Mercurial > repos > ebi-gxa > seurat_run_pca

annotate seurat_macros.xml @ 5:9547ebb03f6f draft

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"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 355bb52d2e9d170b1db237e649657cc14e0a047a"
author ebi-gxa
date Fri, 04 Mar 2022 07:29:26 +0000
parents 3fd59cdcb477
children 8ded486b0014
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df80f3d2f9d4 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 9bf9a6e46a330890be932f60d1d996dd166426c4
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1 <?xml version="1.0"?>
df80f3d2f9d4 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 9bf9a6e46a330890be932f60d1d996dd166426c4
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2 <macros>
5
9547ebb03f6f "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 355bb52d2e9d170b1db237e649657cc14e0a047a"
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3 <token name="@VERSION@">0.3.0</token>
9547ebb03f6f "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 355bb52d2e9d170b1db237e649657cc14e0a047a"
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4 <token name="@SEURAT_VERSION@">3.2.3</token>
0
df80f3d2f9d4 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 9bf9a6e46a330890be932f60d1d996dd166426c4
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5 <xml name="requirements">
df80f3d2f9d4 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 9bf9a6e46a330890be932f60d1d996dd166426c4
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6 <requirements>
df80f3d2f9d4 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 9bf9a6e46a330890be932f60d1d996dd166426c4
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7 <requirement type="package" version="@VERSION@">seurat-scripts</requirement>
df80f3d2f9d4 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 9bf9a6e46a330890be932f60d1d996dd166426c4
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8 </requirements>
df80f3d2f9d4 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 9bf9a6e46a330890be932f60d1d996dd166426c4
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9 </xml>
df80f3d2f9d4 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 9bf9a6e46a330890be932f60d1d996dd166426c4
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10 <xml name="version">
df80f3d2f9d4 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 9bf9a6e46a330890be932f60d1d996dd166426c4
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11 <version_command><![CDATA[
df80f3d2f9d4 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 9bf9a6e46a330890be932f60d1d996dd166426c4
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12 echo $(R --version | grep version | grep -v GNU)", seurat version" $(R --vanilla --slave -e "library(seurat); cat(sessionInfo()\$otherPkgs\$seurat\$Version)" 2> /dev/null | grep -v -i "WARNING: ")
df80f3d2f9d4 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 9bf9a6e46a330890be932f60d1d996dd166426c4
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13 ]]></version_command>
df80f3d2f9d4 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 9bf9a6e46a330890be932f60d1d996dd166426c4
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14 </xml>
df80f3d2f9d4 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 9bf9a6e46a330890be932f60d1d996dd166426c4
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15
1
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16 <xml name="input_object_params">
c4607a42113e planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 0463f230d18201c740851d72e31a5024f391207f
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17 <conditional name="input" label="Input format">
c4607a42113e planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 0463f230d18201c740851d72e31a5024f391207f
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18 <param type="select" name="format" label="Choose the format of the input" help="RData, Loom or AnnData">
c4607a42113e planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 0463f230d18201c740851d72e31a5024f391207f
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19 <option value="rds_seurat" selected="true">RDS with a Seurat object</option>
c4607a42113e planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 0463f230d18201c740851d72e31a5024f391207f
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20 <option value="loom">Loom</option>
c4607a42113e planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 0463f230d18201c740851d72e31a5024f391207f
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21 <option value="anndata">AnnData</option>
c4607a42113e planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 0463f230d18201c740851d72e31a5024f391207f
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22 <option value="rds_sce">RDS with a Single Cell Experiment object</option>
c4607a42113e planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 0463f230d18201c740851d72e31a5024f391207f
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23 </param>
c4607a42113e planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 0463f230d18201c740851d72e31a5024f391207f
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24 <when value="anndata">
c4607a42113e planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 0463f230d18201c740851d72e31a5024f391207f
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25 <param type="data" name="anndata_file" label="AnnData file" help="The AnnData format provided by Scanpy" format="h5,h5ad"/>
c4607a42113e planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 0463f230d18201c740851d72e31a5024f391207f
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26 </when>
c4607a42113e planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 0463f230d18201c740851d72e31a5024f391207f
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27 <when value="loom">
c4607a42113e planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 0463f230d18201c740851d72e31a5024f391207f
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28 <param type="data" name="loom_file" label="Loom file" help="Input as Loom v? file" format="h5,h5loom"/>
c4607a42113e planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 0463f230d18201c740851d72e31a5024f391207f
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29 </when>
c4607a42113e planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 0463f230d18201c740851d72e31a5024f391207f
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30 <when value="rds_seurat">
c4607a42113e planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 0463f230d18201c740851d72e31a5024f391207f
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31 <param type="data" name="rds_seurat_file" label="RDS file" help="Input as RDS file with Seurat 3 object" format="rdata"/>
c4607a42113e planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 0463f230d18201c740851d72e31a5024f391207f
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32 </when>
c4607a42113e planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 0463f230d18201c740851d72e31a5024f391207f
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33 <when value="rds_sce">
c4607a42113e planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 0463f230d18201c740851d72e31a5024f391207f
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34 <param type="data" name="rds_sce_file" label="RDS file" help="Input as RDS file with Single Cell Experiment object" format="rdata"/>
c4607a42113e planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 0463f230d18201c740851d72e31a5024f391207f
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35 </when>
c4607a42113e planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 0463f230d18201c740851d72e31a5024f391207f
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36 </conditional>
c4607a42113e planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 0463f230d18201c740851d72e31a5024f391207f
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37 </xml>
c4607a42113e planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 0463f230d18201c740851d72e31a5024f391207f
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38
c4607a42113e planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 0463f230d18201c740851d72e31a5024f391207f
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39 <token name="@INPUT_OBJECT@">
c4607a42113e planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 0463f230d18201c740851d72e31a5024f391207f
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40 #if $input.format == "anndata"
c4607a42113e planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 0463f230d18201c740851d72e31a5024f391207f
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41 --input-object-file '$input.anndata_file' --input-format anndata
c4607a42113e planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 0463f230d18201c740851d72e31a5024f391207f
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42 #else if $input.format == "loom"
c4607a42113e planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 0463f230d18201c740851d72e31a5024f391207f
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43 --input-object-file '$input.loom_file' --input-format loom
c4607a42113e planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 0463f230d18201c740851d72e31a5024f391207f
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44 #else if $input.format == "rds_seurat"
c4607a42113e planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 0463f230d18201c740851d72e31a5024f391207f
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45 --input-object-file '$input.rds_seurat_file' --input-format seurat
c4607a42113e planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 0463f230d18201c740851d72e31a5024f391207f
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46 #else if $input.format == "rds_sce"
c4607a42113e planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 0463f230d18201c740851d72e31a5024f391207f
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47 --input-object-file '$input.rds_sce_file' --input-format singlecellexperiment
c4607a42113e planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 0463f230d18201c740851d72e31a5024f391207f
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48 #end if
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49 </token>
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50
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51 <xml name="output_object_params">
c4607a42113e planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 0463f230d18201c740851d72e31a5024f391207f
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52 <param type="select" name="format" label="Choose the format of the output" help="Seurat, Single Cell Experiment or Loom">
c4607a42113e planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 0463f230d18201c740851d72e31a5024f391207f
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53 <option value="rds_seurat" selected="true">RDS with a Seurat object</option>
c4607a42113e planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 0463f230d18201c740851d72e31a5024f391207f
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54 <option value="loom">Loom</option>
c4607a42113e planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 0463f230d18201c740851d72e31a5024f391207f
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55 <option value="rds_sce">RDS with a Single Cell Experiment object</option>
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56 </param>
c4607a42113e planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 0463f230d18201c740851d72e31a5024f391207f
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57 </xml>
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58
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59 <xml name="output_files">
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60 <data name="loom_file" from_work_dir="seurat_obj.loom" format="h5" label="${tool.name} on ${on_string}: Seurat Loom">
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61 <filter>format == 'loom'</filter>
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62 </data>
c4607a42113e planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 0463f230d18201c740851d72e31a5024f391207f
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63 <data name="rds_seurat_file" format="rdata" label="${tool.name} on ${on_string}: Seurat RDS">
c4607a42113e planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 0463f230d18201c740851d72e31a5024f391207f
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64 <filter>format == 'rds_seurat'</filter>
c4607a42113e planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 0463f230d18201c740851d72e31a5024f391207f
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65 </data>
c4607a42113e planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 0463f230d18201c740851d72e31a5024f391207f
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66 <data name="rds_sce_file" format="rdata" label="${tool.name} on ${on_string}: Seurat Single Cell Experiment RDS">
c4607a42113e planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 0463f230d18201c740851d72e31a5024f391207f
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67 <filter>format == 'rds_sce'</filter>
c4607a42113e planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 0463f230d18201c740851d72e31a5024f391207f
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68 </data>
c4607a42113e planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 0463f230d18201c740851d72e31a5024f391207f
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69 </xml>
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70
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71 <token name="@OUTPUT_OBJECT@">
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72 #if $format == "anndata"
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73 --output-object-file '$anndata_file' --output-format anndata
c4607a42113e planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 0463f230d18201c740851d72e31a5024f391207f
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74 #else if $format == "loom"
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75 --output-object-file seurat_obj.loom --output-format loom
c4607a42113e planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 0463f230d18201c740851d72e31a5024f391207f
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76 #else if $format == "rds_seurat"
c4607a42113e planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 0463f230d18201c740851d72e31a5024f391207f
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77 --output-object-file '$rds_seurat_file' --output-format seurat
c4607a42113e planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 0463f230d18201c740851d72e31a5024f391207f
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78 #else if $format == "rds_sce"
c4607a42113e planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 0463f230d18201c740851d72e31a5024f391207f
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79 --output-object-file '$rds_sce_file' --output-format singlecellexperiment
c4607a42113e planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 0463f230d18201c740851d72e31a5024f391207f
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80 #end if
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81 </token>
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82
0
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83 <xml name="genes-use-input">
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84 <param name="genes_use" argument="--genes-use" optional="true" type="data" format="tsv,txt,tabular" label="Genes to use" help="A file with gene names to use in construction of SNN graph if building directly based on expression data rather than a dimensionally reduced representation (i.e. PCs)."/>
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85 </xml>
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86 <xml name="dims-use-input">
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87 <param name="dims_use" argument="--dims-use" min="1" optional="true" type="integer" label="PCA Dimensions to use" help="Number of PCs (dimensions) to use in construction of the SNN graph."/>
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88 </xml>
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89
1
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90 <token name="@SEURAT_INTRO@"><![CDATA[
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91 Seurat_ is a toolkit for quality control, analysis, and exploration of single cell RNA sequencing data.
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92 It is developed and maintained by the `Satija Lab`_ at NYGC. Seurat aims to enable users to identify and
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93 interpret sources of heterogeneity from single cell transcriptomic measurements, and to integrate diverse
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94 types of single cell data.
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95 ]]></token>
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96
0
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97 <token name="@VERSION_HISTORY@"><![CDATA[
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98 **Version history**
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99
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100 3.2.3+galaxy0: Moves to Seurat 3.2.3 and introduce convert method, improving format interconversion support.
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101
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102 3.1.2_0.0.8: Update metadata parsing
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103
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104 3.1.1_0.0.7: Exposes perplexity and enables tab input.
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105
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106 3.1.1_0.0.6+galaxy0: Moved to Seurat 3.
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107
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108 Find clusters: removed dims-use, k-param, prune-snn.
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109
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110 2.3.1+galaxy0: Improved documentation and further exposition of all script's options. Pablo Moreno, Jonathan Manning and Ni Huang, Expression Atlas team https://www.ebi.ac.uk/gxa/home at
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111 EMBL-EBI https://www.ebi.ac.uk/. Parts obtained from wrappers from Christophe Antoniewski(github.com/drosofff) and Lea Bellenger(github.com/bellenger-l).
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112
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113 0.0.1: Initial contribution. Maria Doyle (github.com/mblue9).
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114 ]]></token>
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115
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116
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117 <xml name="citations">
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118 <citations>
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119 <citation type="doi">10.1038/nbt.4096</citation>
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120 <citation type="bibtex">
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121 @misc{r-seurat-scripts.git,
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122 author = {Jonathan Manning, Pablo Moreno, EBI Gene Expression Team},
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123 year = {2018},
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124 title = {Seurat-scripts: command line interface for Seurat},
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125 publisher = {GitHub},
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126 journal = {GitHub repository},
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127 url = {https://github.com/ebi-gene-expression-group/r-seurat-scripts.git},
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128 }
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129 </citation>
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130 <citation type="doi">10.1038/s41592-021-01102-w</citation>
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131 </citations>
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132 </xml>
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133 </macros>