Mercurial > repos > ebi-gxa > scanpy_plot_trajectory

annotate scanpy-plot-trajectory.xml @ 26:cb1992d1804b draft default tip

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planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit ee197a80b2d591c393e1662854bc119b2ecab11e-dirty
author ebi-gxa
date Tue, 27 Feb 2024 16:43:29 +0000
parents 9d746af31fe8
children
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f76e8237073a "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 4846776f55931e176f7e77af7c185ec6fec7d142"
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1 <?xml version="1.0" encoding="utf-8"?>
26
cb1992d1804b planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit ee197a80b2d591c393e1662854bc119b2ecab11e-dirty
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2 <tool id="scanpy_plot_trajectory" name="Scanpy PlotTrajectory" version="@TOOL_VERSION@+galaxy0" profile="@PROFILE@">
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3 <description>visualise cell trajectories</description>
f76e8237073a "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 4846776f55931e176f7e77af7c185ec6fec7d142"
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4 <macros>
f76e8237073a "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 4846776f55931e176f7e77af7c185ec6fec7d142"
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5 <import>scanpy_macros2.xml</import>
f76e8237073a "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 4846776f55931e176f7e77af7c185ec6fec7d142"
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6 </macros>
f76e8237073a "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 4846776f55931e176f7e77af7c185ec6fec7d142"
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7 <expand macro="requirements"/>
f76e8237073a "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 4846776f55931e176f7e77af7c185ec6fec7d142"
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8 <command detect_errors="exit_code"><![CDATA[
f76e8237073a "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 4846776f55931e176f7e77af7c185ec6fec7d142"
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9 ln -s '${input_obj_file}' input.h5 &&
f76e8237073a "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 4846776f55931e176f7e77af7c185ec6fec7d142"
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10 PYTHONIOENCODING=utf-8 scanpy-cli plot paga
f76e8237073a "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 4846776f55931e176f7e77af7c185ec6fec7d142"
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11 #if $use_key
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12 --use-key '${use_key}'
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13 #end if
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14 --layout ${layout}
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15 --legend-loc '${legend_loc}'
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16 #if $basis
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17 --basis ${basis}
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18 #end if
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19 #if $settings.default == "false"
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20 --threshold ${settings.threshold}
f76e8237073a "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 4846776f55931e176f7e77af7c185ec6fec7d142"
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21 #if $settings.root
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22 --root ${settings.root}
f76e8237073a "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 4846776f55931e176f7e77af7c185ec6fec7d142"
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23 #end if
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24 ${settings.single_component}
f76e8237073a "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 4846776f55931e176f7e77af7c185ec6fec7d142"
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25 #if $settings.solid_edges
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26 --solid-edges ${settings.solid_edges}
f76e8237073a "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 4846776f55931e176f7e77af7c185ec6fec7d142"
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27 #end if
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28 #if $settings.color
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29 --color '${settings.color}'
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30 #end if
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31 #if $settings.node_size
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32 --node-size-scale ${settings.node_size}
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33 #end if
f76e8237073a "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 4846776f55931e176f7e77af7c185ec6fec7d142"
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34 #if $settings.node_font
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35 --fontsize ${settings.node_font}
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36 #end if
f76e8237073a "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 4846776f55931e176f7e77af7c185ec6fec7d142"
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37 #if $settings.edge_width
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38 --edge-width-scale ${settings.edge_width}
f76e8237073a "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 4846776f55931e176f7e77af7c185ec6fec7d142"
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39 #end if
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40 #end if
17
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41 #if str($output_format).startswith('anndata')
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42 --show-obj stdout --output-format anndata --output-obj output.h5
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43 #else
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44 --show-obj stdout --output-format loom --output-obj output.h5
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45 #end if
0
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46 @INPUT_OPTS@
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47 @PLOT_OPTS@
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48 ]]></command>
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49
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50 <inputs>
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51 <expand macro="input_object_params"/>
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52 <expand macro="output_object_params"/>
0
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53 <param name="use_key" argument="--use-key" type="text" value="paga"
f76e8237073a "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 4846776f55931e176f7e77af7c185ec6fec7d142"
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54 label="The key in `.uns` that contains trajectory information"/>
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55 <param name="layout" argument="--layout" type="select" label="Layout functions">
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56 <option value="fa">ForceAtlas2</option>
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57 <option value="fr" selected="true">Fruchterman-Reingold</option>
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58 <option value="rt">Reingold-Tilford</option>
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59 </param>
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60 <param name="legend_loc" argument="--legend-loc" type="select" label="Location of legend">
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61 <option value="right margin" selected="true">Right margin</option>
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62 <option value="on data">On data</option>
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63 </param>
0
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64 <param name="basis" argument="--basis" type="text" optional="true" label="Name of the embedding to plot"
f76e8237073a "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 4846776f55931e176f7e77af7c185ec6fec7d142"
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65 help="Must be a key of `.obsm` without the prefix 'X_', e.g. 'umap'."/>
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66 <expand macro="output_plot_params"/>
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67 <conditional name="settings">
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68 <param name="default" type="boolean" checked="true" label="Use programme defaults"/>
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69 <when value="true"/>
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70 <when value="false">
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71 <param name="threshold" argument="--threshold" type="float" min="0" value="0.01"
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72 label="Do not draw edges with weights below this threshold"
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73 help="Set to 0 to include all edges."/>
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74 <param name="root" argument="--root" type="integer" min="0" value="0"
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75 label="The index of the root node when choosing a tree layout"/>
f76e8237073a "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 4846776f55931e176f7e77af7c185ec6fec7d142"
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76 <param name="single_component" argument="--single-component" type="boolean" truevalue="--single-component" falsevalue="" checked="false"
f76e8237073a "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 4846776f55931e176f7e77af7c185ec6fec7d142"
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77 label="Restrict to the largest connected component"/>
f76e8237073a "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 4846776f55931e176f7e77af7c185ec6fec7d142"
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78 <param name="solid_edges" argument="--solid-edges" type="select" label="Edges to be drawn in solid black">
f76e8237073a "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 4846776f55931e176f7e77af7c185ec6fec7d142"
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79 <option value="connectivities" selected="true">connectivities</option>
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80 <option value="connectivities_tree">connectivities_tree</option>
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81 </param>
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82 <param name="color" argument="--color" type="text" label="Name of cell annotation or gene that is used to color the nodes"/>
f76e8237073a "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 4846776f55931e176f7e77af7c185ec6fec7d142"
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83 <param name="node_size" argument="--node-size-scale" type="float" value="1.0"
f76e8237073a "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 4846776f55931e176f7e77af7c185ec6fec7d142"
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84 label="Increase or decrease the size of the nodes"/>
f76e8237073a "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 4846776f55931e176f7e77af7c185ec6fec7d142"
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85 <param name="node_font" argument="--fontsize" type="integer" min="1" optional="true"
f76e8237073a "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 4846776f55931e176f7e77af7c185ec6fec7d142"
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86 label="Font size for the node labels"/>
f76e8237073a "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 4846776f55931e176f7e77af7c185ec6fec7d142"
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87 <param name="edge_width" argument="--edge-width-scale" type="float" value="1.0"
f76e8237073a "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 4846776f55931e176f7e77af7c185ec6fec7d142"
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88 label="Increase or decrease the width of the edges"/>
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89 </when>
f76e8237073a "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 4846776f55931e176f7e77af7c185ec6fec7d142"
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90 </conditional>
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91 </inputs>
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92
f76e8237073a "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 4846776f55931e176f7e77af7c185ec6fec7d142"
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93 <outputs>
17
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94 <expand macro="output_data_obj" description="Plotted PAGA"/>
0
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95 <data name="output_png" format="png" from_work_dir="output.png" label="${tool.name} on ${on_string}: trajectory plot"/>
f76e8237073a "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 4846776f55931e176f7e77af7c185ec6fec7d142"
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96 </outputs>
f76e8237073a "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 4846776f55931e176f7e77af7c185ec6fec7d142"
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97
f76e8237073a "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 4846776f55931e176f7e77af7c185ec6fec7d142"
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98 <tests>
f76e8237073a "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 4846776f55931e176f7e77af7c185ec6fec7d142"
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99 <test>
11
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100 <param name="input_obj_file" value="paga.h5"/>
0
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101 <param name="input_format" value="anndata"/>
17
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102 <param name="output_format" value="anndata"/>
26
cb1992d1804b planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit ee197a80b2d591c393e1662854bc119b2ecab11e-dirty
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103 <output name="output_h5" ftype="h5">
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104 <assert_contents>
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105 <has_h5_keys keys="uns/louvain_colors"/>
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106 </assert_contents>
cb1992d1804b planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit ee197a80b2d591c393e1662854bc119b2ecab11e-dirty
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107 </output>
cb1992d1804b planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit ee197a80b2d591c393e1662854bc119b2ecab11e-dirty
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108 <output name="output_png" file="paga_compare.png" ftype="png" compare="sim_size" delta_frac="0.1"/>
0
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109 </test>
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110 </tests>
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111
f76e8237073a "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 4846776f55931e176f7e77af7c185ec6fec7d142"
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112 <help><![CDATA[
f76e8237073a "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 4846776f55931e176f7e77af7c185ec6fec7d142"
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113 ===============================================================
f76e8237073a "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 4846776f55931e176f7e77af7c185ec6fec7d142"
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114 Plot PAGA-inferred trajectories (`scanpy.pl.paga/paga_compare`)
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115 ===============================================================
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116
f76e8237073a "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 4846776f55931e176f7e77af7c185ec6fec7d142"
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117 Depending on the selected options, it yields a plot of a graph representing
f76e8237073a "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 4846776f55931e176f7e77af7c185ec6fec7d142"
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118 inferred trajectory, or a trajectory graph side-by-side with a scatter plot of
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119 cells embedded to space of reduced dimensionality in png format.
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120
f76e8237073a "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 4846776f55931e176f7e77af7c185ec6fec7d142"
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121 It requires running PAGA, first.
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122
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123 @HELP@
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124
f76e8237073a "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 4846776f55931e176f7e77af7c185ec6fec7d142"
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125 @VERSION_HISTORY@
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126 ]]></help>
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127 <expand macro="citations"/>
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128 </tool>