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planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit 9fb5578191db8a559191e45156cfb95350f01aea
author goeckslab
date Mon, 10 Jun 2024 18:45:07 +0000
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834ee9481948 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit 9fb5578191db8a559191e45156cfb95350f01aea
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1 <tool id="scimap_plotting" name="Spatial plotting functions" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
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2 <description>from Scimap</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
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7 <expand macro="scimap_requirements"/>
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8 <expand macro="macro_stdio" />
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9 <version_command>echo "@VERSION@"</version_command>
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10 <command detect_errors="aggressive">
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11 <![CDATA[
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12 python '$__tool_directory__/scimap_plotting.py'
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13 --inputs '$inputs'
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14 --anndata '$anndata'
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15 --output '$output'
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16
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17 ]]>
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18 </command>
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19 <configfiles>
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20 <inputs name="inputs" />
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21 </configfiles>
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22 <inputs>
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23 <param name="anndata" type="data" format="h5ad" label="Select the input anndata" />
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24 <conditional name="analyses">
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25 <param name="selected_tool" type="select" label="Select a plotting function to run">
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26 <option value="stacked_barplot">Stacked barplot</option>
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27 <option value="voronoi">Voronoi</option>
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28 </param>
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29 <when value="stacked_barplot">
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30 <param argument="x_axis" type="text" value="imageid" label="Categorical column in adata.obs to be plotted on the x axis" />
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31 <param argument="y_axis" type="text" value="phenotype" label="Categorical column in adata.obs to be plotted on the y axis" />
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32 <param name="method" type="select" label="Select the metric for plotting">
834ee9481948 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit 9fb5578191db8a559191e45156cfb95350f01aea
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33 <option value="percent" selected="true">Percent abundance</option>
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34 <option value="absolute">Absolute abundance</option>
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35 </param>
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36 <section name="options" title="Advanced Options" expanded="false">
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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" />
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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" />
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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" />
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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" />
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41 </section>
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42 </when>
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43 <when value="voronoi">
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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" />
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45 <param argument="x_coordinate" type="text" value="X_centroid" optional="false" label="Pass the name of the column containing cell X coordinates" />
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46 <param argument="y_coordinate" type="text" value="Y_centroid" optional="false" label="Pass the name of the column containing cell Y coordinates" />
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47 <section name="options" title="Advanced Options" expanded="false">
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48 <param argument="imageid" type="text" value="imageid" optional="true" label="Pass the name of the column containing image IDs" help="Only necessary if subsetting one image out of a multi-image file" />
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49 <param argument="subset" type="text" value="" optional="true" label="Image ID of a single image to be subsetted for plotting" />
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50 <param argument="x_lim" type="text" value="" optional="true" label="Type in a list of limits for the x-axis" help="Optional. Comma delimited: xmin,xmax" />
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51 <param argument="y_lim" type="text" value="" optional="true" label="Type in a list of limits for the y-axis" help="Optional. Comma delimited: ymin,ymax" />
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52 <param argument="flip_y" type="boolean" truevalue="True" falsevalue="False" label="Flip Y-axis" />
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53 <param argument="voronoi_edge_color" type="text" value="black" optional="true" label="Specify a Matplotlib color for marking the edges of the voronoi cells" />
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54 <param argument="voronoi_line_width" type="float" value="0.1" optional="true" label="The linewidth of the marker edges" />
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55 <param argument="voronoi_alpha" type="float" value="0.5" optional="true" label="The alpha blending value for voronoi cells" help="between 0 (transparent) and 1 (opaque)" />
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56 <param argument="size_max" type="float" value="" optional="true" label="The maximum size for the Voronoi cells" help="Default is Inf" />
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57 <param argument="overlay_points" type="text" value="" optional="true" label="Pass the name of the column which contains categorical variable to be overlayed" help="overlays a scatter plot on top of the voronoi diagram" />
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58 <param argument="overlay_points_categories" type="text" value="" optional="true" label="Subset overlay categories to plotting. Type in a list of categories to include" help="Optional. Comma delimited. Default is all categories" />
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59 <param argument="overlay_drop_categories" type="text" value="" optional="true" label="Specify a list of categories to exclude from overlay plotting." help="Convenience alternative to specifying categories to keep" />
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60 <param argument="overlay_point_size" type="integer" value="5" optional="true" label="Overlay point size" />
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61 <param argument="overlay_point_alpha" type="float" value="1" optional="true" label="The alpha blending value for overlay points" help="between 0 (transparent) and 1 (opaque)" />
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62 <param argument="plot_legend" type="boolean" checked="true" truevalue="True" falsevalue="False" label="Whether to include a legend" />
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63 <param argument="legend_size" type="integer" value="6" label="Point size of legend text" />
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64 </section>
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65 </when>
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66 </conditional>
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67 </inputs>
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68 <outputs>
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69 <data from_work_dir="out.png" format="png" name="output" label="Scimap.pl.${analyses.selected_tool} on ${on_string}" />
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70 </outputs>
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71 <tests>
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72 <test>
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73 <param name="anndata" value="tutorial_data_pheno.h5ad" />
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74 <conditional name="analyses">
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75 <param name="selected_tool" value="stacked_barplot" />
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76 <param name="method" value="percent" />
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77 </conditional>
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78 <output name="output">
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79 <assert_contents>
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80 <has_size value="147000" delta="10000" />
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81 </assert_contents>
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82 </output>
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83 </test>
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84 <test>
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85 <param name="anndata" value="tutorial_data_pheno.h5ad" />
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86 <conditional name="analyses">
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87 <param name="selected_tool" value="voronoi" />
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88 </conditional>
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89 <output name="output">
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90 <assert_contents>
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91 <has_size value="510000" delta="10000" />
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92 </assert_contents>
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93 </output>
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94 </test>
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95 </tests>
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96 <help>
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97 <![CDATA[
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98 **What it does**
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99
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100 This tool does various single cell spatial analyses with Scimap.
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101
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102 **Input**
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103
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104 AnnData.
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105
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106 **Output**
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107
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108 Anndata with a corresponding key added.
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109
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110
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111 ]]>
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112 </help>
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113 <expand macro="citations" />
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114 </tool>