Mercurial > repos > ebi-gxa > scanpy_run_pca

annotate scanpy-run-pca.xml @ 10:4a54b92af339 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 ba0c88ab1b077a0b1c60c8d3c529e72ca6946226"
author ebi-gxa
date Thu, 12 Mar 2020 05:16:30 -0400
parents 2dd53b944e78
children 3e7ede8e1c94
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5063cd7f8c89 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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2dd53b944e78 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit edcca4677d954001b33ad15e22603ea452031d76
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2 <tool id="scanpy_run_pca" name="Scanpy RunPCA" version="@TOOL_VERSION@+galaxy10" profile="@PROFILE@">
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5063cd7f8c89 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>for dimensionality reduction</description>
5063cd7f8c89 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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5063cd7f8c89 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>
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7 <expand macro="requirements"/>
5063cd7f8c89 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[
5063cd7f8c89 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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9 ln -s '${input_obj_file}' input.h5 &&
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7798c318e7d7 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 4846776f55931e176f7e77af7c185ec6fec7d142"
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10 PYTHONIOENCODING=utf-8 scanpy-run-pca
7798c318e7d7 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 4846776f55931e176f7e77af7c185ec6fec7d142"
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11 --n-comps '${n_pcs}'
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12 #if $run_mode.chunked
7798c318e7d7 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 4846776f55931e176f7e77af7c185ec6fec7d142"
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13 --chunked
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14 --chunk-size '${run_mode.chunk_size}'
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15 #else
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16 ${run_mode.zero_center}
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17 #if $run_mode.svd_solver
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18 --svd-solver '${run_mode.svd_solver}'
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19 #end if
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7798c318e7d7 "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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20 #if $run_mode.random_seed is not None
7798c318e7d7 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 4846776f55931e176f7e77af7c185ec6fec7d142"
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21 --random-state '${run_mode.random_seed}'
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22 #end if
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23 #end if
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24 #if $extra_outputs and "embeddings" in str($extra_outputs).split(','):
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25 --export-embedding embeddings.tsv
7798c318e7d7 "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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26 #end if
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27 @INPUT_OPTS@
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28 @OUTPUT_OPTS@
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29 ]]></command>
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30
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31 <inputs>
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32 <expand macro="input_object_params"/>
5063cd7f8c89 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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33 <expand macro="output_object_params"/>
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34 <param name="n_pcs" argument="--n-comps" type="integer" min="2" value="50" label="Number of PCs to produce"/>
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35 <conditional name="run_mode">
5063cd7f8c89 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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36 <param name="chunked" argument="--chunked" type="boolean" checked="false" label="Perform incremental PCA by chunks"/>
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37 <when value="true">
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38 <param name="chunk_size" argument="--chunk-size" type="integer" value="0" label="Chunk size"/>
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39 </when>
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40 <when value="false">
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41 <param name="zero_center" argument="--zero-center" type="boolean" truevalue="" falsevalue="--no-zero-center" checked="true"
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42 label="Zero center data before scaling"/>
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43 <param name="svd_solver" argument="--svd-solver" type="select" optional="true" label="SVD solver">
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44 <option value="arpack">ARPACK</option>
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45 <option value="randomized">Randomised</option>
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46 </param>
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47 <param name="random_seed" argument="--random-state" type="integer" value="0" label="random seed for numpy random number generator"/>
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48 </when>
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49 </conditional>
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50
1
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51 <param name="extra_outputs" type="select" multiple="true" display="checkboxes" optional="true" label="Export extra output">
0
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52 <option value="embeddings">PCA embeddings</option>
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53 </param>
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54
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55 </inputs>
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56
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57 <outputs>
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58 <expand macro="output_data_obj" description="PCA object"/>
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59 <data name="output_embed" format="tsv" from_work_dir="embeddings.tsv" label="${tool.name} on ${on_string}: PCA embeddings">
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60 <filter>extra_outputs and 'embeddings' in extra_outputs.split(',')</filter>
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61 </data>
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62 </outputs>
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63
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64 <tests>
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65 <test>
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66 <param name="input_obj_file" value="scale_data.h5"/>
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67 <param name="input_format" value="anndata"/>
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68 <param name="output_format" value="anndata"/>
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69 <param name="extra_outputs" value="embeddings"/>
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70 <param name="n_pcs" value="50"/>
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71 <param name="zero_center" value="true"/>
5063cd7f8c89 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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72 <param name="svd_solver" value="arpack"/>
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73 <param name="random_seed" value="0"/>
5063cd7f8c89 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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74 <param name="chunked" value="false"/>
5063cd7f8c89 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 <output name="output_h5" file="run_pca.h5" ftype="h5" compare="sim_size"/>
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76 <output name="output_embed" file="run_pca.embeddings.csv" ftype="csv" compare="sim_size">
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77 <assert_contents>
5063cd7f8c89 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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78 <has_n_columns n="50" sep=","/>
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79 </assert_contents>
5063cd7f8c89 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 </output>
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81 </test>
5063cd7f8c89 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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82 </tests>
5063cd7f8c89 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
5063cd7f8c89 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 <help><![CDATA[
1
7798c318e7d7 "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 ================================================================================
7798c318e7d7 "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 Dimensionality reduction by PCA (principal component analysis) (`scanpy.pp.pca`)
7798c318e7d7 "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 ================================================================================
0
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88
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89 It uses the implementation of *scikit-learn*.
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90
5063cd7f8c89 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 @HELP@
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92
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93 @VERSION_HISTORY@
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94 ]]></help>
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95 <expand macro="citations"/>
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96 </tool>