Mercurial > repos > ebi-gxa > scanpy_plot_embed

annotate scanpy-plot-embedding.xml @ 19:1be0fc4d8654 draft

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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 cecd3663ae841b026216f01003d58ea7c3bfde3e-dirty"
author ebi-gxa
date Tue, 03 Aug 2021 09:02:11 +0000
parents 9fafbfcdee0d
children a71086d2e55f
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c63bc0b71865 "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"?>
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2 <tool id="scanpy_plot_embed" name="Scanpy PlotEmbed" version="@TOOL_VERSION@+galaxy0" profile="@PROFILE@">
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3 <description>visualise cell embeddings</description>
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4 <macros>
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5 <import>scanpy_macros2.xml</import>
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6 </macros>
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7 <expand macro="requirements"/>
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8 <command detect_errors="exit_code"><![CDATA[
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9 ln -s '${input_obj_file}' input.h5 &&
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10 PYTHONIOENCODING=utf-8 scanpy-cli plot embed
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11 @INPUT_OPTS@
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12 #if $color_by
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13 --color '${color_by}'
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14 #end if
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15 ${use_raw}
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16 --legend-loc '${legend_loc}'
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17 --legend-fontsize '${legend_fontsize}'
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18 #if $basis
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19 --basis '${basis}'
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20 #end if
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21 #if $groups
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22 --groups $groups
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23 #end if
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24 #if $neighbors_key
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25 --neighbors-key '${neighbors_key}'
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26 #end if
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27 #if $layer
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28 --layer '${layer}'
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29 #end if
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30 #if $point_size
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31 --size ${point_size}
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32 #end if
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33 #if $gene_symbols_field
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34 --gene-symbols ${gene_symbols_field}
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35 #end if
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36 ${edges} --edges-width ${edges_width}
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37 #if $edges_color
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38 --edges-color ${edges_color}
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39 #end if
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40 #if $components
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41 --components ${components}
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42 #end if
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43 --projection $projection
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44 $sort_order
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45 @PLOT_OPTS@
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46 ]]></command>
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47
c63bc0b71865 "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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48 <inputs>
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49 <expand macro="input_object_params"/>
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50 <param name="basis" argument="--basis" type="text" value='umap' label="name of the embedding to plot"/>
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51 <param name="color_by" argument="--color" type="text" label="color by attributes, comma separated texts">
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b2410da4e381 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 1d069e25584e436d7628694cb8853a15f1f85604
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52 <sanitizer>
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53 <valid initial="string.printable"/>
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54 </sanitizer>
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55 </param>
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56 <param name="groups" argument="--groups" type="text" value="" label="Key for categorical in `.obs`" help="You can pass your predefined groups by choosing any categorical annotation of observations."/>
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57 <param name="gene_symbols_field" argument="--gene-symbols" type="text" optional="true" label="Field for gene symbols" help="The field used in the AnnData object to store gene symbols, leave blank for the default (index), else a common value is 'gene_symbols'"/>
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58 <param name="use_raw" argument="--use-raw" type="boolean" checked="true" truevalue="--use-raw" falsevalue="--no-raw" label="Use raw attributes if present"/>
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59 <param name="layer" argument="--layer" value="" type="text"
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60 label="Name of the AnnData object layer to plot" help="By default adata.raw.X is plotted. If use_raw=False is set, then adata.X is plotted. If layer is set to a valid layer name, then the layer is plotted. layer takes precedence over use_raw." />
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61 <param name="neighbors_key" argument="--neighbors-key" value="" type="text"
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62 label="Where to look for neighbors connectivities." help="If not specified, this looks in .obsp[‘connectivities’] for connectivities (default storage place for pp.neighbors). If specified, this looks .obsp[.uns[neighbors_key][‘connectivities_key’]] for connectivities."/>
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63 <param name="legend_loc" argument="--legend-loc" type="select" label="Location of legend">
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64 <option value="right margin" selected="true">Right margin</option>
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65 <option value="on data">On data</option>
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66 </param>
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67 <param name="legend_fontsize" argument="--legend-fontsize" type="integer" value="15" label="Legend font size"/>
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68 <param name="point_size" argument="--size" type="integer" optional="true" label="Point size"
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69 help="Automatically determined if not specified."/>
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70 <param name="edges" argument="--edges" type="boolean" checked="False" truevalue="--edges" falsevalue="" label="Show edges?"/>
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71 <param name="edges_width" argument="--edges-width" type="float" value="0.1" label="Width of edges"/>
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72 <param name="edges_color" argument="--edges-color" type="text" value="" label="Color of edges"/>
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73 <param name="sort_order" argument="--no-sort-order" type="boolean" checked="False" truevalue="" falsevalue="--no-sort-order" label="Plot in order?" help="For continuous annotations used as 'color parameter, plot data points with higher values on top of others."/>
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74 <param name="components" argument="--components" type="text" value="" label="Components to plot" help="Comma-separated list, e.g. '1,2', '2,3'. To plot all available components use 'all'."/>
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75 <param name="projection" argument="--projection" type="select" label="Plot projection">
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76 <option value="2d" selected="true">2D</option>
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77 <option value="3d">3D</option>
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78 </param>
0
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79 <expand macro="output_plot_params"/>
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80 </inputs>
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81
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82 <outputs>
4
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83 <data name="output_png" format="png" from_work_dir="output.png" label="${tool.name} on ${on_string}: ${basis} embedding plot"/>
0
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84 </outputs>
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85
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86 <tests>
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87 <test>
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88 <param name="input_obj_file" value="find_cluster.h5"/>
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89 <param name="input_format" value="anndata"/>
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90 <param name="basis" value="X_pca"/>
0
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91 <param name="color_by" value="louvain"/>
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92 <param name="use_raw" value="false"/>
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93 <output name="output_png" file="plot_embed.png" ftype="png" compare="sim_size"/>
0
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94 </test>
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95 </tests>
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96
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97 <help><![CDATA[
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98 =============================================================
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99 Plot embeddings of a given method of dimensionality reduction
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100 =============================================================
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101
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102 It yields a scatter plot in png format, wherein cells are placed in space of
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103 reduced dimensionality and coloured by attribute of choice.
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104
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105 Requires calculating the specified embeddings first. For example, to make
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106 UMAP/TSNE plots, run `Scanpy RunUMAP`/`Scanpy RunTSNE` first, then enter
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107 "umap"/"tsne" as the name of the embedding to plot here.
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108
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109 @HELP@
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110
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111 @VERSION_HISTORY@
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112 ]]></help>
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113 <expand macro="citations"/>
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114 </tool>