Mercurial > repos > iuc > seurat_integrate

annotate integrate.xml @ 0:4341b8ff2a46 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
author iuc
date Wed, 11 Sep 2024 10:20:51 +0000
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4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
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1 <tool id="seurat_integrate" name="Seurat Integrate" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
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2 <description> and manipulate layers </description>
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
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3 <macros>
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
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4 <import>macros.xml</import>
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
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5 </macros>
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
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6 <expand macro="requirements"/>
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
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7 <expand macro="version_command"/>
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
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8 <command detect_errors="exit_code"><![CDATA[
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
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9 @CMD@
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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10 ]]></command>
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
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11 <configfiles>
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
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12 <configfile name="script_file"><![CDATA[
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
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13 @CMD_imports@
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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14 @CMD_read_inputs@
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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15
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
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16 #if $method.method == 'SplitLayers'
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
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17 seurat_obj[['$method.assay']]<-split(
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
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18 seurat_obj[['$method.assay']],
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
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19 f = seurat_obj[['$method.factor', drop = TRUE]]
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
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20 )
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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21
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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22 #else if $method.method == 'IntegrateLayers'
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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23
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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24 #if $method.features
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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25 features_list<-paste(readLines('$method.features'), collapse=",")
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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26 #end if
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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27
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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28 seurat_obj<-IntegrateLayers(
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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29 seurat_obj,
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
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30 method = $method.integration.integration_method,
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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31 #if $method.integration.integration_method == 'CCAIntegration'
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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32 #if $method.integration.adv.k_filter
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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33 k.filter = $method.integration.adv.k_filter,
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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34 #else
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
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35 k.filter = NA,
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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36 #end if
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
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37 dims = 1:$method.integration.adv.dims,
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
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38 #if $method.integration.adv.dims_to_integrate
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
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39 dims.to.integrate = $method.integration.adv.dims_to_integrate,
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
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40 #end if
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
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41 k.weight = $method.integration.adv.k_weight,
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
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42 #if $method.integration.adv.weight_reduction != ''
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
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43 weight.reduction = c(unlist(strsplit(gsub(" ", "", '$method.integration.adv.weight_reduction'), ","))),
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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44 #end if
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
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45 sd.weight = $method.integration.adv.sd_weight,
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
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46 preserve.order = $method.integration.adv.preserve_order,
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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47 #else if $method.integration.integration_method == 'HarmonyIntegration'
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
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48 npcs = $method.integration.adv.npcs,
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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49 key = '$method.integration.adv.key',
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50 #if $method.integration.adv.theta
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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51 theta = $method.integration.adv.theta,
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52 #end if
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53 #if $method.integration.adv.lambda
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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54 lambda = $method.integration.adv.lambda,
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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55 #end if
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56 sigma = $method.integration.adv.sigma,
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57 #if $method.integration.adv.nclust
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58 nclust = $method.integration.adv.nclust,
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59 #end if
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60 max_iter = $method.integration.adv.max_iter,
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61 #else if $method.integration.integration_method == 'JointPCAIntegration'
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62 k.anchor = $method.integration.adv.k_anchor,
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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63 dims = 1:$method.integration.adv.dims,
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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64 #if $method.integration.adv.dims_to_integrate
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iuc
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65 dims.to.integrate = $method.integration.adv.dims_to_integrate,
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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66 #end if
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67 k.weight = $method.integration.adv.k_weight,
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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68 #if $method.integration.adv.weight_reduction != ''
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69 weight.reduction = c(unlist(strsplit(gsub(" ", "", '$method.integration.adv.weight_reduction'), ","))),
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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70 #end if
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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71 sd.weight = $method.integration.adv.sd_weight,
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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72 preserve.order = $method.integration.adv.preserve_order,
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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73 #else if $method.integration.integration_method == 'RPCAIntegration'
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74 #if $method.integration.adv.k_filter
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
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75 k.filter = $method.integration.adv.k_filter,
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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76 #else
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iuc
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77 k.filter = NA,
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78 #end if
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79 dims = 1:$method.integration.adv.dims,
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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80 #if $method.integration.adv.dims_to_integrate
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iuc
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81 dims.to.integrate = $method.integration.adv.dims_to_integrate,
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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82 #end if
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83 k.weight = $method.integration.adv.k_weight,
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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84 #if $method.integration.adv.weight_reduction != ''
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85 weight.reduction = c(unlist(strsplit(gsub(" ", "", '$method.integration.adv.weight_reduction'), ","))),
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86 #end if
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87 sd.weight = $method.integration.adv.sd_weight,
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88 preserve.order = $method.integration.adv.preserve_order,
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89 #end if
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90 orig.reduction = '$method.orig_reduction',
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91 new.reduction = '$method.new_reduction',
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92 #if $method.assay != ''
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93 assay = '$method.assay',
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94 #end if
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95 #if $method.features
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96 features = c(unlist(strsplit(features_list, ","))),
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97 #end if
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98 #if $method.layers != ''
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99 layers = c(unlist(strsplit(gsub(" ", "", '$method.layers'), ","))),
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100 #end if
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101 #if $method.scale_layers != ''
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102 scale_layers = c(unlist(strsplit(gsub(" ", "", '$method.scale_layers'), ","))),
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103 #end if
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104 #if $method.normalization_method == 'true'
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105 normalization.method = 'SCT'
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106 #end if
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107 )
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108
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109 #else if $method.method == 'JoinLayers'
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110 seurat_obj[['$method.assay']]<-JoinLayers(
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111 seurat_obj[['$method.assay']]
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112 )
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113
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114 #else if $method.method == 'PrepSCTFindMarkers'
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115 seurat_obj<-PrepSCTFindMarkers(
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116 seurat_obj,
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117 assay = '$method.assay'
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118 )
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119
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120 #end if
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121
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122 @CMD_rds_write_outputs@
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123
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124 ]]></configfile>
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125 </configfiles>
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126 <inputs>
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127 <expand macro="input_rds"/>
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128 <conditional name="method">
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129 <param name="method" type="select" label="Method used">
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130 <option value="SplitLayers">Split data into layers using 'split'</option>
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131 <option value="IntegrateLayers" selected="true">Apply integration methods with 'IntegrateLayers'</option>
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132 <option value="JoinLayers">Join layers with 'JoinLayers'</option>
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133 <option value="PrepSCTFindMarkers">Prepare to run DE on SCT Assay with 'PrepSCTFindMarkers'</option>
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134 </param>
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135 <when value="SplitLayers">
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136 <param argument="assay" type="text" value="RNA" label="Name of assay to use">
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137 <expand macro="valid_name"/>
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138 </param>
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139 <param name="factor" type="text" value="" label="Factor or group to use to split data" help="(f)">
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140 <expand macro="valid_name"/>
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141 </param>
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142 </when>
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143 <when value="IntegrateLayers">
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144 <conditional name="integration">
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145 <param name="integration_method" type="select" label="Integration method to use" help="(method)">
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146 <option value="CCAIntegration">CCA Integration</option>
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147 <option value="HarmonyIntegration">Harmony Integration</option>
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148 <option value="JointPCAIntegration">Joint PCA Integration</option>
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149 <option value="RPCAIntegration">RPCA Integration</option>
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150 </param>
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151 <when value="CCAIntegration">
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152 <section name="adv" title="Advanced Options">
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153 <param name="k_filter" type="integer" optional="true" value="" label="Number of anchors to filter" help="leave blank to use all (k.filter)"/>
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154 <expand macro="integration_inputs"/>
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155 </section>
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156 </when>
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157 <when value="HarmonyIntegration">
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158 <section name="adv" title="Advanced Options">
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159 <param argument="npcs" type="integer" optional="true" value="50" label="Number of PCs to compute if doing PCA on input matrix"/>
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160 <param argument="key" type="text" value="harmony_" label="Dimensional reduction key" help="specifies the string before the number for the dimension names (reduction.key)">
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161 <expand macro="valid_reduction_key"/>
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162 </param>
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163 <param argument="theta" type="float" optional="true" value="" label="Diversity clustering penalty parameter"/>
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164 <param argument="lambda" type="float" optional="true" value="" label="Ridge regression penalty parameter"/>
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165 <param argument="sigma" type="float" value="0.1" label="Width of soft kmeans clusters"/>
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166 <param argument="nclust" type="integer" optional="true" value="" label="Number of clusters in model"/>
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167 <param argument="max_iter" type="integer" value="10" label="Maximum number of rounds to run Harmony"/>
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168 </section>
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169 </when>
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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170 <when value="JointPCAIntegration">
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
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171 <section name="adv" title="Advanced Options">
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
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172 <param name="k_anchor" type="integer" value="20" label="How many neighbors (k) to use when picking anchors"/>
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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173 <expand macro="integration_inputs"/>
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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174 </section>
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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175 </when>
4341b8ff2a46 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 <when value="RPCAIntegration">
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
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177 <section name="adv" title="Advanced Options">
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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178 <param name="k_filter" type="integer" optional="true" value="" label="Number of anchors to filter" help="leave blank to use all (k.filter)"/>
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
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diff changeset
179 <expand macro="integration_inputs"/>
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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180 </section>
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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181 </when>
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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182 </conditional>
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
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183 <param name="orig_reduction" type="text" value="pca" label="Dimensional reduction to use for correction" help="(orig.reduction)">
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
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184 <expand macro="valid_name"/>
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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185 </param>
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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186 <param name="new_reduction" type="text" value="integrated.dr" label="Name for new dimensional reduction" help="(new.reduction)">
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
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187 <expand macro="valid_name"/>
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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188 </param>
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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189 <expand macro="select_assay"/>
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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190 <param argument="features" type="data" format="txt,tabular" optional="true" label="List of features to use for integration" help="text file with one feature on each line"/>
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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191 <param argument="layers" type="text" optional="true" value="" label="Names of normalized layer(s) in assay">
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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192 <expand macro="valid_list"/>
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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193 </param>
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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194 <param name="scale_layers" type="text" optional="true" value="" label="Names of scaled layer(s) in assay" help="(scale.layer)">
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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195 <expand macro="valid_list"/>
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196 </param>
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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197 <param name="normalization_method" type="boolean" truevalue="true" falsevalue="false" label="Use SCT as Normalization Method" help="after using SCTransform (normalization.method)"/>
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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198 </when>
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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199 <when value="JoinLayers">
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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200 <param argument="assay" type="text" value="RNA" label="Name of assay to join">
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
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201 <expand macro="valid_name"/>
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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202 </param>
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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203 </when>
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
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204 <when value="PrepSCTFindMarkers">
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
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205 <param argument="assay" type="text" value="SCT" label="Name of Assay where SCT objects are stored">
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
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diff changeset
206 <expand macro="valid_name"/>
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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207 </param>
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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208 </when>
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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209 </conditional>
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
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210 <expand macro="inputs_common_advanced"/>
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
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211 </inputs>
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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212 <outputs>
4341b8ff2a46 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 <expand macro="seurat_outputs"/>
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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214 </outputs>
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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215 <tests>
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
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diff changeset
216 <test expect_num_outputs="2">
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
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diff changeset
217 <!-- test1: SplitLayers -->
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
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218 <param name="seurat_rds" location="https://zenodo.org/records/13732784/files/added_metadata.rds"/>
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
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diff changeset
219 <conditional name="method">
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
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220 <param name="method" value="SplitLayers"/>
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
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diff changeset
221 <param name="assay" value="RNA"/>
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
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diff changeset
222 <param name="factor" value="Group"/>
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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223 </conditional>
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
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diff changeset
224 <section name="advanced_common">
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
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225 <param name="show_log" value="true"/>
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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226 </section>
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
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diff changeset
227 <output name="hidden_output">
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
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228 <assert_contents>
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
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229 <has_text_matching expression="split"/>
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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230 </assert_contents>
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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231 </output>
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
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diff changeset
232 <output name="rds_out" location="https://zenodo.org/records/13732784/files/splitdata.rds" ftype="rds"/>
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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parents:
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233 </test>
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
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234 <test expect_num_outputs="2">
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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parents:
diff changeset
235 <!-- test2: IntegrateLayers-->
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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diff changeset
236 <param name="seurat_rds" location="https://zenodo.org/records/13732784/files/unintegrated_umap.rds"/>
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
237 <conditional name="method">
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
238 <param name="method" value="IntegrateLayers"/>
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
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diff changeset
239 <conditional name="integration">
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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parents:
diff changeset
240 <param name="integration_method" value="CCAIntegration"/>
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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diff changeset
241 </conditional>
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
242 <param name="orig_reduction" value="pca"/>
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
243 <param name="new_reduction" value="integrated.cca"/>
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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244 </conditional>
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
245 <section name="advanced_common">
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
246 <param name="show_log" value="true"/>
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
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diff changeset
247 </section>
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
248 <output name="hidden_output">
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
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diff changeset
249 <assert_contents>
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
250 <has_text_matching expression="IntegrateLayers"/>
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
251 </assert_contents>
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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252 </output>
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
253 <output name="rds_out" location="https://zenodo.org/records/13732784/files/cca_integrated.rds" ftype="rds"/>
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
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diff changeset
254 </test>
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
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255 <test expect_num_outputs="2">
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256 <!-- test3: IntegrateLayers - Harmony Installed-->
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257 <param name="seurat_rds" location="https://zenodo.org/records/13732784/files/unintegrated_umap.rds"/>
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258 <conditional name="method">
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259 <param name="method" value="IntegrateLayers"/>
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260 <conditional name="integration">
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261 <param name="integration_method" value="HarmonyIntegration"/>
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262 </conditional>
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263 <param name="orig_reduction" value="pca"/>
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264 <param name="new_reduction" value="integrated.harm"/>
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265 </conditional>
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266 <section name="advanced_common">
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267 <param name="show_log" value="true"/>
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268 </section>
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269 <output name="hidden_output">
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270 <assert_contents>
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271 <has_text_matching expression="IntegrateLayers"/>
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272 </assert_contents>
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273 </output>
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274 <output name="rds_out" location="https://zenodo.org/records/13732784/files/harm_integrated.rds" ftype="rds" compare="sim_size"/>
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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275 </test>
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276 <test expect_num_outputs="2">
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277 <!-- test4: JoinLayers-->
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278 <param name="seurat_rds" location="https://zenodo.org/records/13732784/files/integrated_umap.rds"/>
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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279 <conditional name="method">
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280 <param name="method" value="JoinLayers"/>
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281 </conditional>
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282 <section name="advanced_common">
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283 <param name="show_log" value="true"/>
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284 </section>
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285 <output name="hidden_output">
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286 <assert_contents>
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287 <has_text_matching expression="JoinLayers"/>
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288 </assert_contents>
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289 </output>
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290 <output name="rds_out" location="https://zenodo.org/records/13732784/files/joined.rds" ftype="rds"/>
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291 </test>
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292 <test expect_num_outputs="2">
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293 <!-- test5: PrepSCTFindMarkers-->
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294 <param name="seurat_rds" location="https://zenodo.org/records/13732784/files/SCT_integrated_umap.rds"/>
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295 <conditional name="method">
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296 <param name="method" value="PrepSCTFindMarkers"/>
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297 </conditional>
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298 <section name="advanced_common">
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299 <param name="show_log" value="true"/>
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300 </section>
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301 <output name="hidden_output">
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302 <assert_contents>
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303 <has_text_matching expression="PrepSCTFindMarkers"/>
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304 </assert_contents>
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305 </output>
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306 <output name="rds_out" location="https://zenodo.org/records/13732784/files/PrepSCTFindMarkers.rds" ftype="rds"/>
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307 </test>
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308 </tests>
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309 <help><![CDATA[
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310 Seurat
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311 ======
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312
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313 Seurat is an R package designed for QC, analysis, and exploration of single-cell RNA-seq data.
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314
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315 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.
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316
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317
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318 Split
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319 =====
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320
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321 The split function is used here to split the data into separate layers based on the groups defined by f. Each group becomes its own layer in the Seurat Object.
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322
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323 More details on the `R documentation
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324 <https://rdrr.io/r/base/split.html>`__
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325
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326
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327 Integrate
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328 =========
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329
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330 Multiple layers are integrated to enable them to be analysed together.
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331
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332 Available methods are: CCA, Harmony, JointPCA, RPCA, FastMNN and scVI.
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333
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334 More details on the `seurat documentation
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335 <https://satijalab.github.io/seurat-object/reference/CreateSeuratObject.html>`__
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336
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337 JoinLayers
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338 ==========
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339
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340 Multiple layers (e.g. those created using the split function) can be joined together in a single layer. No integration is performed by this function.
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341
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342 More details on the `seurat documentation
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343 <https://satijalab.github.io/seurat-object/reference/SplitLayers.html>`__
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344
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345 PrepSCTFindMarkers
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346 ==================
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347
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348 Given a merged object with multiple SCT models, this function uses minimum of the median UMI (calculated using the raw UMI counts) of individual objects to reverse the individual SCT regression model using minimum of median UMI as the sequencing depth covariate.
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349 The counts slot of the SCT assay is replaced with recorrected counts and the data slot is replaced with log1p of recorrected counts.
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350
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351 More details on the `seurat documentation
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352 <https://satijalab.org/seurat/reference/prepsctfindmarkers>`__
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353
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354 ]]></help>
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355 <expand macro="citations"/>
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356 </tool>