Mercurial > repos > ebi-gxa > scanpy_multiplet_scrublet

annotate scanpy-multiplet-scrublet.xml @ 5:b8126b3bf5d0 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 6c9d530aa653101e9e21804393ec11f38cddf027-dirty
author ebi-gxa
date Thu, 16 Feb 2023 13:29:18 +0000
parents 8ca3ab8300ce
children fadc4fbf8025
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9f8381c5d808 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 3365d5d4f7930e736fa6814df36d68e578d45d46-dirty"
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1 <?xml version="1.0" encoding="utf-8"?>
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b8126b3bf5d0 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 6c9d530aa653101e9e21804393ec11f38cddf027-dirty
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2 <tool id="scanpy_multiplet_scrublet" name="Scanpy Scrublet" version="@TOOL_VERSION@+galaxy9" profile="@PROFILE@">
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9f8381c5d808 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 3365d5d4f7930e736fa6814df36d68e578d45d46-dirty"
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3 <description>remove multiplets from annData objects with Scrublet</description>
9f8381c5d808 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 3365d5d4f7930e736fa6814df36d68e578d45d46-dirty"
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4 <macros>
9f8381c5d808 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 3365d5d4f7930e736fa6814df36d68e578d45d46-dirty"
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5 <import>scanpy_macros2.xml</import>
9f8381c5d808 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 3365d5d4f7930e736fa6814df36d68e578d45d46-dirty"
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6 </macros>
9f8381c5d808 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 3365d5d4f7930e736fa6814df36d68e578d45d46-dirty"
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7 <expand macro="requirements"/>
9f8381c5d808 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 3365d5d4f7930e736fa6814df36d68e578d45d46-dirty"
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8 <command detect_errors="exit_code"><![CDATA[
9f8381c5d808 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 3365d5d4f7930e736fa6814df36d68e578d45d46-dirty"
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9 ln -s '${input_obj_file}' input.h5 &&
9f8381c5d808 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 3365d5d4f7930e736fa6814df36d68e578d45d46-dirty"
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10 PYTHONIOENCODING=utf-8 scanpy-multiplet scrublet
9f8381c5d808 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 3365d5d4f7930e736fa6814df36d68e578d45d46-dirty"
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11 #if $threshold
9f8381c5d808 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 3365d5d4f7930e736fa6814df36d68e578d45d46-dirty"
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12 --threshold '${threshold}'
9f8381c5d808 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 3365d5d4f7930e736fa6814df36d68e578d45d46-dirty"
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13 #end if
9f8381c5d808 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 3365d5d4f7930e736fa6814df36d68e578d45d46-dirty"
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14 #if $batch_key
9f8381c5d808 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 3365d5d4f7930e736fa6814df36d68e578d45d46-dirty"
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15 --batch-key '${batch_key}'
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b8126b3bf5d0 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 6c9d530aa653101e9e21804393ec11f38cddf027-dirty
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16 #else if $sample_key
b8126b3bf5d0 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 6c9d530aa653101e9e21804393ec11f38cddf027-dirty
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17 --batch-key '${sample_key}'
0
9f8381c5d808 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 3365d5d4f7930e736fa6814df36d68e578d45d46-dirty"
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18 #end if
9f8381c5d808 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 3365d5d4f7930e736fa6814df36d68e578d45d46-dirty"
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19 $filter
9f8381c5d808 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 3365d5d4f7930e736fa6814df36d68e578d45d46-dirty"
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20 #if $settings.default == "false"
9f8381c5d808 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 3365d5d4f7930e736fa6814df36d68e578d45d46-dirty"
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21 #if $settings.n_neighbors
9f8381c5d808 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 3365d5d4f7930e736fa6814df36d68e578d45d46-dirty"
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22 --n-neighbours '${settings.n_neighbors}'
9f8381c5d808 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 3365d5d4f7930e736fa6814df36d68e578d45d46-dirty"
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23 #end if
9f8381c5d808 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 3365d5d4f7930e736fa6814df36d68e578d45d46-dirty"
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24 --sim-doublet-ratio '${settings.sim_doublet_ratio}'
9f8381c5d808 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 3365d5d4f7930e736fa6814df36d68e578d45d46-dirty"
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25 --synthetic-doublet-umi-subsampling '${settings.synthetic_doublet_umi_subsampling}'
9f8381c5d808 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 3365d5d4f7930e736fa6814df36d68e578d45d46-dirty"
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26 --expected-doublet-rate '${settings.expected_doublet_rate}'
9f8381c5d808 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 3365d5d4f7930e736fa6814df36d68e578d45d46-dirty"
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27 --stdev-doublet-rate '${settings.stdev_doublet_rate}'
9f8381c5d808 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 3365d5d4f7930e736fa6814df36d68e578d45d46-dirty"
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28 --knn-dist-metric "${settings.knn_dist_metric}"
9f8381c5d808 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 3365d5d4f7930e736fa6814df36d68e578d45d46-dirty"
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29 --n-pcs '${settings.n_pcs}'
9f8381c5d808 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 3365d5d4f7930e736fa6814df36d68e578d45d46-dirty"
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30 --random-state '${settings.random_state}'
9f8381c5d808 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 3365d5d4f7930e736fa6814df36d68e578d45d46-dirty"
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31 ${settings.normalise_variance} ${settings.log_transform} ${settings.mean_center}
9f8381c5d808 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 3365d5d4f7930e736fa6814df36d68e578d45d46-dirty"
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32 ${settings.approx} ${settings.get_doublet_neighbor_parents}
9f8381c5d808 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 3365d5d4f7930e736fa6814df36d68e578d45d46-dirty"
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33 #end if
9f8381c5d808 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 3365d5d4f7930e736fa6814df36d68e578d45d46-dirty"
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34 @INPUT_OPTS@
9f8381c5d808 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 3365d5d4f7930e736fa6814df36d68e578d45d46-dirty"
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35 @OUTPUT_OPTS@
9f8381c5d808 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 3365d5d4f7930e736fa6814df36d68e578d45d46-dirty"
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36 ]]></command>
9f8381c5d808 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 3365d5d4f7930e736fa6814df36d68e578d45d46-dirty"
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37
9f8381c5d808 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 3365d5d4f7930e736fa6814df36d68e578d45d46-dirty"
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38 <inputs>
9f8381c5d808 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 3365d5d4f7930e736fa6814df36d68e578d45d46-dirty"
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39 <expand macro="input_object_params"/>
9f8381c5d808 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 3365d5d4f7930e736fa6814df36d68e578d45d46-dirty"
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40 <expand macro="output_object_params"/>
9f8381c5d808 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 3365d5d4f7930e736fa6814df36d68e578d45d46-dirty"
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41 <param name="threshold" argument="--threshold" type="float" optional="true" label="Doublet score threshold." help="Threshold for calling a transcriptome a doublet. If not set, this is set automatically by looking for the minimum between the two modes of the doublet_scores_sim_ histogram. It is best practice to check the threshold visually using the doublet_scores_sim_ histogram and/or based on co-localization of predicted doublets in a 2-D embedding."/>
9f8381c5d808 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 3365d5d4f7930e736fa6814df36d68e578d45d46-dirty"
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42 <param name="filter" argument="--filter" type="boolean" truevalue="--filter" falsevalue="" checked="False"
9f8381c5d808 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 3365d5d4f7930e736fa6814df36d68e578d45d46-dirty"
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43 label="Remove predicted multiplets?" help="By default, the output object is annotated but not filtered according to the scrublet status."/>
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b8126b3bf5d0 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 6c9d530aa653101e9e21804393ec11f38cddf027-dirty
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44 <param name="batch_key" type="text" argument="--batch-key" optional="true" label="Where batches are present, the name of the column in adata.obs that differentiates among experiments/batches."/>
b8126b3bf5d0 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 6c9d530aa653101e9e21804393ec11f38cddf027-dirty
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45 <param name="sample_key" type="text" argument="--batch-key" optional="true" label="The name of the column in adata.obs that differentiates among samples. This is a convenience for workflows, this is overriden if the batch key is set. It is an Scrubblet best practice to operate per samples rather than on the complete dataset (and it should use less memory)."/>
0
9f8381c5d808 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 3365d5d4f7930e736fa6814df36d68e578d45d46-dirty"
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46 <conditional name="settings">
9f8381c5d808 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 3365d5d4f7930e736fa6814df36d68e578d45d46-dirty"
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47 <param name="default" type="boolean" checked="true" label="Use programme defaults"/>
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48 <when value="true"/>
9f8381c5d808 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 3365d5d4f7930e736fa6814df36d68e578d45d46-dirty"
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49 <when value="false">
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50 <param name="sim_doublet_ratio" argument="--sim-doublet-ratio" type="float" value="2.0" label="Number of doublets to simulate relative to the number of observed transcriptomes."/>
9f8381c5d808 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 3365d5d4f7930e736fa6814df36d68e578d45d46-dirty"
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51 <param name="synthetic_doublet_umi_subsampling" argument="--synthetic-doublet-umi-subsampling" type="float" value="1.0" label="Rate for sampling UMIs when creating synthetic doublets." help="If 1.0, each doublet is created by simply adding the UMI counts from two randomly sampled observed transcriptomes. For values less than 1, the UMI counts are added and then randomly sampled at the specified rate."/>
9f8381c5d808 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 3365d5d4f7930e736fa6814df36d68e578d45d46-dirty"
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52 <param name="expected_doublet_rate" argument="--expected-doublet-rate" type="float" value="0.05" label="Estimated doublet rate for the experiment."/>
9f8381c5d808 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 3365d5d4f7930e736fa6814df36d68e578d45d46-dirty"
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53 <param name="stdev_doublet_rate" argument="--stdev-doublet-rate" type="float" value="0.02" label="Uncertainty in the expected doublet rate."/>
9f8381c5d808 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 3365d5d4f7930e736fa6814df36d68e578d45d46-dirty"
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54 <param name="knn_dist_metric" argument="--knn-dist-metric" type="select" label="A known metric’s name.">
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55 <option value="euclidean" selected="true">Euclidean</option>
9f8381c5d808 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 3365d5d4f7930e736fa6814df36d68e578d45d46-dirty"
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56 <option value="angular">angular</option>
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57 <option value="cityblock">cityblock</option>
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58 <option value="cosine">cosine</option>
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59 <option value="l1">l1</option>
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60 <option value="l2">l2</option>
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61 <option value="manhattan">manhattan</option>
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62 <option value="braycurtis">braycurtis</option>
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63 <option value="canberra">canberra</option>
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64 <option value="chebyshev">chebyshev</option>
9f8381c5d808 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 3365d5d4f7930e736fa6814df36d68e578d45d46-dirty"
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65 <option value="correlation">correlation</option>
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66 <option value="dice">dice</option>
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67 <option value="hamming">hamming</option>
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68 <option value="jaccard">jaccard</option>
9f8381c5d808 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 3365d5d4f7930e736fa6814df36d68e578d45d46-dirty"
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69 <option value="kulsinski">kulsinski</option>
9f8381c5d808 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 3365d5d4f7930e736fa6814df36d68e578d45d46-dirty"
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70 <option value="mahalanobis">mahalanobis</option>
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71 <option value="minkowski">minkowski</option>
9f8381c5d808 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 3365d5d4f7930e736fa6814df36d68e578d45d46-dirty"
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72 <option value="rogerstanimoto">rogerstanimoto</option>
9f8381c5d808 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 3365d5d4f7930e736fa6814df36d68e578d45d46-dirty"
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73 <option value="russelrao">russelrao</option>
9f8381c5d808 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 3365d5d4f7930e736fa6814df36d68e578d45d46-dirty"
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74 <option value="seuclidan">seuclidian</option>
9f8381c5d808 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 3365d5d4f7930e736fa6814df36d68e578d45d46-dirty"
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75 <option value="sokalmichener">sokalmichener</option>
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76 <option value="sokalsneath">sokalsneath</option>
9f8381c5d808 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 3365d5d4f7930e736fa6814df36d68e578d45d46-dirty"
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77 <option value="sqeuclidean">sqeuclidean</option>
9f8381c5d808 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 3365d5d4f7930e736fa6814df36d68e578d45d46-dirty"
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78 <option value="yule">yule</option>
9f8381c5d808 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 3365d5d4f7930e736fa6814df36d68e578d45d46-dirty"
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79 </param>
9f8381c5d808 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 3365d5d4f7930e736fa6814df36d68e578d45d46-dirty"
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80 <param name="normalise_variance" argument="--no-normalize-variance" type="boolean" truevalue="" falsevalue="--no-normalize-variance" checked="True"
9f8381c5d808 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 3365d5d4f7930e736fa6814df36d68e578d45d46-dirty"
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81 label="Normalize the data such that each gene has a variance of 1?" help="klearn.decomposition.TruncatedSVD will be used for dimensionality reduction, if --no-mean-center is set. Use this flag to disable that behaviour." />
9f8381c5d808 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 3365d5d4f7930e736fa6814df36d68e578d45d46-dirty"
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82 <param name="log_transform" argument="--log-transform" type="boolean" truevalue="--log-transform" falsevalue="" checked="False"
9f8381c5d808 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 3365d5d4f7930e736fa6814df36d68e578d45d46-dirty"
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83 label="Apply log transform?" help="Whether to use :func:~scanpy.pp.log1p to log-transform the data prior to PCA."/>
9f8381c5d808 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 3365d5d4f7930e736fa6814df36d68e578d45d46-dirty"
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84 <param name="mean_center" argument="--no-mean-center" type="boolean" truevalue="" falsevalue="--no-mean-center" checked="True"
9f8381c5d808 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 3365d5d4f7930e736fa6814df36d68e578d45d46-dirty"
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85 label="Center the data such that each gene has a mean of 0" help="sklearn.decomposition.PCA will be used for dimensionality reduction."/>
9f8381c5d808 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 3365d5d4f7930e736fa6814df36d68e578d45d46-dirty"
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86 <param name="n_pcs" argument="--n-pcs" type="integer" value="30" optional="true" label="Number of principal components." help="Used to embed the transcriptomes prior to k-nearest-neighbor graph construction."/>
9f8381c5d808 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 3365d5d4f7930e736fa6814df36d68e578d45d46-dirty"
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87 <param name="approx" argument="--no-approx" type="boolean" truevalue="" falsevalue="--no-approx" checked="True"
9f8381c5d808 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 3365d5d4f7930e736fa6814df36d68e578d45d46-dirty"
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88 label="Use approximate nearest neighbor (annoy) method for the KNN classifier"/>
9f8381c5d808 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 3365d5d4f7930e736fa6814df36d68e578d45d46-dirty"
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89 <param name="get_doublet_neighbor_parents" argument="--get-doublet-neighbor-parents" type="boolean" truevalue="--get-doublet-neighbor-parents " falsevalue="" checked="False"
9f8381c5d808 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 3365d5d4f7930e736fa6814df36d68e578d45d46-dirty"
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90 label="Get doublet neighbor parents" help="Return (in .uns) the parent transcriptomes that generated the doublet neighbors of each observed transcriptome. This information can be used to infer the cell states that generated a given doublet state."/>
9f8381c5d808 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 3365d5d4f7930e736fa6814df36d68e578d45d46-dirty"
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91 <param name="n_neighbors" argument="--n-neighbors" type="integer" optional="true" label="Number of neighbors." help="Used to construct the KNN graph of observed transcriptomes and simulated doublets. If not set, this is automatically set to np.round(0.5 * np.sqrt(n_obs))."/>
9f8381c5d808 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 3365d5d4f7930e736fa6814df36d68e578d45d46-dirty"
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92 <param name="random_state" argument="--random-state" type="integer" value="0" label="Seed for random number generator." />
9f8381c5d808 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 3365d5d4f7930e736fa6814df36d68e578d45d46-dirty"
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93 </when>
9f8381c5d808 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 3365d5d4f7930e736fa6814df36d68e578d45d46-dirty"
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94 </conditional>
9f8381c5d808 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 3365d5d4f7930e736fa6814df36d68e578d45d46-dirty"
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95 </inputs>
9f8381c5d808 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 3365d5d4f7930e736fa6814df36d68e578d45d46-dirty"
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96
9f8381c5d808 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 3365d5d4f7930e736fa6814df36d68e578d45d46-dirty"
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97 <outputs>
9f8381c5d808 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 3365d5d4f7930e736fa6814df36d68e578d45d46-dirty"
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98 <expand macro="output_data_obj" description="Scrublet-processed annData"/>
9f8381c5d808 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 3365d5d4f7930e736fa6814df36d68e578d45d46-dirty"
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99 </outputs>
9f8381c5d808 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 3365d5d4f7930e736fa6814df36d68e578d45d46-dirty"
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100
9f8381c5d808 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 3365d5d4f7930e736fa6814df36d68e578d45d46-dirty"
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101 <tests>
9f8381c5d808 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 3365d5d4f7930e736fa6814df36d68e578d45d46-dirty"
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102 <test>
9f8381c5d808 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 3365d5d4f7930e736fa6814df36d68e578d45d46-dirty"
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103 <param name="input_obj_file" value="read_10x.h5"/>
9f8381c5d808 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 3365d5d4f7930e736fa6814df36d68e578d45d46-dirty"
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104 <param name="input_format" value="anndata"/>
9f8381c5d808 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 3365d5d4f7930e736fa6814df36d68e578d45d46-dirty"
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105 <param name="output_format" value="anndata"/>
9f8381c5d808 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 3365d5d4f7930e736fa6814df36d68e578d45d46-dirty"
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106 <output name="output_h5" file="scrublet.h5" ftype="h5" compare="sim_size"/>
9f8381c5d808 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 3365d5d4f7930e736fa6814df36d68e578d45d46-dirty"
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107 </test>
9f8381c5d808 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 3365d5d4f7930e736fa6814df36d68e578d45d46-dirty"
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108 </tests>
9f8381c5d808 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 3365d5d4f7930e736fa6814df36d68e578d45d46-dirty"
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109
9f8381c5d808 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 3365d5d4f7930e736fa6814df36d68e578d45d46-dirty"
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110 <help><![CDATA[
9f8381c5d808 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 3365d5d4f7930e736fa6814df36d68e578d45d46-dirty"
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111 .. class:: infomark
9f8381c5d808 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 3365d5d4f7930e736fa6814df36d68e578d45d46-dirty"
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112
9f8381c5d808 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 3365d5d4f7930e736fa6814df36d68e578d45d46-dirty"
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113 **What it does**
9f8381c5d808 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 3365d5d4f7930e736fa6814df36d68e578d45d46-dirty"
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114
9f8381c5d808 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 3365d5d4f7930e736fa6814df36d68e578d45d46-dirty"
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115 Predict cell doublets using a nearest-neighbor classifier of observed transcriptomes and simulated doublets. Works best if the input is a raw (unnormalized) counts matrix from a single sample or a collection of similar samples from the same experiment. This function is a wrapper around functions that pre-process using Scanpy and directly call functions of Scrublet().
9f8381c5d808 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 3365d5d4f7930e736fa6814df36d68e578d45d46-dirty"
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116
9f8381c5d808 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 3365d5d4f7930e736fa6814df36d68e578d45d46-dirty"
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117 This is a wrapper around the Scanpy wrapper for Scrublet- see https://scanpy.readthedocs.io/en/docsearch/external/scanpy.external.pp.scrublet.html.
9f8381c5d808 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 3365d5d4f7930e736fa6814df36d68e578d45d46-dirty"
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118
4
8ca3ab8300ce "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 9ea121884e1aecd2ee66a0686057cb3ed904b9eb-dirty"
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119 **Note**
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120
8ca3ab8300ce "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 9ea121884e1aecd2ee66a0686057cb3ed904b9eb-dirty"
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121 Where a threshold is not provided, Scrublet will try to automatically set one based on simulations, but this does not always work. There will be a warning, and no 'threshold' slot will be populated in .uns['scrublet']. The 'predicted_doublets' slot in .obs will be set to False for all cells such that no filtering will occur if this column is supplied to filtering steps. You can use the 'Scanpy Plot Scrublet' tool to plot the distribution of scores yourself and estimate a threshold to override this behaviour.
8ca3ab8300ce "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 9ea121884e1aecd2ee66a0686057cb3ed904b9eb-dirty"
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122
0
9f8381c5d808 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 3365d5d4f7930e736fa6814df36d68e578d45d46-dirty"
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123 @HELP@
9f8381c5d808 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 3365d5d4f7930e736fa6814df36d68e578d45d46-dirty"
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124
9f8381c5d808 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 3365d5d4f7930e736fa6814df36d68e578d45d46-dirty"
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125 @VERSION_HISTORY@
9f8381c5d808 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 3365d5d4f7930e736fa6814df36d68e578d45d46-dirty"
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126 ]]></help>
9f8381c5d808 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 3365d5d4f7930e736fa6814df36d68e578d45d46-dirty"
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127 <expand macro="citations"/>
9f8381c5d808 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 3365d5d4f7930e736fa6814df36d68e578d45d46-dirty"
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128 </tool>