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