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annotate main_macros.xml @ 2:4a058bd23a12 draft

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planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/squidpy commit ae0f7f9e0f265031ce1a9c1cadea109b0e1b81aa
author goeckslab
date Mon, 29 Apr 2024 20:42:57 +0000
parents bad34051dc8a
children d30ef0613122
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1 <macros>
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2 <token name="@TOOL_VERSION@">1.4.1</token>
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3 <token name="@PROFILE@">20.01</token>
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4 <token name="@VERSION_SUFFIX@">0</token>
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6 <xml name="macro_stdio">
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7 <stdio>
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8 <exit_code range="1:" level="fatal" description="Error occurred. Please check Tool Standard Error" />
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9 </stdio>
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10 </xml>
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12 <xml name="squidpy_requirements">
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13 <requirements>
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14 <container type="docker">quay.io/goeckslab/squidpy:@TOOL_VERSION@</container>
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15 </requirements>
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16 </xml>
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18 <xml name="citations">
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19 <citations>
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20 <citation type="doi">10.1038/s41592-021-01358-2</citation>
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21 </citations>
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22 </xml>
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24 <xml name="squidpy_spatial_options">
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25 <section name="options" title="Advanced Graph Options" expanded="false">
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26 <yield/>
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27 <!-- <param argument="copy" type="hidden" value="false" help="If True, return the result, otherwise save it to the adata object." /> -->
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28 </section>
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29 </xml>
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31 <xml name="squidpy_plotting_options">
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32 <section name="plotting_options" title="Plotting Options" expanded="false">
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33 <yield />
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34 <!-- <param argument="legend_kwargs" type="text" value="" optional="true" label="Keyword arguments for matplotlib.pyplot.legend()" /> -->
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35 <param argument="figsize" type="text" value="" optional="true" label="Size of the figure in inches" help="Optional. e.g.: (12, 12)." />
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36 <param argument="dpi" type="integer" value="" optional="true" label="Dots per inch" help="Optional" />
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37 </section>
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38 </xml>
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40 <xml name="squidpy_plotting_option_palette">
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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." />
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42 </xml>
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44 <xml name="squidpy_plotting_options_more">
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45 <expand macro="squidpy_plotting_options">
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46 <yield />
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47 <param argument="annotate" type="boolean" checked="false" label="Whether to annotate the cells of the heatmap?" />
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48 <param argument="method" type="select" label="The linkage method to be used for dendrogram/clustering" help="see scipy.cluster.hierarchy.linkage().">
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49 <option value="none" selected="true">None</option>
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50 <option value="single">single</option>
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51 <option value="complete">complete</option>
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52 <option value="average">average</option>
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53 <option value="weighted">weighted</option>
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54 <option value="centroid">centroid</option>
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55 <option value="median">median</option>
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56 <option value="ward">ward</option>
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57 </param>
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58 <param argument="title" type="text" value="" optional="true" label="The title of the plot" help="Optional." />
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59 <param argument="cmap" type="text" value="viridis" label="Continuous colormap to use" help="Refer to `matplotlib.pyplot.cmap`." />
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60 <!-- <param argument="cbar_kwargs" type="text" value="" label="Keyword arguments for matplotlib.figure.Figure.colorbar()" /> -->
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61 <expand macro="squidpy_plotting_option_palette" />
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62 </expand>
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63 </xml>
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64 </macros>