Mercurial > repos > iuc > seurat_data

annotate inspect_and_manipulate.xml @ 1:4ec52a83ec82 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit 566984b588e88225f0b3f2dae88c6fd084315e7c
author iuc
date Tue, 05 Nov 2024 11:55:01 +0000
parents 50c5abeb08ba
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50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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1 <tool id="seurat_data" name="Seurat Data Management" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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2 <description>- Inspect and Manipulate </description>
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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3 <macros>
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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4 <import>macros.xml</import>
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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5 </macros>
1
4ec52a83ec82 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit 566984b588e88225f0b3f2dae88c6fd084315e7c
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6 <expand macro="bio_tools"/>
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50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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7 <expand macro="requirements"/>
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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8 <expand macro="version_command"/>
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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9 <command detect_errors="exit_code"><![CDATA[
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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10 @CMD@
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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11 ]]></command>
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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12 <configfiles>
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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13 <configfile name="script_file"><![CDATA[
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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14 @CMD_imports@
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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15 @CMD_read_inputs@
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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16
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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17 #if $method.method == 'Inspect'
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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18 #if $method.inspect.inspect == 'General'
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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19 sink('inspect.txt')
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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20 seurat_obj
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21 sink()
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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22
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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23 #else if $method.inspect.inspect == 'Features'
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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24 inspect<-Features(seurat_obj[['$method.inspect.assay']])
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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25 row.names = FALSE
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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26 col.names = FALSE
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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27 @CMD_inspect_rds_outputs@
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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28
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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29 #else if $method.inspect.inspect == 'Cells'
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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30 inspect<-Cells(
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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31 seurat_obj,
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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32 #if $method.layer != ''
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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33 layer = $method.layer
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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34 #end if
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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35 )
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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36 row.names = FALSE
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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37 col.names = FALSE
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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38 @CMD_inspect_rds_outputs@
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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39
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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40 #else if $method.inspect.inspect == 'Idents'
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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41 inspect<-Idents(seurat_obj)
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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42 row.names = TRUE
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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43 col.names = FALSE
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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44 @CMD_inspect_rds_outputs@
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45
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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46 #else if $method.inspect.inspect == 'Metadata'
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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47 #if $method.inspect.view_metadata != ''
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48 inspect<-seurat_obj[['$method.inspect.view_metadata']]
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49 #else
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50 inspect<-seurat_obj[[]]
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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51 #end if
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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52 row.names = TRUE
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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53 col.names = TRUE
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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54 @CMD_inspect_rds_outputs@
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55
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56 #else if $method.inspect.inspect == 'Matrix'
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57 inspect<-LayerData(
1
4ec52a83ec82 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit 566984b588e88225f0b3f2dae88c6fd084315e7c
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58 seurat_obj,
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59 assay='$method.inspect.assay',
0
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60 layer='$method.inspect.layer'
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61 )
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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62 row.names = TRUE
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63 col.names = TRUE
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64 @CMD_inspect_rds_outputs@
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65
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66 #end if
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67
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68 #else if $method.method == 'Manipulate'
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69 #if $method.manipulate.manipulate == 'Change_Idents'
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70 Idents(seurat_obj)<- '$method.manipulate.change'
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71
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72 #else if $method.manipulate.manipulate == 'Rename_Idents'
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73 #if $method.manipulate.stash_idents.stash_idents == 'true'
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74 seurat_obj[['$method.manipulate.stash_idents.old_ident']]<-Idents(seurat_obj)
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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75 #end if
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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76 #if $method.manipulate.rename.rename_all == 'true'
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77 new_names = c(unlist(strsplit(gsub(" ", "", '$method.manipulate.rename.new_names'), ",")))
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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78 names(new_names)<-levels(seurat_obj)
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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79 seurat_obj<-RenameIdents(
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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80 seurat_obj,
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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81 new_names
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82 )
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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83 #else if $method.manipulate.rename.rename_all == 'false'
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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84 seurat_obj<-RenameIdents(
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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85 seurat_obj,
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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86 '$method.manipulate.rename.old_name' = '$method.manipulate.rename.new_name'
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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87 )
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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88 #end if
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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89
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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90 #else if $method.manipulate.manipulate == 'Add_Metadata'
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
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91 meta_data<-read.table(
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
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diff changeset
92 "$method.manipulate.metadata",
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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93 header = TRUE,
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
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94 row.names = 1,
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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diff changeset
95 sep = "\t"
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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diff changeset
96 )
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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97 seurat_obj<-AddMetaData(
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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98 seurat_obj,
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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99 metadata = meta_data,
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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100 )
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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101
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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102 #else if $method.manipulate.manipulate == 'Merge'
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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103 y = list()
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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104 #for $file in $method.manipulate.add_seurat
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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105 y<-append(y, readRDS('${file}'))
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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106 #end for
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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107 seurat_obj<-merge(x = seurat_obj, y)
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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108
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109 #if $method.manipulate.join.join == 'true'
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110 seurat_obj[['$method.manipulate.join.assay']]<-JoinLayers(
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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111 seurat_obj[['$method.manipulate.join.assay']]
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112 )
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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113 #end if
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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114
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115 #else if $method.manipulate.manipulate == 'Subset_Ident'
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116 seurat_obj<-subset(
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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117 seurat_obj,
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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118 idents = c(unlist(strsplit(gsub(" ", "", '$method.manipulate.idents'), ","))),
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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119 )
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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120
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121 #else if $method.manipulate.manipulate == 'Subset_Group'
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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122 seurat_obj<-subset(
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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123 seurat_obj,
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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124 subset = $method.manipulate.grouping == '$method.manipulate.groups',
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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125 )
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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126
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127 #else if $method.manipulate.manipulate == 'DietSeurat'
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128
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129 #if $method.manipulate.features
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130 features_list<-paste(readLines('$method.manipulate.features'), collapse=",")
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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131 #end if
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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132
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133 seurat_obj<-DietSeurat(
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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134 seurat_obj,
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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135 #if $method.manipulate.layers != ''
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136 layers = c(unlist(strsplit(gsub(" ", "", '$method.manipulate.layers'), ","))),
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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137 #else if $method.manipulate.features
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diff changeset
138 features = c(unlist(strsplit(features_list, ","))),
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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139 #else if $method.manipulate.assays != ''
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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140 assays = c(unlist(strsplit(gsub(" ", "", '$method.manipulate.assays'), ","))),
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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141 #else if $method.manipulate.dimreducs != ''
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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142 dimreducs = c(unlist(strsplit(gsub(" ", "", '$method.manipulate.dimreducs'), ","))),
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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143 #else if $method.manipulate.graphs != ''
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144 graphs = c(unlist(strsplit(gsub(" ", "", '$method.manipulate.graphs'), ","))),
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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145 #else if $method.manipulate.features != ''
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146 misc = $method.manipulate.misc
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147 #end if
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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148 )
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149
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150 #else if $method.manipulate.manipulate == 'AggregateExpression'
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151
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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152 #if $method.manipulate.features
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153 features_list<-paste(readLines('$method.manipulate.features'), collapse=",")
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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154 #end if
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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155
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156 seurat_obj<-AggregateExpression(
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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diff changeset
157 seurat_obj,
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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158 group.by = c(unlist(strsplit(gsub(" ", "", '$method.manipulate.group_by'), ","))),
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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159 #if $method.assays != ''
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160 assays = c(unlist(strsplit(gsub(" ", "", '$method.manipulate.assays'), ","))),
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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161 #end if
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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162 #if $method.manipulate.features
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163 features = c(unlist(strsplit(features_list, ","))),
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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164 #end if
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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165 normalization.method = '$method.manipulate.normalization_method.normalization_method',
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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166 #if $method.manipulate.normalization_method.normalization_method == 'CLR'
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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167 margin = $method.manipulate.normalization_method.margin,
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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168 #end if
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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169 scale.factor = $method.manipulate.scale_factor,
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170 #if $method.manipulate.block_size
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171 block.size = $method.manipulate.block_size,
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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172 #end if
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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diff changeset
173 return.seurat = TRUE
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
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diff changeset
174 )
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
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diff changeset
175
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
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diff changeset
176 #else if $method.manipulate.manipulate == 'DefaultAssay'
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
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diff changeset
177 DefaultAssay(object = seurat_obj)<-'$method.manipulate.default_assay'
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
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diff changeset
178
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
179 #end if
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
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diff changeset
180
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
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diff changeset
181 #end if
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
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182
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
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diff changeset
183 @CMD_rds_write_outputs@
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
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diff changeset
184
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
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diff changeset
185 ]]></configfile>
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
186 </configfiles>
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
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diff changeset
187 <inputs>
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
188 <expand macro="input_rds"/>
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
189 <conditional name="method">
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
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diff changeset
190 <param name="method" type="select" label="Method used">
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
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diff changeset
191 <option value="Inspect">Inspect Seurat Object</option>
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
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192 <option value="Manipulate">Manipulate Seurat Object</option>
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
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diff changeset
193 </param>
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
194 <when value="Inspect">
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
195 <conditional name="inspect">
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
196 <param name="inspect" type="select" label="Display information about">
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
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diff changeset
197 <option value="General">General</option>
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
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198 <option value="Features">Features</option>
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
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diff changeset
199 <option value="Cells">Cells</option>
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
200 <option value="Idents">Cell Identities</option>
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
201 <option value="Metadata">Cell Metadata</option>
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
202 <option value="Matrix">Matrix</option>
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
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diff changeset
203 </param>
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
204 <when value="General">
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
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diff changeset
205 </when>
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
206 <when value="Features">
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
207 <param name="assay" type="text" value="RNA" label="Assay to display features for">
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
208 <expand macro="valid_name"/>
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
209 </param>
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
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diff changeset
210 </when>
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
211 <when value="Cells">
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
212 <expand macro="select_layer"/>
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
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diff changeset
213 </when>
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
214 <when value="Idents">
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
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diff changeset
215 </when>
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
216 <when value="Metadata">
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
217 <param name="view_metadata" type="text" optional="true" value="" label="Metadata to view" help="leave blank to view all metadata"/>
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
218 </when>
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
219 <when value="Matrix">
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
220 <param name="assay" type="text" value="RNA" label="Assay to display matrix for">
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
221 <expand macro="valid_name"/>
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
222 </param>
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
223 <param name="layer" type="text" value="data" label="Layer to display matrix for">
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
224 <expand macro="valid_name"/>
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
225 </param>
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
226 </when>
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
227 </conditional>
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
228 </when>
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
229 <when value="Manipulate">
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
230 <conditional name="manipulate">
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
231 <param name="manipulate" type="select" label="Manipulation to perform">
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
232 <option value="Change_Idents">Change annotation used as idents</option>
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
233 <option value="Rename_Idents">Rename idents</option>
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
234 <option value="Add_Metadata">Add metadata</option>
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
235 <option value="Merge">Merge Seurat Objects</option>
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
236 <option value="Subset_Ident">Subset by Ident</option>
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
237 <option value="Subset_Group">Subset by Group</option>
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
238 <option value="DietSeurat">Choose elements to keep with 'DietSeurat'</option>
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
239 <option value="AggregateExpression">Pseudobulk cells with 'AggregateExpression'</option>
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
240 <option value="DefaultAssay">Set default assay</option>
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
241 </param>
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
242 <when value="Change_Idents">
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
243 <param name="change" type="text" value="" label="New annotation to use as ident"/>
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
244 </when>
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
245 <when value="Rename_Idents">
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
246 <conditional name="rename">
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
247 <param name="rename_all" type="select" label="Rename all idents">
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
248 <option value="true" selected="true">Yes</option>
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
249 <option value="false">No - just rename one ident</option>
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
250 </param>
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
251 <when value="true">
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
252 <param name="new_names" type="text" value="" label="New names" help="comma-separated list, must be same as number of idents">
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
253 <expand macro="valid_list"/>
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
254 </param>
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
255 </when>
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
256 <when value="false">
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
257 <param name="old_name" type="text" value="" label="Name of ident to change"/>
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
258 <param name="new_name" type="text" value="" label="New name for ident">
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
259 <expand macro="valid_name"/>
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
260 </param>
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
261 </when>
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
262 </conditional>
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
263 <conditional name="stash_idents">
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
264 <param name="stash_idents" type="select" label="Save copy of old idents first">
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
265 <option value="false" selected="true">No</option>
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
266 <option value="true">Yes</option>
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
267 </param>
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
268 <when value="false">
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
269 </when>
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
270 <when value="true">
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
271 <param name="old_ident" type="text" value="old.ident" label="Name to store old idents under"/>
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
272 </when>
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
273 </conditional>
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
274 </when>
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
275 <when value="Add_Metadata">
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
276 <param name="metadata" type="data" format="tabular,tsv" label="Cell metadata to add" help="table with cell names in first column"/>
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
277 </when>
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
278 <when value="Merge">
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
279 <param name="add_seurat" type="data" format="rds" multiple="true" label="Seurat object to merge"/>
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
280 <conditional name="join">
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
281 <param name="join" type="select" label="Join layers after merging">
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
282 <option value="false" selected="true">No</option>
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
283 <option value="true">Yes</option>
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
284 </param>
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
285 <when value="false">
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
286 </when>
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
287 <when value="true">
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
288 <param argument="assay" type="text" value="RNA" label="Name of assay to join">
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
289 <expand macro="valid_name"/>
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
290 </param>
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
291 </when>
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
292 </conditional>
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
293 </when>
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
294 <when value="Subset_Ident">
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
295 <param name="idents" type="text" value="" label="Idents to keep" help="comma-separated list of clusters or idents">
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
296 <expand macro="valid_list"/>
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
297 </param>
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
298 </when>
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
299 <when value="Subset_Group">
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
300 <param name="grouping" type="text" value="" label="Grouping to use to select cells" help="from the object metadata e.g. batch, donor"/>
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
301 <param name="groups" type="text" value="" label="Group to keep" help="enter a single category from the grouping"/>
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
302 </when>
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
303 <when value="DietSeurat">
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
304 <param argument="layers" type="text" value="counts" label="Layers to keep" help="comma-separated list">
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
305 <expand macro="valid_list"/>
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
306 </param>
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
307 <param argument="assays" type="text" value="RNA" label="Assays to keep" help="comma-separated list">
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
308 <expand macro="valid_list"/>
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
309 </param>
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
310 <param argument="features" type="data" format="txt,tabular" optional="true" label="List of features to keep" help="text file with one feature on each line, leave blank to keep all"/>
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
311 <param argument="dimreducs" type="text" optional="true" value="" label="Dimensional Reductions to keep" help="comma-separated list, leave blank to remove all">
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
312 <expand macro="valid_list"/>
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
313 </param>
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
314 <param argument="graphs" type="text" optional="true" value="" label="Graphs to keep" help="comma-separated list, leave blank to remove all">
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
315 <expand macro="valid_list"/>
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
316 </param>
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
317 <param argument="misc" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="true" label="Keep misc slot"/>
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
318 </when>
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
319 <when value="AggregateExpression">
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
320 <param name="group_by" type="text" value="ident" label="Aggregate expression for these categories" help="comma-separated list of group/condition names (group.by)"/>
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
321 <param argument="assays" type="text" optional="true" value="" label="Assays to use" help="comma-separated list, leave blank to use all assays">
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
322 <expand macro="valid_list"/>
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
323 </param>
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
324 <param argument="features" type="data" format="txt,tabular" optional="true" label="Features to use" help="text file with one feature on each line, leave blank to use all features"/>
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
325 <expand macro="normalize"/>
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
326 </when>
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
327 <when value="DefaultAssay">
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
328 <param name="default_assay" type="text" value="RNA" label="Assay to use as default">
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
329 <expand macro="valid_name"/>
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
330 </param>
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
331 </when>
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
332 </conditional>
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
333 </when>
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
334 </conditional>
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
335 <expand macro="inputs_common_advanced"/>
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
336 </inputs>
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
337 <outputs>
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
338 <expand macro="seurat_outputs"/>
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
339 <expand macro="inspect_out"/>
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
340 </outputs>
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
341 <tests>
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
342 <test expect_num_outputs="2">
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
343 <!-- test1: Inspect General-->
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
344 <param name="seurat_rds" location="https://zenodo.org/records/13732784/files/integrated_umap.rds"/>
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
345 <conditional name="method">
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
346 <param name="method" value="Inspect"/>
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
347 <conditional name="inspect">
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
348 <param name="inspect" value="General"/>
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
349 </conditional>
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
350 </conditional>
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
351 <section name="advanced_common">
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
352 <param name="show_log" value="true"/>
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
353 </section>
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
354 <output name="hidden_output">
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
355 <assert_contents>
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
356 <has_text_matching expression="seurat_obj"/>
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
357 </assert_contents>
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
358 </output>
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
359 <output name="inspect_general" location="https://zenodo.org/records/13732784/files/inspect.txt" ftype="txt">
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
360 <assert_contents>
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
361 <has_text_matching expression="An object of class Seurat"/>
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
362 </assert_contents>
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
363 </output>
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
364 </test>
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
365 <test expect_num_outputs="2">
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
366 <!-- test2: Inspect Cells-->
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
367 <param name="seurat_rds" location="https://zenodo.org/records/13732784/files/rawdata.rds"/>
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
368 <conditional name="method">
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
369 <param name="method" value="Inspect"/>
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
370 <conditional name="inspect">
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
371 <param name="inspect" value="Cells"/>
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
372 </conditional>
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
373 </conditional>
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
374 <section name="advanced_common">
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
375 <param name="show_log" value="true"/>
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
376 </section>
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
377 <output name="hidden_output">
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
378 <assert_contents>
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
379 <has_text_matching expression="Cells"/>
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
380 </assert_contents>
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
381 </output>
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
382 <output name="inspect_tabular" location="https://zenodo.org/records/13732784/files/inspect_cells.tabular" ftype="tabular">
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
383 <assert_contents>
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
384 <has_n_columns n="1"/>
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
385 </assert_contents>
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
386 </output>
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
387 </test>
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
388 <test expect_num_outputs="2">
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
389 <!-- test3: Inspect Features-->
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
390 <param name="seurat_rds" location="https://zenodo.org/records/13732784/files/citeseq.rds"/>
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
391 <conditional name="method">
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
392 <param name="method" value="Inspect"/>
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
393 <conditional name="inspect">
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
394 <param name="inspect" value="Features"/>
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
395 <param name="assay" value="ADT"/>
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
396 </conditional>
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
397 </conditional>
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
398 <section name="advanced_common">
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
399 <param name="show_log" value="true"/>
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
400 </section>
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
401 <output name="hidden_output">
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
402 <assert_contents>
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
403 <has_text_matching expression="Features"/>
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
404 </assert_contents>
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
405 </output>
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
406 <output name="inspect_tabular" location="https://zenodo.org/records/13732784/files/inspect_features.tabular" ftype="tabular">
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
407 <assert_contents>
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
408 <has_n_columns n="1"/>
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
409 </assert_contents>
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
410 </output>
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
411 </test>
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
412 <test expect_num_outputs="2">
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
413 <!-- test4: Inspect Metadata-->
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
414 <param name="seurat_rds" location="https://zenodo.org/records/13732784/files/added_metadata.rds"/>
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
415 <conditional name="method">
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
416 <param name="method" value="Inspect"/>
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
417 <conditional name="inspect">
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
418 <param name="inspect" value="Metadata"/>
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
419 <param name="view_metadata" value="Group"/>
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
420 </conditional>
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
421 </conditional>
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
422 <section name="advanced_common">
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
423 <param name="show_log" value="true"/>
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
424 </section>
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
425 <output name="hidden_output">
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
426 <assert_contents>
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
427 <has_text_matching expression="seurat_obj"/>
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
428 </assert_contents>
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
429 </output>
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
430 <output name="inspect_tabular" location="https://zenodo.org/records/13732784/files/inspect_metadata_group.tabular" ftype="tabular">
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
431 <assert_contents>
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
432 <has_n_columns n="1"/>
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
433 </assert_contents>
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
434 </output>
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
435 </test>
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
436 <test expect_num_outputs="2">
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
437 <!-- test5: Inspect Idents-->
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
438 <param name="seurat_rds" location="https://zenodo.org/records/13732784/files/renamed_clusters.rds"/>
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
439 <conditional name="method">
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
440 <param name="method" value="Inspect"/>
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
441 <conditional name="inspect">
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
442 <param name="inspect" value="Idents"/>
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
443 </conditional>
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
444 </conditional>
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
445 <section name="advanced_common">
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
446 <param name="show_log" value="true"/>
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
447 </section>
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
448 <output name="hidden_output">
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
449 <assert_contents>
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
450 <has_text_matching expression="Idents"/>
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
451 </assert_contents>
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
452 </output>
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
453 <output name="inspect_tabular" location="https://zenodo.org/records/13732784/files/inspect_idents.tabular" ftype="tabular">
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
454 <assert_contents>
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
455 <has_n_columns n="2"/>
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
456 </assert_contents>
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
457 </output>
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
458 </test>
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
459 <test expect_num_outputs="2">
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
460 <!-- test6: Inspect Matrix-->
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
461 <param name="seurat_rds" location="https://zenodo.org/records/13732784/files/clusters.rds"/>
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
462 <conditional name="method">
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
463 <param name="method" value="Inspect"/>
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
464 <conditional name="inspect">
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
465 <param name="inspect" value="Matrix"/>
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
466 </conditional>
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
467 </conditional>
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
468 <section name="advanced_common">
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
469 <param name="show_log" value="true"/>
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
470 </section>
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
471 <output name="hidden_output">
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
472 <assert_contents>
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
473 <has_text_matching expression="seurat_obj"/>
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
474 </assert_contents>
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
475 </output>
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
476 <output name="inspect_tabular" location="https://zenodo.org/records/13732784/files/inspect_matrix.tabular" ftype="tabular">
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
477 <assert_contents>
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
478 <has_n_columns n="249"/>
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
479 </assert_contents>
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
480 </output>
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
481 </test>
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
482 <test expect_num_outputs="2">
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
483 <!-- test7: Change Idents-->
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
484 <param name="seurat_rds" location="https://zenodo.org/records/13732784/files/clusters.rds"/>
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
485 <conditional name="method">
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
486 <param name="method" value="Manipulate"/>
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
487 <conditional name="manipulate">
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
488 <param name="manipulate" value="Change_Idents"/>
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
489 <param name="change" value="orig.idents"/>
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
490 </conditional>
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
491 </conditional>
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
492 <section name="advanced_common">
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
493 <param name="show_log" value="true"/>
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
494 </section>
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
495 <output name="hidden_output">
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
496 <assert_contents>
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
497 <has_text_matching expression="Idents"/>
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
498 </assert_contents>
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
499 </output>
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
500 <output name="rds_out" location="https://zenodo.org/records/13732784/files/changed_idents.rds" ftype="rds"/>
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
501 </test>
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
502 <test expect_num_outputs="2">
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
503 <!-- test8: Rename Idents-->
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
504 <param name="seurat_rds" location="https://zenodo.org/records/13732784/files/clusters.rds"/>
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
505 <conditional name="method">
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
506 <param name="method" value="Manipulate"/>
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
507 <conditional name="manipulate">
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
508 <param name="manipulate" value="Rename_Idents"/>
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
509 <conditional name="rename">
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
510 <param name="rename_all" value="true"/>
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
511 <param name="new_names" value="Cell A, Cell B, Cell C, Cell D"/>
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
512 </conditional>
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
513 <conditional name="stash_idents">
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
514 <param name="stash_idents" value="true"/>
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
515 <param name="old_ident" value="renamed"/>
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
516 </conditional>
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
517 </conditional>
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
518 </conditional>
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
519 <section name="advanced_common">
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
520 <param name="show_log" value="true"/>
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
521 </section>
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
522 <output name="hidden_output">
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
523 <assert_contents>
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
524 <has_text_matching expression="Idents"/>
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
525 </assert_contents>
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
526 </output>
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
527 <output name="rds_out" location="https://zenodo.org/records/13732784/files/renamed_clusters.rds" ftype="rds"/>
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
528 </test>
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
529 <test expect_num_outputs="2">
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
530 <!-- test9: Add Metadata-->
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
531 <param name="seurat_rds" location="https://zenodo.org/records/13732784/files/rawdata.rds"/>
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
532 <conditional name="method">
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
533 <param name="method" value="Manipulate"/>
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
534 <conditional name="manipulate">
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
535 <param name="manipulate" value="Add_Metadata"/>
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
536 <param name="metadata" location="https://zenodo.org/records/13732784/files/metadata.tsv"/>
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
537 </conditional>
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
538 </conditional>
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
539 <section name="advanced_common">
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
540 <param name="show_log" value="true"/>
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
541 </section>
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
542 <output name="hidden_output">
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
543 <assert_contents>
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
544 <has_text_matching expression="AddMetaData"/>
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
545 </assert_contents>
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
546 </output>
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
547 <output name="rds_out" location="https://zenodo.org/records/13732784/files/added_metadata.rds" ftype="rds"/>
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
548 </test>
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
549 <test expect_num_outputs="2">
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
550 <!-- test10: Merge-->
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
551 <param name="seurat_rds" location="https://zenodo.org/records/13732784/files/subset_Group_A.rds"/>
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
552 <conditional name="method">
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
553 <param name="method" value="Manipulate"/>
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
554 <conditional name="manipulate">
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
555 <param name="manipulate" value="Merge"/>
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
556 <param name="add_seurat" location="https://zenodo.org/records/13732784/files/subset_B16.rds,https://zenodo.org/records/13732784/files/subset_B8.rds"/>
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
557 </conditional>
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
558 </conditional>
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
559 <section name="advanced_common">
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
560 <param name="show_log" value="true"/>
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
561 </section>
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
562 <output name="hidden_output">
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
563 <assert_contents>
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
564 <has_text_matching expression="merge"/>
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
565 </assert_contents>
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
566 </output>
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
567 <output name="rds_out" location="https://zenodo.org/records/13736785/files/merged.rds" ftype="rds"/>
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
568 </test>
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
569 <test expect_num_outputs="2">
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
570 <!-- test11: Subset Ident-->
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
571 <param name="seurat_rds" location="https://zenodo.org/records/13732784/files/clusters.rds"/>
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
572 <conditional name="method">
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
573 <param name="method" value="Manipulate"/>
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
574 <conditional name="manipulate">
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
575 <param name="manipulate" value="Subset_Ident"/>
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
576 <param name="idents" value="2, 3"/>
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
577 </conditional>
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
578 </conditional>
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
579 <section name="advanced_common">
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
580 <param name="show_log" value="true"/>
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
581 </section>
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
582 <output name="hidden_output">
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
583 <assert_contents>
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
584 <has_text_matching expression="subset"/>
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
585 </assert_contents>
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
586 </output>
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
587 <output name="rds_out" location="https://zenodo.org/records/13732784/files/subset_cluster.rds" ftype="rds"/>
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
588 </test>
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
589 <test expect_num_outputs="2">
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
590 <!-- test12: Subset Group-->
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
591 <param name="seurat_rds" location="https://zenodo.org/records/13732784/files/added_metadata.rds"/>
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
592 <conditional name="method">
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
593 <param name="method" value="Manipulate"/>
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
594 <conditional name="manipulate">
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
595 <param name="manipulate" value="Subset_Group"/>
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
596 <param name="grouping" value="Group"/>
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
597 <param name="groups" value="Group_A"/>
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
598 </conditional>
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
599 </conditional>
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
600 <section name="advanced_common">
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
601 <param name="show_log" value="true"/>
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
602 </section>
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
603 <output name="hidden_output">
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
604 <assert_contents>
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
605 <has_text_matching expression="subset"/>
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
606 </assert_contents>
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
607 </output>
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
608 <output name="rds_out" location="https://zenodo.org/records/13732784/files/subset_Group_A.rds" ftype="rds"/>
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
609 </test>
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
610 <test expect_num_outputs="2">
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
611 <!-- test13: DietSeurat-->
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
612 <param name="seurat_rds" location="https://zenodo.org/records/13732784/files/integrated_umap.rds"/>
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
613 <conditional name="method">
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
614 <param name="method" value="Manipulate"/>
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
615 <conditional name="manipulate">
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
616 <param name="manipulate" value="DietSeurat"/>
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
617 <param name="assays" value="ADT"/>
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
618 <param name="dimreducs" value="pca, umap"/>
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
619 </conditional>
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
620 </conditional>
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
621 <section name="advanced_common">
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
622 <param name="show_log" value="true"/>
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
623 </section>
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
624 <output name="hidden_output">
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
625 <assert_contents>
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
626 <has_text_matching expression="DietSeurat"/>
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
627 </assert_contents>
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
628 </output>
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
629 <output name="rds_out" location="https://zenodo.org/records/13732784/files/diet_seurat.rds" ftype="rds"/>
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
630 </test>
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
631 <test expect_num_outputs="2">
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
632 <!-- test14: AggregateExpression-->
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
633 <param name="seurat_rds" location="https://zenodo.org/records/13732784/files/integrated_umap.rds"/>
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
634 <conditional name="method">
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
635 <param name="method" value="Manipulate"/>
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
636 <conditional name="manipulate">
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
637 <param name="manipulate" value="AggregateExpression"/>
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
638 <param name="group_by" value="Group"/>
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
639 </conditional>
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
640 </conditional>
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
641 <section name="advanced_common">
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
642 <param name="show_log" value="true"/>
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
643 </section>
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
644 <output name="hidden_output">
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
645 <assert_contents>
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
646 <has_text_matching expression="AggregateExpression"/>
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
647 </assert_contents>
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
648 </output>
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
649 <output name="rds_out" location="https://zenodo.org/records/13732784/files/aggregated.rds" ftype="rds" compare="sim_size"/>
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
650 </test>
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
651 <test expect_num_outputs="2">
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
652 <!-- test15: Default Assay-->
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
653 <param name="seurat_rds" location="https://zenodo.org/records/13732784/files/citeseq.rds"/>
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
654 <conditional name="method">
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
655 <param name="method" value="Manipulate"/>
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
656 <conditional name="manipulate">
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
657 <param name="manipulate" value="DefaultAssay"/>
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
658 <param name="default_assay" value="ADT"/>
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
659 </conditional>
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
660 </conditional>
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
661 <section name="advanced_common">
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
662 <param name="show_log" value="true"/>
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
663 </section>
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
664 <output name="hidden_output">
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
665 <assert_contents>
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
666 <has_text_matching expression="DefaultAssay"/>
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
667 </assert_contents>
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
668 </output>
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
669 <output name="rds_out" location="https://zenodo.org/records/13732784/files/default.rds" ftype="rds"/>
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
670 </test>
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
671 </tests>
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
672 <help><![CDATA[
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
673 Seurat
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
674 ======
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
675
1
4ec52a83ec82 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit 566984b588e88225f0b3f2dae88c6fd084315e7c
iuc
parents: 0
diff changeset
676 Seurat is an R package designed for QC, analysis, and exploration of single-cell RNA-seq data.
0
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
677
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
678 Seurat aims to enable users to identify and interpret sources of heterogeneity from single-cell transcriptomic measurements, and to integrate diverse types of single-cell data.
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
679
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
680 Inspect and Manipulate
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
681 ======================
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
682
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
683 A selection of essential functions to display information about a Seurat Object or make basic changes to the object.
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
684
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
685 More details on these essential commands can be found in the `seurat documentation
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
686 <https://satijalab.org/seurat/articles/essential_commands>`__
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
687
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
688 Inspect
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
689 =======
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
690
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
691 General - basic information about the Seurat Object
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
692 Features - list of features, select which assay to display features from if object contains multimodal data
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
693 Cells - list of cell barcodes/ids, select layer to display cells for if object contains multiple layers
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
694 Idents - list showing Ident for each cell
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
695 Metadata - table of cell metadata
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
696 Matrix - show the full matrix
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
697
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
698 Manipulate
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
699 ==========
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
700
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
701 Functions to add, change, or remove selected elements of a Seurat Object.
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
702
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
703 Change Idents
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
704 =============
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
705
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
706 Change which annotation in your cell metadata is used as the Ident column.
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
707
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
708 Rename Idents
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
709 =============
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
710
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
711 Rename the classes in the Ident column (e.g. to replace cluster numbers with cell types).
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
712
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
713 You have the option to stash the original idents in a new column called 'old.ident' before renaming the classes in the Ident column.
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
714
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
715 AddMetaData
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
716 ===========
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
717
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
718 Merge
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
719 =====
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
720
1
4ec52a83ec82 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit 566984b588e88225f0b3f2dae88c6fd084315e7c
iuc
parents: 0
diff changeset
721 Combine two Seurat Objects into a single Seurat Object.
0
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
722 Each object will be placed in a separate layer, but you can choose to run the JoinLayers function after merging to combine the objects into a single layer.
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
723
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
724 Subset
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
725 ======
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
726
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
727 Subset a group of cells based on their ident or another grouping in your cell metadata.
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
728
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
729 DietSeurat
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
730 ==========
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
731
1
4ec52a83ec82 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit 566984b588e88225f0b3f2dae88c6fd084315e7c
iuc
parents: 0
diff changeset
732 Keep only certain aspects of the Seurat object.
0
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
733 Can be useful in functions that utilize merge as it reduces the amount of data in the merge
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
734
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
735 More details on these essential commands can be found in the `seurat documentation
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
736 <https://satijalab.org/seurat/reference/dietseurat>`__
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
737
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
738 AggregateExpression
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
739 ===================
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
740
1
4ec52a83ec82 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit 566984b588e88225f0b3f2dae88c6fd084315e7c
iuc
parents: 0
diff changeset
741 Returns summed counts ("pseudobulk") for each identity class.
0
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
742
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
743 More details on the `seurat documentation
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
744 <https://satijalab.org/seurat/reference/aggregateexpression>`__
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
745
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
746
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
747 DefaultAssay
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
748 ============
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
749
1
4ec52a83ec82 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit 566984b588e88225f0b3f2dae88c6fd084315e7c
iuc
parents: 0
diff changeset
750 Set the default assay for multimodal data.
0
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
751
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
752 You can use the Inspect - General function to check which assay is currently active and which other assays are available.
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
753
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
754 ]]></help>
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
755 <expand macro="citations"/>
50c5abeb08ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
756 </tool>