787aa3b04d96ad91f6b4540f26b23949
goeckslab
parents:
diff
changeset
|
60 </test> |
6fe0d4f464f4
planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/squidpy commit 721eaced787aa3b04d96ad91f6b4540f26b23949
goeckslab
parents:
diff
changeset
|
61 </tests> |
6fe0d4f464f4
planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/squidpy commit 721eaced787aa3b04d96ad91f6b4540f26b23949
goeckslab
parents:
diff
changeset
|
62 <help> |
6fe0d4f464f4
planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/squidpy commit 721eaced787aa3b04d96ad91f6b4540f26b23949
goeckslab
parents:
diff
changeset
|
63 <![CDATA[ |
6fe0d4f464f4
planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/squidpy commit 721eaced787aa3b04d96ad91f6b4540f26b23949
goeckslab
parents:
diff
changeset
|
64 This is a limited implementation of the squidpy.pl.spatial_scatter() function |
6fe0d4f464f4
planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/squidpy commit 721eaced787aa3b04d96ad91f6b4540f26b23949
goeckslab
parents:
diff
changeset
|
65 |
6fe0d4f464f4
planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/squidpy commit 721eaced787aa3b04d96ad91f6b4540f26b23949
goeckslab
parents:
diff
changeset
|
66 See Squidpy documentation for more information: |
6fe0d4f464f4
planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/squidpy commit 721eaced787aa3b04d96ad91f6b4540f26b23949
goeckslab
parents:
diff
changeset
|
67 |
6fe0d4f464f4
planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/squidpy commit 721eaced787aa3b04d96ad91f6b4540f26b23949
goeckslab
parents:
diff
changeset
|
68 https://squidpy.readthedocs.io/en/stable/index.html |
6fe0d4f464f4
planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/squidpy commit 721eaced787aa3b04d96ad91f6b4540f26b23949
goeckslab
parents:
diff
changeset
|
69 ]]> |
6fe0d4f464f4
planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/squidpy commit 721eaced787aa3b04d96ad91f6b4540f26b23949
goeckslab
parents:
diff
changeset
|
70 </help> |
6fe0d4f464f4
planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/squidpy commit 721eaced787aa3b04d96ad91f6b4540f26b23949
goeckslab
parents:
diff
changeset
|
71 <expand macro="citations" /> |
6fe0d4f464f4
planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/squidpy commit 721eaced787aa3b04d96ad91f6b4540f26b23949
goeckslab
parents:
diff
changeset
|
72 </tool> |