annotate scanpy-integrate-bbknn.xml @ 6:89eef46fce58 draft

"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 858a2398f1dbbd60110867c593c237358c794615-dirty"
author ebi-gxa
date Mon, 12 Apr 2021 14:42:26 +0000
parents c2be8a21eaa2
children 1fb88fd7dce5
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e6d5b3fed639 "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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1 <?xml version="1.0" encoding="utf-8"?>
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2 <tool id="scanpy_integrate_bbknn" name="Scanpy BBKNN" version="@TOOL_VERSION@+galaxy0" profile="@PROFILE@">
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3 <description>batch-balanced K-nearest neighbours</description>
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4 <macros>
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5 <import>scanpy_macros2.xml</import>
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6 </macros>
e6d5b3fed639 "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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7 <expand macro="requirements"/>
e6d5b3fed639 "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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8 <command detect_errors="exit_code"><![CDATA[
e6d5b3fed639 "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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9 #if $batch_key
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10 ln -s '${input_obj_file}' input.h5 &&
e6d5b3fed639 "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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11 PYTHONIOENCODING=utf-8 scanpy-integrate bbknn
e6d5b3fed639 "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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12 --batch-key '${batch_key}'
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13 #if $settings.default == "false"
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14 #if $settings.use_rep
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15 --use-rep '${settings.use_rep}'
e6d5b3fed639 "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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16 #end if
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17 #if $settings.key_added
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18 --key-added '${settings.key_added}'
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19 #end if
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20 #if $settings.n_pcs
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21 --n-pcs '${settings.n_pcs}'
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22 #end if
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23 #if not $settings.approx
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24 ${settings.approx}
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25 #end if
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26 #if $settings.metric
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27 --metric '${settings.metric}'
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28 #end if
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29 #if $settings.neighbors_within_batch
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30 --neighbors-within-batch '${settings.neighbors_within_batch}'
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31 #end if
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32 #if $settings.trim
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33 --trim '${settings.trim}'
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34 #end if
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35 #if $settings.n_trees
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36 --n-trees '${settings.n_trees}'
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37 #end if
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38 #if not $settings.use_faiss
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39 ${settings.use_faiss}
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40 #end if
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41 #if $settings.set_op_mix_ratio
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42 --set-op-mix-ratio '${settings.set_op_mix_ratio}'
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43 #end if
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44 #if $settings.local_connectivity
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45 --local-connectivity '${settings.local_connectivity}'
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46 #end if
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47 #end if
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48 @INPUT_OPTS@
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49 @OUTPUT_OPTS@
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50 #else
1
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51 echo "No batch variables passed, simply passing original input as output unchanged." && cp '${input_obj_file}' output.h5
0
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52 #end if
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53 ]]></command>
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54
e6d5b3fed639 "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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55 <inputs>
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56 <expand macro="input_object_params"/>
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57 <expand macro="output_object_params"/>
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58 <param name="batch_key" type="text" argument="--batch-key" label="The name of the column in adata.obs that differentiates among experiments/batches.">
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59 <sanitizer>
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60 <valid initial="string.printable"/>
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61 </sanitizer>
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62 </param>
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63 <conditional name="settings">
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64 <param name="default" type="boolean" checked="true" label="Use programme defaults"/>
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65 <when value="true"/>
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66 <when value="false">
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67 <param name="use_rep" argument="--use-rep" type="text" value='X_pca' label="The dimensionality reduction in .obsm to use for neighbour detection.">
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68 <sanitizer>
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69 <valid initial="string.printable"/>
e6d5b3fed639 "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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70 </sanitizer>
e6d5b3fed639 "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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71 </param>
e6d5b3fed639 "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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72 <param name="key_added" argument="--key-added" type="text" optional="true" label="Key under which to add the computed results." help="If not specified, the neighbors data is stored in .uns[‘neighbors’], distances and connectivities are stored in .obsp[‘distances’] and .obsp[‘connectivities’] respectively. If specified, the neighbors data is added to .uns[key_added], distances are stored in .obsp[key_added+’_distances’] and connectivities in .obsp[key_added+’_connectivities’].">
e6d5b3fed639 "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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73 <sanitizer>
e6d5b3fed639 "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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74 <valid initial="string.printable"/>
e6d5b3fed639 "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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75 </sanitizer>
e6d5b3fed639 "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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76 </param>
e6d5b3fed639 "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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77 <param name="n_pcs" argument="--n-pcs" type="integer" value="50" optional="true" label="Number of PCs to use"/>
e6d5b3fed639 "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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78 <param name="approx" argument="--no-approx" type="boolean" truevalue="" falsevalue="--no-approx" checked="True"
e6d5b3fed639 "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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79 label="Use annoy’s approximate neighbour finding?" help="This results in a quicker run time for large datasets while also potentially increasing the degree of batch correction."/>
e6d5b3fed639 "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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80 <param name="metric" argument="--metric" type="select" label="A known metric’s name">
e6d5b3fed639 "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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81 <option value="angular" selected="true">angular</option>
e6d5b3fed639 "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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82 <option value="euclidean">Euclidean</option>
e6d5b3fed639 "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 <option value="cityblock">cityblock</option>
e6d5b3fed639 "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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84 <option value="cosine">cosine</option>
e6d5b3fed639 "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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85 <option value="l1">l1</option>
e6d5b3fed639 "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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86 <option value="l2">l2</option>
e6d5b3fed639 "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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87 <option value="manhattan">manhattan</option>
e6d5b3fed639 "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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88 <option value="braycurtis">braycurtis</option>
e6d5b3fed639 "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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89 <option value="canberra">canberra</option>
e6d5b3fed639 "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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90 <option value="chebyshev">chebyshev</option>
e6d5b3fed639 "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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91 <option value="correlation">correlation</option>
e6d5b3fed639 "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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92 <option value="dice">dice</option>
e6d5b3fed639 "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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93 <option value="hamming">hamming</option>
e6d5b3fed639 "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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94 <option value="jaccard">jaccard</option>
e6d5b3fed639 "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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95 <option value="kulsinski">kulsinski</option>
e6d5b3fed639 "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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96 <option value="mahalanobis">mahalanobis</option>
e6d5b3fed639 "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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97 <option value="minkowski">minkowski</option>
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98 <option value="rogerstanimoto">rogerstanimoto</option>
e6d5b3fed639 "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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99 <option value="russelrao">russelrao</option>
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100 <option value="seuclidan">seuclidian</option>
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101 <option value="sokalmichener">sokalmichener</option>
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102 <option value="sokalsneath">sokalsneath</option>
e6d5b3fed639 "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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103 <option value="sqeuclidean">sqeuclidean</option>
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104 <option value="yule">yule</option>
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105 </param>
e6d5b3fed639 "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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106 <param name="neighbors_within_batch" argument="--neighbors-within-batch" type="integer" value="3" optional="true" label="How many top neighbours to report for each batch" help="Total number of neighbours will be this number times the number of batches."/>
e6d5b3fed639 "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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107 <param name="trim" argument="--trim" type="integer" value="" optional="true" label="Trim the neighbours of each cell to these many top connectivities." help="May help with population independence and improve the tidiness of clustering. The lower the value the more independent the individual populations, at the cost of more conserved batch effect. If not set, sets the parameter value automatically to 10 times the total number of neighbours for each cell. Set to 0 to skip."/>
e6d5b3fed639 "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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108 <param name="n_trees" argument="--n-trees" type="integer" value="10" optional="true" label="The number of trees to construct in the annoy forest." help="More trees give higher precision when querying, at the cost of increased run time and resource intensity."/>
e6d5b3fed639 "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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109 <param name="use_faiss" argument="--no-use-faiss" type="boolean" truevalue="" falsevalue="--no-use-faiss" checked="True"
e6d5b3fed639 "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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110 label="Use the faiss package to compute nearest neighbours if installed" help="If approx=False and the metric is 'euclidean' use the faiss package to compute nearest neighbours if installed. This improves performance at a minor cost to numerical precision as faiss operates on float32."/>
e6d5b3fed639 "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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111 <param name="set_op_mix_ratio" argument="--set-op-mix-ratio" type="float" value="1" min="0" max="1" label="UMAP connectivity computation parameter" help="Float between 0 and 1, controlling the blend between a connectivity matrix formed exclusively from mutual nearest neighbour pairs (0) and a union of all observed neighbour relationships with the mutual pairs emphasised (1)."/>
e6d5b3fed639 "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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112 <param name="local_connectivity" argument="--local-connectivity" type="integer" value="1" label="UMAP connectivity computation parameter, how many nearest neighbors of each cell are assumed to be fully connected (and given a connectivity value of 1)."/>
e6d5b3fed639 "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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113 </when>
e6d5b3fed639 "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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114 </conditional>
e6d5b3fed639 "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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115 </inputs>
e6d5b3fed639 "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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116
e6d5b3fed639 "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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117 <outputs>
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118 <expand macro="output_data_obj" description="Batch-corrected for ${batch_key}"/>
e6d5b3fed639 "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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119 </outputs>
e6d5b3fed639 "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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120
e6d5b3fed639 "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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121 <tests>
e6d5b3fed639 "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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122 <test>
e6d5b3fed639 "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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123 <param name="input_obj_file" value="find_cluster.h5"/>
e6d5b3fed639 "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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124 <param name="input_format" value="anndata"/>
e6d5b3fed639 "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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125 <param name="output_format" value="anndata"/>
e6d5b3fed639 "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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126 <param name="batch_key" value="louvain"/>
e6d5b3fed639 "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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127 <output name="output_h5" file="bbknn.h5" ftype="h5" compare="sim_size"/>
e6d5b3fed639 "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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128 </test>
1
c2be8a21eaa2 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 9028e8fa3761fd640dcace5d36bf9b7d558319f7-dirty"
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129 <test>
c2be8a21eaa2 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 9028e8fa3761fd640dcace5d36bf9b7d558319f7-dirty"
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130 <param name="input_obj_file" value="find_cluster.h5"/>
c2be8a21eaa2 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 9028e8fa3761fd640dcace5d36bf9b7d558319f7-dirty"
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131 <param name="input_format" value="anndata"/>
c2be8a21eaa2 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 9028e8fa3761fd640dcace5d36bf9b7d558319f7-dirty"
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132 <param name="output_format" value="anndata"/>
c2be8a21eaa2 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 9028e8fa3761fd640dcace5d36bf9b7d558319f7-dirty"
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133 <output name="output_h5" file="bbknn_copy.h5" ftype="h5" compare="sim_size"/>
c2be8a21eaa2 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 9028e8fa3761fd640dcace5d36bf9b7d558319f7-dirty"
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134 </test>
0
e6d5b3fed639 "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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135 </tests>
e6d5b3fed639 "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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136
e6d5b3fed639 "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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137 <help><![CDATA[
e6d5b3fed639 "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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138 .. class:: infomark
e6d5b3fed639 "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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139
e6d5b3fed639 "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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140 **What it does**
e6d5b3fed639 "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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141
e6d5b3fed639 "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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142 Batch balanced kNN alters the kNN procedure to identify each cell’s top neighbours in each batch separately instead of the entire cell pool with no accounting for batch. Aligns batches in a quick and lightweight manner.
e6d5b3fed639 "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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143
e6d5b3fed639 "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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144 Use as an alternative to Scanpy ComputeGraph.
e6d5b3fed639 "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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145
e6d5b3fed639 "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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146 @HELP@
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147
e6d5b3fed639 "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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148 @VERSION_HISTORY@
e6d5b3fed639 "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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149 ]]></help>
e6d5b3fed639 "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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150 <expand macro="citations"/>
e6d5b3fed639 "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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151 </tool>