Mercurial > repos > ebi-gxa > scanpy_run_tsne

annotate scanpy-run-tsne.xml @ 25:753bf41cc2e3 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 9748fb7ca203206ecac97461f60ce75890d00fa4-dirty"
author ebi-gxa
date Fri, 15 Oct 2021 15:09:06 +0000
parents a147dce191e9
children 181d61d2f3cd
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f6f189ce4ebc planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 9bf9a6e46a330890be932f60d1d996dd166426c4
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1 <?xml version="1.0" encoding="utf-8"?>
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a147dce191e9 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 85dcbc74a856bd55865bd372601de39af72dfd29-dirty"
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2 <tool id="scanpy_run_tsne" name="Scanpy RunTSNE" version="@TOOL_VERSION@+galaxy0" profile="@PROFILE@">
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f6f189ce4ebc planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 9bf9a6e46a330890be932f60d1d996dd166426c4
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3 <description>visualise cell clusters using tSNE</description>
f6f189ce4ebc planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 9bf9a6e46a330890be932f60d1d996dd166426c4
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4 <macros>
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5 <import>scanpy_macros2.xml</import>
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f6f189ce4ebc planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 9bf9a6e46a330890be932f60d1d996dd166426c4
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6 </macros>
f6f189ce4ebc planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 9bf9a6e46a330890be932f60d1d996dd166426c4
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7 <expand macro="requirements"/>
f6f189ce4ebc planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 9bf9a6e46a330890be932f60d1d996dd166426c4
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8 <command detect_errors="exit_code"><![CDATA[
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9 #set embeddings_tsv='embeddings.tsv'
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f6f189ce4ebc planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 9bf9a6e46a330890be932f60d1d996dd166426c4
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10 ln -s '${input_obj_file}' input.h5 &&
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11 PYTHONIOENCODING=utf-8 scanpy-run-tsne
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8b0d6f6f44c8 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 4332e90fa9f269bf4a8b912366eeace9c040b4c4-dirty"
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12 #if $use_rep
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13 --use-rep '${use_rep}'
2e74fd7b5f45 "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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14 #end if
2e74fd7b5f45 "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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15 #if $embeddings
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16 --export-embedding embeddings.tsv
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17 #end if
2e74fd7b5f45 "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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18 #if $settings.default == "false"
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19 #if $settings.perplexity_file
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20 #set f = open($settings.perplexity_file.__str__)
9d2b6c6f9e07 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit c02d457c74016980672e64832e6cad31d703edcd-dirty"
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21 #set perplexity = f.read().strip()
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22 #silent f.close
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23 #elif $settings.perplexity
b5e1939cc155 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit e572b5425460d57f1bd13ab6374674c1c6801ab3-dirty"
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24 #set perplexity = $settings.perplexity.__str__.strip()
b5e1939cc155 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit e572b5425460d57f1bd13ab6374674c1c6801ab3-dirty"
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25 #end if
b5e1939cc155 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit e572b5425460d57f1bd13ab6374674c1c6801ab3-dirty"
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26 #if $perplexity
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27 --perplexity '$perplexity'
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28 #end if
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29 #if $settings.key_added
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30 #set key_added = $settings.key_added
b5e1939cc155 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit e572b5425460d57f1bd13ab6374674c1c6801ab3-dirty"
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31 #if $perplexity
b5e1939cc155 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit e572b5425460d57f1bd13ab6374674c1c6801ab3-dirty"
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32 #set key_added = $key_added.replace('PERPLEXITY', $perplexity.__str__)
b5e1939cc155 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit e572b5425460d57f1bd13ab6374674c1c6801ab3-dirty"
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33 #end if
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34 --key-added '${key_added}'
b5e1939cc155 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit e572b5425460d57f1bd13ab6374674c1c6801ab3-dirty"
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35 #set embeddings_tsv="embeddings_" + $key_added.__str__ + ".tsv"
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36 #end if
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37 --early-exaggeration '${settings.early_exaggeration}'
2e74fd7b5f45 "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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38 --learning-rate '${settings.learning_rate}'
2e74fd7b5f45 "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 #if $settings.n_pc
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40 --n-pcs ${settings.n_pc}
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41 #end if
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42 #if not $settings.fast_tsne
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43 --no-fast-tsne
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44 #end if
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45 #if $settings.n_job
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46 --n-jobs ${settings.n_job}
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47 #end if
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48 #if $settings.random_seed is not None
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49 --random-state ${settings.random_seed}
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50 #end if
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51 #end if
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52 @INPUT_OPTS@
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53 @OUTPUT_OPTS@
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54 #if $embeddings
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55 #if $embeddings_tsv != 'embeddings.tsv'
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56 && mv '${embeddings_tsv}' embeddings.tsv
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57 #end if
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58 #end if
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59
f6f189ce4ebc planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 9bf9a6e46a330890be932f60d1d996dd166426c4
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60 ]]></command>
f6f189ce4ebc planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 9bf9a6e46a330890be932f60d1d996dd166426c4
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61
f6f189ce4ebc planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 9bf9a6e46a330890be932f60d1d996dd166426c4
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62 <inputs>
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63 <expand macro="input_object_params"/>
f6f189ce4ebc planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 9bf9a6e46a330890be932f60d1d996dd166426c4
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64 <expand macro="output_object_params"/>
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65 <param name="embeddings" type="boolean" checked="true" label="Output embeddings in tsv format"/>
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66
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67 <param name="use_rep" argument="--use-rep" type="text" optional="true" label="Use the indicated representation" help="Use the indicated representation. 'X' (for the content of .X, usuaally normalised expression values) or any key for .obsm (e.g. X_pca for PCA) is valid. If not set, the representation is chosen automatically: For .n_vars less than 50, .X is used, otherwise ‘X_pca’ is used. If ‘X_pca’ is not present, it’s computed with default parameters."/>
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f6f189ce4ebc planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 9bf9a6e46a330890be932f60d1d996dd166426c4
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68 <conditional name="settings">
f6f189ce4ebc planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 9bf9a6e46a330890be932f60d1d996dd166426c4
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69 <param name="default" type="boolean" checked="true" label="Use programme defaults"/>
f6f189ce4ebc planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 9bf9a6e46a330890be932f60d1d996dd166426c4
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70 <when value="true"/>
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71 <when value="false">
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72 <param name="key_added" argument="--key-added" type="text" optional="true"
b5e1939cc155 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit e572b5425460d57f1bd13ab6374674c1c6801ab3-dirty"
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73 label="Additional suffix to the name of the slot to save the embedding" help="If included, PERPLEXITY will be substituted with the value of the perplexity setting."/>
0
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74 <param name="perplexity" argument="--perplexity" type="float" value="30" label="The perplexity is related to the number of nearest neighbours, select a value between 5 and 50"/>
f6f189ce4ebc planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 9bf9a6e46a330890be932f60d1d996dd166426c4
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75 <param name="perplexity_file" argument="--perplexity" type="data" format="txt,tsv" label="The perplexity is related to the number of nearest neighbours" help="For use with the parameter iterator. Overrides the persplexity option above" optional="true"/>
f6f189ce4ebc planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 9bf9a6e46a330890be932f60d1d996dd166426c4
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76 <param name="early_exaggeration" argument="--early-exaggeration" type="float" value="12" label="Controls the tightness within and between clusters"/>
f6f189ce4ebc planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 9bf9a6e46a330890be932f60d1d996dd166426c4
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77 <param name="learning_rate" argument="--learning-rate" type="float" value="1000" label="Learning rate, should be between 100 and 1000"/>
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78 <param name="fast_tsne" type="boolean" checked="false" label="Use multicoreTSNE" help="Depending on the setup and version, the availability of the needed library might vary and hence fail."/>
0
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79 <param name="n_job" argument="--n-jobs" type="integer" optional="true" label="The number of jobs"/>
f6f189ce4ebc planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 9bf9a6e46a330890be932f60d1d996dd166426c4
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80 <param name="n_pc" argument="--n-pcs" type="integer" optional="true" label="The number of PCs to use"/>
f6f189ce4ebc planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 9bf9a6e46a330890be932f60d1d996dd166426c4
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81 <param name="random_seed" argument="--random-seed" type="integer" value="0" label="Seed for random number generator"/>
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82 </when>
f6f189ce4ebc planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 9bf9a6e46a330890be932f60d1d996dd166426c4
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83 </conditional>
f6f189ce4ebc planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 9bf9a6e46a330890be932f60d1d996dd166426c4
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84
f6f189ce4ebc planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 9bf9a6e46a330890be932f60d1d996dd166426c4
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85 </inputs>
f6f189ce4ebc planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 9bf9a6e46a330890be932f60d1d996dd166426c4
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86
f6f189ce4ebc planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 9bf9a6e46a330890be932f60d1d996dd166426c4
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87 <outputs>
5
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88 <expand macro="output_data_obj" description="tSNE object"/>
12
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89 <data name="output_embed" format="tabular" from_work_dir="embeddings.tsv" label="${tool.name} on ${on_string}: tSNE embeddings">
0
f6f189ce4ebc planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 9bf9a6e46a330890be932f60d1d996dd166426c4
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90 <filter>embeddings</filter>
f6f189ce4ebc planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 9bf9a6e46a330890be932f60d1d996dd166426c4
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91 </data>
f6f189ce4ebc planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 9bf9a6e46a330890be932f60d1d996dd166426c4
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92 </outputs>
f6f189ce4ebc planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 9bf9a6e46a330890be932f60d1d996dd166426c4
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93
f6f189ce4ebc planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 9bf9a6e46a330890be932f60d1d996dd166426c4
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94 <tests>
f6f189ce4ebc planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 9bf9a6e46a330890be932f60d1d996dd166426c4
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95 <test>
f6f189ce4ebc planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 9bf9a6e46a330890be932f60d1d996dd166426c4
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96 <param name="input_obj_file" value="find_cluster.h5"/>
f6f189ce4ebc planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 9bf9a6e46a330890be932f60d1d996dd166426c4
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97 <param name="input_format" value="anndata"/>
f6f189ce4ebc planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 9bf9a6e46a330890be932f60d1d996dd166426c4
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98 <param name="output_format" value="anndata"/>
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99 <param name="default" value="false"/>
16
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100 <param name="perplexity_file" value="perplexity.txt"/>
9d2b6c6f9e07 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit c02d457c74016980672e64832e6cad31d703edcd-dirty"
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101 <param name="embeddings" value="true"/>
9d2b6c6f9e07 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit c02d457c74016980672e64832e6cad31d703edcd-dirty"
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102 <param name="random_seed" value="0"/>
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103 <output name="output_h5" file="run_tsne.h5" ftype="h5" compare="sim_size"/>
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104 <output name="output_embed" file="run_tsne.embeddings.tsv" ftype="tabular" compare="sim_size">
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105 <assert_contents>
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106 <has_n_columns n="3"/>
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107 </assert_contents>
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108 </output>
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109 </test>
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110 <test>
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111 <param name="input_obj_file" value="find_cluster.h5"/>
9d2b6c6f9e07 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit c02d457c74016980672e64832e6cad31d703edcd-dirty"
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112 <param name="input_format" value="anndata"/>
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113 <param name="output_format" value="anndata"/>
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114 <param name="default" value="false"/>
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115 <param name="perplexity" value="30"/>
0
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116 <param name="embeddings" value="true"/>
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117 <param name="random_seed" value="0"/>
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118 <output name="output_h5" file="run_tsne.h5" ftype="h5" compare="sim_size"/>
12
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119 <output name="output_embed" file="run_tsne.embeddings.tsv" ftype="tabular" compare="sim_size">
0
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120 <assert_contents>
12
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121 <has_n_columns n="3"/>
0
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122 </assert_contents>
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123 </output>
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124 </test>
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125 </tests>
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126
f6f189ce4ebc planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 9bf9a6e46a330890be932f60d1d996dd166426c4
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127 <help><![CDATA[
1
2e74fd7b5f45 "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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128 =========================================================================
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129 t-distributed stochastic neighborhood embedding (tSNE) (`scanpy.tl.tsne`)
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130 =========================================================================
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131
2e74fd7b5f45 "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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132 For making TSNE plots, please use `Scanpy PlotEmbed` with the output of this tool and enter "tsne" as the
2e74fd7b5f45 "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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133 name of the embedding to plot.
0
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134
f6f189ce4ebc planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 9bf9a6e46a330890be932f60d1d996dd166426c4
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135 t-distributed stochastic neighborhood embedding (tSNE) (Maaten et al, 2008) has been
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136 proposed for visualizating single-cell data by (Amir et al, 2013). Here, by default,
f6f189ce4ebc planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 9bf9a6e46a330890be932f60d1d996dd166426c4
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137 we use the implementation of *scikit-learn* (Pedregosa et al, 2011).
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138
f6f189ce4ebc planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 9bf9a6e46a330890be932f60d1d996dd166426c4
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139 It yields `X_tsne`, tSNE coordinates of data.
f6f189ce4ebc planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 9bf9a6e46a330890be932f60d1d996dd166426c4
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140
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141 @HELP@
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142
f6f189ce4ebc planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 9bf9a6e46a330890be932f60d1d996dd166426c4
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143 @VERSION_HISTORY@
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144 ]]></help>
f6f189ce4ebc planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 9bf9a6e46a330890be932f60d1d996dd166426c4
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145 <expand macro="citations"/>
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146 </tool>