Mercurial > repos > ebi-gxa > scanpy_run_fdg

annotate scanpy-run-fdg.xml @ 25:cef0ddd01875 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 162313dc6ba68efc5003b1bd9b71a40aec87d826-dirty
author ebi-gxa
date Fri, 13 Oct 2023 14:09:25 +0000
parents 7c6581b57ad4
children be019b069e31
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1 <?xml version="1.0" encoding="utf-8"?>
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cef0ddd01875 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 162313dc6ba68efc5003b1bd9b71a40aec87d826-dirty
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2 <tool id="scanpy_run_fdg" name="Scanpy RunFDG" version="@TOOL_VERSION@+galaxy93" profile="@PROFILE@">
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3 <description>visualise cell clusters using force-directed graph</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 '${input_obj_file}' input.h5 &&
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10 PYTHONIOENCODING=utf-8 scanpy-cli embed fdg
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11 --key-added-ext '${key_added_ext}'
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12 #if $embeddings
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13 --export-embedding embeddings.tsv
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14 #end if
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15 #if $settings.default == "false"
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16 #if $settings.neighbors_key
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17 --neighbors-key '${settings.neighbors_key}'
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18 #end if
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19 #if $settings.obsp
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20 --obsp '${settings.obsp}'
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21 #end if
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22 --random-state ${settings.random_seed}
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23 --layout ${settings.layout}
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24 #if $settings.init_pos
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25 --init-pos '${settings.init_pos}'
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26 #end if
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27 #if $settings.root
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28 --root '${settings.root}'
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29 #end if
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30 #end if
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31 @INPUT_OPTS@
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32 @OUTPUT_OPTS@
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33
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34 ]]></command>
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35
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36 <inputs>
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37 <expand macro="input_object_params"/>
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38 <expand macro="output_object_params"/>
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39 <param name="embeddings" type="boolean" checked="true" label="Output embeddings in tsv format"/>
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40 <param name="key_added_ext" argument="--key-added-ext" type="text" optional="true"
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41 label="Additional suffix to the name of the slot to save the embedding"/>
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42
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43 <conditional name="settings">
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44 <param name="default" type="boolean" checked="true" label="Use programme defaults"/>
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45 <when value="true"/>
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46 <when value="false">
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47 <param name="neighbors_key" argument="--neighbors-key" value="neighbors" type="text"
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48 label="Name of the slot that holds the KNN graph"/>
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49 <param name="obsp" type="boolean" checked="false" label="Use .obsp[obsp] as adjacency" help="You can’t specify both obsp and neighbors-key at the same time."/>
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50 <param name="init_pos" argument="--init-pos" type="text" label="Method to initialise embedding, any key for adata.obsm or choose from the preset methods"/>
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51 <param name="layout" argument="--layout" type="select" label="Graph layout">
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52 <option value="fa">fa</option>
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53 <option value="fr" selected="true">fr</option>
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54 <option value="grid_fr">grid fr</option>
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55 <option value="kk">kk</option>
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56 <option value="lgl">lgl</option>
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57 <option value="drl">drl</option>
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58 <option value="rt">rt</option>
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59 <option value="rt_circular">rt_circular</option>
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60 </param>
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61 <param name="root" argument="--root" type="integer" optional="true" label="Root for tree layouts"/>
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62 <param name="random_seed" argument="--random-state" type="integer" value="0" label="Seed for numpy random number generator"/>
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63 </when>
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64 </conditional>
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65 </inputs>
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66
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67 <outputs>
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68 <expand macro="output_data_obj" description="FDG object"/>
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69 <data name="output_embed" format="tabular" from_work_dir="embeddings.tsv" label="${tool.name} on ${on_string}: FDG embeddings">
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70 <filter>embeddings</filter>
96af0059b974 "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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71 </data>
96af0059b974 "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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72 </outputs>
96af0059b974 "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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73
96af0059b974 "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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74 <tests>
96af0059b974 "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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75 <test>
96af0059b974 "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="input_obj_file" value="find_cluster.h5"/>
96af0059b974 "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 <param name="input_format" value="anndata"/>
96af0059b974 "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="output_format" value="anndata"/>
96af0059b974 "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 <param name="default" value="false"/>
96af0059b974 "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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80 <param name="embeddings" value="true"/>
96af0059b974 "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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81 <param name="random_seed" value="0"/>
96af0059b974 "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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82 <output name="output_h5" file="run_fdg.h5" ftype="h5" compare="sim_size"/>
11
dd27b39c5c12 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 62f47287c7e8449c59a1f1f454852ddc669b1b1e-dirty"
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83 <output name="output_embed" file="run_fdg.embeddings.tsv" ftype="tabular" compare="sim_size">
0
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84 <assert_contents>
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85 <has_n_columns n="3"/>
0
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86 </assert_contents>
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87 </output>
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88 </test>
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89 </tests>
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90
96af0059b974 "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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91 <help><![CDATA[
96af0059b974 "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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92 ================================================================================
96af0059b974 "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 Embed the neighborhood graph using Force-directed Graph (`scanpy.tl.draw_graph`)
96af0059b974 "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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94 ================================================================================
96af0059b974 "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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95
96af0059b974 "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 For making FDG plots, please use `Scanpy PlotEmbed` with the output of this
96af0059b974 "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 tool and enter "draw_graph_{layout}" as the name of the embedding to plot.
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98
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99 It yields `X_draw_graph_{layout}`, FDG coordinates of data.
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100
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101 @HELP@
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102
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103 @VERSION_HISTORY@
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104 ]]></help>
96af0059b974 "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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105 <expand macro="citations"/>
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106 </tool>