Mercurial > repos > iuc > seurat_create

annotate create_seurat.xml @ 1:a7af4acac32c draft

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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 11:54:55 +0000
parents d0c26c9430f2
children af8bdeb89691
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d0c26c9430f2 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_create" name="Seurat Create" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
d0c26c9430f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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2 <description>- Prepare data for the pipeline</description>
d0c26c9430f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
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3 <macros>
d0c26c9430f2 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>
d0c26c9430f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
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5 </macros>
1
a7af4acac32c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit 566984b588e88225f0b3f2dae88c6fd084315e7c
iuc
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6 <expand macro="bio_tools"/>
0
d0c26c9430f2 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="requirements"/>
d0c26c9430f2 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"/>
d0c26c9430f2 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[
d0c26c9430f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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10 #if str($method.method) == 'CreateSeuratObject':
d0c26c9430f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
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11 #if str($method.input_type.input_type) == 'mtx':
d0c26c9430f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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12 ln -s '$method.input_type.matrix' matrix.mtx &&
d0c26c9430f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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13 ln -s '$method.input_type.gene_names' genes.tsv &&
d0c26c9430f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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14 ln -s '$method.input_type.cell_barcodes' barcodes.tsv &&
d0c26c9430f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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15 #else if str($method.input_type.input_type) == 'tab':
d0c26c9430f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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16 ln -s '$method.input_type.input_tab' input.tab;
d0c26c9430f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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17 #if str($method.input_type.citeseq.citeseq) == 'true':
d0c26c9430f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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18 ln -s '$method.input_type.citeseq.citeseq_table' citeseq.tab &&
d0c26c9430f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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19 #end if
d0c26c9430f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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20 #end if
d0c26c9430f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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21 cat '$script_file' > $hidden_output &&
d0c26c9430f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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22 Rscript '$script_file' >> $hidden_output
d0c26c9430f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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23 #else:
d0c26c9430f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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24 @CMD@
d0c26c9430f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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25 #end if
d0c26c9430f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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26 ]]></command>
d0c26c9430f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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27 <configfiles>
d0c26c9430f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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28 <configfile name="script_file"><![CDATA[
d0c26c9430f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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29 @CMD_imports@
d0c26c9430f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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30
d0c26c9430f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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31 #if $method.method == 'CreateSeuratObject'
d0c26c9430f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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32 #if $method.input_type.input_type == 'mtx'
d0c26c9430f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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33 counts<-Read10X(
d0c26c9430f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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34 data.dir = '.',
d0c26c9430f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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35 gene.column = $method.input_type.gene_column,
d0c26c9430f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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36 cell.column = $method.input_type.cell_column,
d0c26c9430f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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37 unique.features = $method.input_type.unique_features,
d0c26c9430f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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38 strip.suffix = $method.input_type.strip_suffix
d0c26c9430f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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39 )
d0c26c9430f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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40
d0c26c9430f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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41 #if $method.meta_data
d0c26c9430f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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42 meta_data<-read.table(
d0c26c9430f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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43 "$method.meta_data",
d0c26c9430f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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44 header = TRUE,
d0c26c9430f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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45 row.names = 1,
d0c26c9430f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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46 sep = "\t"
d0c26c9430f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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47 )
d0c26c9430f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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48 for (name in colnames(meta_data)) {
d0c26c9430f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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49 meta_data[[name]]<-gsub("^$", "N/A", trimws(meta_data[[name]]))
d0c26c9430f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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50 meta_data[[name]][is.na(meta_data[[name]])]<-"N/A"
d0c26c9430f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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51 }
d0c26c9430f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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52 #end if
d0c26c9430f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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53
d0c26c9430f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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54 seurat_obj<-CreateSeuratObject(
d0c26c9430f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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55 counts,
d0c26c9430f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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56 assay = '$method.assay',
d0c26c9430f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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57 #if $method.names_field != ''
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58 names.field = $method.names_field,
d0c26c9430f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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59 #end if
d0c26c9430f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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60 #if $method.names_delim != ''
d0c26c9430f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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61 names.delim = '$method.names_delim',
d0c26c9430f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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62 #end if
d0c26c9430f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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63 #if $method.min_cells
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64 min.cells = $method.min_cells,
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65 #end if
d0c26c9430f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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66 #if $method.min_features
d0c26c9430f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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67 min.features = $method.min_features,
d0c26c9430f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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68 #end if
d0c26c9430f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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69 #if $method.meta_data
d0c26c9430f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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70 meta.data = meta_data
d0c26c9430f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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71 #end if
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72 )
d0c26c9430f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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73
d0c26c9430f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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74 #if $method.percent_mt.percent_mt == 'true'
d0c26c9430f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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75 seurat_obj[["percent.mt"]]<-PercentageFeatureSet(
d0c26c9430f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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76 seurat_obj,
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77 pattern = '$method.percent_mt.pattern',
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78 )
d0c26c9430f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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79 #end if
d0c26c9430f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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80
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81 #if $method.input_type.citeseq_boolean == 'true'
d0c26c9430f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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82 seurat_obj[['ADT']]<-CreateAssayObject(counts[['Antibody Capture']], colnames(x = seurat_obj))
d0c26c9430f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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83 #end if
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84
d0c26c9430f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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parents:
diff changeset
85 #else if $method.input_type.input_type == 'tab'
d0c26c9430f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
86 counts<-read.table(
d0c26c9430f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
87 'input.tab',
d0c26c9430f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
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diff changeset
88 header = TRUE,
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iuc
parents:
diff changeset
89 row.names = 1,
d0c26c9430f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
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90 sep = "\t"
d0c26c9430f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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91 )
d0c26c9430f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
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92
d0c26c9430f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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93 #if $method.meta_data
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iuc
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94 meta_data<-read.table(
d0c26c9430f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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95 "$method.meta_data",
d0c26c9430f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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96 header = TRUE,
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97 row.names = 1,
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iuc
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98 sep = "\t"
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iuc
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99 )
d0c26c9430f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
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100 for (name in colnames(meta_data)) {
d0c26c9430f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
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101 meta_data[[name]]<-gsub("^$", "N/A", trimws(meta_data[[name]]))
d0c26c9430f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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102 meta_data[[name]][is.na(meta_data[[name]])]<-"N/A"
d0c26c9430f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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103 }
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104 #end if
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105
d0c26c9430f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
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106 seurat_obj<-CreateSeuratObject(
d0c26c9430f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
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107 counts,
d0c26c9430f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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108 assay = '$method.assay',
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109 #if $method.names_field != ''
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iuc
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110 names.field = $method.names_field,
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111 #end if
d0c26c9430f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
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112 #if $method.names_delim != ''
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iuc
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113 names.delim = '$method.names_delim',
d0c26c9430f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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114 #end if
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115 #if $method.min_cells
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116 min.cells = $method.min_cells,
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117 #end if
d0c26c9430f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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118 #if $method.min_features
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iuc
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119 min.features = $method.min_features,
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iuc
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120 #end if
d0c26c9430f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
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121 #if $method.meta_data
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iuc
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122 meta.data = meta_data
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iuc
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123 #end if
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124 )
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125
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126 #if $method.percent_mt.percent_mt == 'true'
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127 seurat_obj[["percent.mt"]]<-PercentageFeatureSet(
d0c26c9430f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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128 seurat_obj,
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129 pattern = '$method.percent_mt.pattern',
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130 )
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131 #end if
1
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132
0
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133 #if $method.input_type.citeseq.citeseq == 'true'
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134 citeseq<-read.table(
d0c26c9430f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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135 'citeseq.tab',
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136 header = TRUE,
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iuc
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137 row.names = 1,
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iuc
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138 sep = "\t"
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139 )
1
a7af4acac32c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit 566984b588e88225f0b3f2dae88c6fd084315e7c
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140
0
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iuc
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141 seurat_obj[['ADT']]<-CreateAssay5Object(counts = citeseq)
d0c26c9430f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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142 #end if
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143 #end if
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144
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145 #else if $method.method == 'Add_QC_Metrics'
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iuc
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146 @CMD_read_inputs@
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147
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148 #if $method.match.match == 'list'
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iuc
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149 features_list<-paste(readLines('$method.match.features'), collapse=",")
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150 #end if
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151
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152 seurat_obj[['$method.col_name']]<-PercentageFeatureSet(
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153 seurat_obj,
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iuc
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154 #if $method.match.match == 'pattern'
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iuc
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155 pattern = '$method.match.pattern',
d0c26c9430f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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156 #else if $method.match.match == 'list'
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157 features = c(unlist(strsplit(features_list, ","))),
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158 #end if
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159 #if $method.assay != ''
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160 assay = '$method.assay'
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iuc
parents:
diff changeset
161 #end if
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162 )
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163
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diff changeset
164 #else if $method.method == 'FilterCells'
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165 @CMD_read_inputs@
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iuc
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166 #if $method.minimum_nFeature_RNA
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iuc
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167 seurat_obj<-subset(
d0c26c9430f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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168 seurat_obj,
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169 subset = nFeature_RNA > $method.minimum_nFeature_RNA
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170 )
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171 #end if
d0c26c9430f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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diff changeset
172 #if $method.maximum_nFeature_RNA
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iuc
parents:
diff changeset
173 seurat_obj<-subset(
d0c26c9430f2 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 seurat_obj,
d0c26c9430f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
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175 subset = nFeature_RNA < $method.maximum_nFeature_RNA
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iuc
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diff changeset
176 )
d0c26c9430f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
177 #end if
d0c26c9430f2 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 #if $method.minimum_nCount_RNA
d0c26c9430f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
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179 seurat_obj<-subset(
d0c26c9430f2 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 seurat_obj,
d0c26c9430f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
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181 subset = nCount_RNA > $method.minimum_nCount_RNA
d0c26c9430f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
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182 )
d0c26c9430f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
183 #end if
d0c26c9430f2 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 #if $method.maximum_nCount_RNA
d0c26c9430f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
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185 seurat_obj<-subset(
d0c26c9430f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
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diff changeset
186 seurat_obj,
d0c26c9430f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
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187 subset = nCount_RNA < $method.maximum_nCount_RNA
d0c26c9430f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
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188 )
d0c26c9430f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
189 #end if
d0c26c9430f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
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190 #if $method.minimum_percent_mt
d0c26c9430f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
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191 seurat_obj<-subset(
d0c26c9430f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
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192 seurat_obj,
d0c26c9430f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
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193 subset = percent.mt> $method.minimum_percent_mt
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iuc
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194 )
d0c26c9430f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
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195 #end if
d0c26c9430f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
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196 #if $method.maximum_percent_mt
d0c26c9430f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
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197 seurat_obj<-subset(
d0c26c9430f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
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198 seurat_obj,
d0c26c9430f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
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199 subset = percent.mt < $method.maximum_percent_mt
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iuc
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200 )
d0c26c9430f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
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201 #end if
d0c26c9430f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
202 #if $method.other.other == 'true'
d0c26c9430f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
203 #if $method.other.minimum
d0c26c9430f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
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204 seurat_obj<-subset(
d0c26c9430f2 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 seurat_obj,
d0c26c9430f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
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206 subset = $method.other.other_variable > $method.other.minimum
d0c26c9430f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
207 )
d0c26c9430f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
208 #end if
d0c26c9430f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
209 #if $method.other.maximum
d0c26c9430f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
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210 seurat_obj<-subset(
d0c26c9430f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
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211 seurat_obj,
d0c26c9430f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
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212 subset = $method.other.other_variable < $method.other.maximum
d0c26c9430f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
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213 )
d0c26c9430f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
214 #end if
d0c26c9430f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
215 #end if
d0c26c9430f2 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
d0c26c9430f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
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217 #end if
d0c26c9430f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
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218
d0c26c9430f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
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219 @CMD_rds_write_outputs@
d0c26c9430f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
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220
d0c26c9430f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
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221 ]]></configfile>
d0c26c9430f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
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222 </configfiles>
d0c26c9430f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
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223 <inputs>
d0c26c9430f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
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224 <conditional name="method">
d0c26c9430f2 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="method" type="select" label="Method used">
d0c26c9430f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
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226 <option value="CreateSeuratObject">Create Seurat Object</option>
d0c26c9430f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
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227 <option value="Add_QC_Metrics">Add QC Metrics</option>
d0c26c9430f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
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228 <option value="FilterCells">Filter cells by QC metrics</option>
d0c26c9430f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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229 </param>
d0c26c9430f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
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230 <when value="CreateSeuratObject">
d0c26c9430f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
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231 <conditional name="input_type">
d0c26c9430f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
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232 <param name="input_type" type="select" label="Select format of input">
d0c26c9430f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
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233 <option value="mtx" selected="true">matrix market (for e.g. 10x data)</option>
d0c26c9430f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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234 <option value="tab">tab-delimited text</option>
d0c26c9430f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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235 </param>
d0c26c9430f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
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236 <when value="mtx">
d0c26c9430f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
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237 <param name="matrix" type="data" format="mtx" label="Counts matrix with features as rows, cells as columns (.mtx)"/>
d0c26c9430f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
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238 <param name="citeseq_boolean" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Matrix includes citeseq data"/>
d0c26c9430f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
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239 <param name="gene_names" type="data" format="tsv,tabular" label="List of gene names (for rows)"/>
d0c26c9430f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
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240 <param name="cell_barcodes" type="data" format="tsv,tabular" label="List of cell barcodes (for columns)"/>
d0c26c9430f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
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241 <param name="gene_column" type="integer" value="2" label="Column of gene table to use as gene names" help="(gene.column)"/>
d0c26c9430f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
242 <param name="cell_column" type="integer" value="1" label="Column of cell table to use as cell names" help="(cell.column)"/>
d0c26c9430f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
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243 <param name="unique_features" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="true" label="Make feature names unique" help="(unique.features)"/>
d0c26c9430f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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244 <param name="strip_suffix" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="false" label="Remove trailing -1 if present in all cell barcodes" help="(strip.suffix)"/>
d0c26c9430f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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245 </when>
d0c26c9430f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
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246 <when value="tab">
d0c26c9430f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
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247 <param name="input_tab" type="data" format="tsv,tabular" label="Expression table with features as rows, cells as columns" help="(file)"/>
d0c26c9430f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
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diff changeset
248 <conditional name="citeseq">
d0c26c9430f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
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249 <param name="citeseq" type="select" label="Add citeseq assay">
d0c26c9430f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
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250 <option value="false" selected="true">No</option>
d0c26c9430f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
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251 <option value="true">Yes</option>
d0c26c9430f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
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252 </param>
d0c26c9430f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
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253 <when value="false"></when>
d0c26c9430f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
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254 <when value="true">
d0c26c9430f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
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255 <param name="citeseq_table" type="data" format ="tsv,tabular" label="CITE-Seq data to add"/>
d0c26c9430f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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256 </when>
d0c26c9430f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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257 </conditional>
d0c26c9430f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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258 </when>
d0c26c9430f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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259 </conditional>
d0c26c9430f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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260 <param name="meta_data" type="data" format="tsv,tabular" optional="true" label="Additional cell metadata to add" help="table with cell names in first column (meta.data)"/>
d0c26c9430f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
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diff changeset
261 <param argument="assay" type="text" value="RNA" label="Name of assay to create">
d0c26c9430f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
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262 <expand macro="valid_name"/>
d0c26c9430f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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263 </param>
d0c26c9430f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
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264 <param name="min_cells" type="integer" optional="true" value="0" label="Include features detected in at least this many cells" help="(min.cells)"/>
d0c26c9430f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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265 <param name="min_features" type="integer" optional="true" value="0" label="Include cells where at least this many features are detected" help="(min.features)"/>
d0c26c9430f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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266 <param name="names_field" type="integer" optional="true" value="" label="Field of cell names to use as cell identity class" help="(names.field)"/>
d0c26c9430f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
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diff changeset
267 <param name="names_delim" type="text" optional="true" value="" label="Delimiter for cell names" help="(names.delim)"/>
d0c26c9430f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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268 <conditional name="percent_mt">
d0c26c9430f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
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269 <param name="percent_mt" type="select" label="Calculate percentage of mito genes in each cell">
d0c26c9430f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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270 <option value="false" selected="true">No</option>
d0c26c9430f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
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271 <option value="true">Yes</option>
d0c26c9430f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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272 </param>
d0c26c9430f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
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273 <when value="false">
d0c26c9430f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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274 </when>
d0c26c9430f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
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275 <when value="true">
d0c26c9430f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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276 <param argument="pattern" type="text" value="^MT-" label="Pattern/regex to match in gene names" help="e.g. the default '^MT-' matches gene names starting with 'MT-' which are human mitochondrial genes"/>
d0c26c9430f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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277 </when>
d0c26c9430f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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278 </conditional>
d0c26c9430f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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279 </when>
d0c26c9430f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
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280 <when value="Add_QC_Metrics">
d0c26c9430f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
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281 <expand macro="input_rds"/>
d0c26c9430f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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282 <conditional name="match">
d0c26c9430f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
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283 <param name="match" type="select" label="Calculate percentage of reads based on">
d0c26c9430f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
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284 <option value="pattern" selected="true">Pattern in gene names</option>
d0c26c9430f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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285 <option value="list">List of features</option>
d0c26c9430f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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286 </param>
d0c26c9430f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
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diff changeset
287 <when value="pattern">
d0c26c9430f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
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288 <param argument="pattern" type="text" value="^MT-" label="Pattern/regex to match in gene names" help="e.g. the default '^MT-' matches gene names starting with 'MT-' which are human mitochondrial genes"/>
d0c26c9430f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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289 </when>
d0c26c9430f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
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290 <when value="list">
d0c26c9430f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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291 <param argument="features" type="data" format="txt,tabular" label="List of genes to match" help="text file with one feature on each line"/>
d0c26c9430f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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292 </when>
d0c26c9430f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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293 </conditional>
d0c26c9430f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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294 <param name="col_name" type="text" value="percent.mt" label="Name to store the variable as">
d0c26c9430f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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295 <expand macro="valid_name"/>
d0c26c9430f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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296 </param>
d0c26c9430f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
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297 <expand macro="select_assay"/>
d0c26c9430f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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298 </when>
d0c26c9430f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
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299 <when value="FilterCells">
d0c26c9430f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
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300 <expand macro="input_rds"/>
d0c26c9430f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
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301 <param name="minimum_nFeature_RNA" type="integer" optional="true" value="" label="Minimum nFeature_RNA"/>
d0c26c9430f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
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302 <param name="maximum_nFeature_RNA" type="integer" optional="true" value="" label="Maximum nFeature_RNA"/>
d0c26c9430f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
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303 <param name="minimum_nCount_RNA" type="integer" optional="true" value="" label="Minimum nCount_RNA"/>
d0c26c9430f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
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304 <param name="maximum_nCount_RNA" type="integer" optional="true" value="" label="Maximum nCount_RNA"/>
d0c26c9430f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
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305 <param name="minimum_percent_mt" type="float" optional="true" value="" label="Minimum percent.mt"/>
d0c26c9430f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
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306 <param name="maximum_percent_mt" type="float" optional="true" value="" label="Maximum percent.mt"/>
d0c26c9430f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
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307 <conditional name="other">
d0c26c9430f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
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308 <param name="other" type="select" label="Filter by a different metric">
d0c26c9430f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
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309 <option value="false" selected="true">No</option>
d0c26c9430f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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310 <option value="true">Yes</option>
d0c26c9430f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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311 </param>
d0c26c9430f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
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diff changeset
312 <when value="false">
d0c26c9430f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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313 </when>
d0c26c9430f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
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314 <when value="true">
d0c26c9430f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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315 <param name="other_variable" type="text" value="" label="Enter name of cell metric to filter" help="e.g. percent.ribo or other metrics calculated using 'Add QC Metrics'"/>
d0c26c9430f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
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316 <param name="minimum" type="float" optional="true" value="" label="Minimum"/>
d0c26c9430f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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317 <param name="maximum" type="float" optional="true" value="" label="Maximum"/>
d0c26c9430f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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318 </when>
d0c26c9430f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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319 </conditional>
d0c26c9430f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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320 </when>
d0c26c9430f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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321 </conditional>
d0c26c9430f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
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322 <expand macro="inputs_common_advanced"/>
d0c26c9430f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
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323 </inputs>
d0c26c9430f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
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324 <outputs>
d0c26c9430f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
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325 <expand macro="seurat_outputs"/>
d0c26c9430f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
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326 </outputs>
d0c26c9430f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
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327 <tests>
d0c26c9430f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
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328 <test expect_num_outputs="2">
d0c26c9430f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
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329 <!-- test1: CreateSeuratObject from matrix -->
d0c26c9430f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
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330 <conditional name="method">
d0c26c9430f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
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331 <param name="method" value="CreateSeuratObject"/>
d0c26c9430f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
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332 <conditional name="input_type">
d0c26c9430f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
333 <param name="input_type" value="mtx"/>
d0c26c9430f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
334 <param name="matrix" location="https://zenodo.org/records/13732784/files/matrix.mtx"/>
d0c26c9430f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
335 <param name="gene_names" location="https://zenodo.org/records/13732784/files/genes.tsv"/>
d0c26c9430f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
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336 <param name="cell_barcodes" location="https://zenodo.org/records/13732784/files/barcodes.tsv"/>
d0c26c9430f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
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337 <param name="gene_column" value="1"/>
d0c26c9430f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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338 </conditional>
d0c26c9430f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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diff changeset
339 <conditional name="percent_mt">
d0c26c9430f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
340 <param name="percent_mt" value="true"/>
d0c26c9430f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
341 <param name="pattern" value="^Mt"/>
d0c26c9430f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
342 </conditional>
d0c26c9430f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
343 </conditional>
d0c26c9430f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
344 <section name="advanced_common">
d0c26c9430f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
345 <param name="show_log" value="true"/>
d0c26c9430f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
346 </section>
d0c26c9430f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
347 <output name="hidden_output">
d0c26c9430f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
348 <assert_contents>
d0c26c9430f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
349 <has_text_matching expression="Read10X"/>
d0c26c9430f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
350 <has_text_matching expression="CreateSeuratObject"/>
d0c26c9430f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
351 </assert_contents>
d0c26c9430f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
352 </output>
d0c26c9430f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
353 <output name="rds_out" location="https://zenodo.org/records/13732784/files/rawdata.rds" ftype="rds"/>
d0c26c9430f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
354 </test>
d0c26c9430f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
355 <test expect_num_outputs="2">
d0c26c9430f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
356 <!-- test2: CreateSeuratObject from tabular -->
d0c26c9430f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
357 <conditional name="method">
d0c26c9430f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
358 <param name="method" value="CreateSeuratObject"/>
d0c26c9430f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
359 <conditional name="input_type">
d0c26c9430f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
360 <param name="input_type" value="tab"/>
d0c26c9430f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
361 <param name="input_tab" location="https://zenodo.org/records/13732784/files/counts.tsv"/>
d0c26c9430f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
362 </conditional>
d0c26c9430f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
363 </conditional>
d0c26c9430f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
364 <section name="advanced_common">
d0c26c9430f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
365 <param name="show_log" value="true"/>
d0c26c9430f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
366 </section>
d0c26c9430f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
367 <output name="hidden_output">
d0c26c9430f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
368 <assert_contents>
d0c26c9430f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
369 <has_text_matching expression="read.table"/>
d0c26c9430f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
370 <has_text_matching expression="CreateSeuratObject"/>
d0c26c9430f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
371 </assert_contents>
d0c26c9430f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
372 </output>
d0c26c9430f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
373 <output name="rds_out" location="https://zenodo.org/records/13732784/files/rawdata2.rds" ftype="rds"/>
d0c26c9430f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
374 </test>
d0c26c9430f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
375 <test expect_num_outputs="2">
d0c26c9430f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
376 <!-- test3: CreateSeuratObject with CITE-Seq -->
d0c26c9430f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
377 <conditional name="method">
d0c26c9430f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
378 <param name="method" value="CreateSeuratObject"/>
d0c26c9430f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
379 <conditional name="input_type">
d0c26c9430f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
380 <param name="input_type" value="tab"/>
d0c26c9430f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
381 <param name="input_tab" location="https://zenodo.org/records/13732784/files/rna.tab"/>
d0c26c9430f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
382 <conditional name="citeseq">
d0c26c9430f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
383 <param name="citeseq" value="true"/>
d0c26c9430f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
384 <param name="citeseq_table" location="https://zenodo.org/records/13732784/files/adt.tab"/>
d0c26c9430f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
385 </conditional>
d0c26c9430f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
386 </conditional>
d0c26c9430f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
387 </conditional>
d0c26c9430f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
388 <param name="min_features" value=""/>
d0c26c9430f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
389 <section name="advanced_common">
d0c26c9430f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
390 <param name="show_log" value="true"/>
d0c26c9430f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
391 </section>
d0c26c9430f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
392 <output name="hidden_output">
d0c26c9430f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
393 <assert_contents>
d0c26c9430f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
394 <has_text_matching expression="read.table"/>
d0c26c9430f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
395 <has_text_matching expression="CreateSeuratObject"/>
d0c26c9430f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
396 </assert_contents>
d0c26c9430f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
397 </output>
d0c26c9430f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
398 <output name="rds_out" location="https://zenodo.org/records/13732784/files/citeseq.rds" ftype="rds"/>
d0c26c9430f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
399 </test>
d0c26c9430f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
400 <test expect_num_outputs="2">
d0c26c9430f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
401 <!-- test4: Add_QC_Metrics -->
d0c26c9430f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
402 <param name="seurat_rds" location="https://zenodo.org/records/13732784/files/rawdata.rds"/>
d0c26c9430f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
403 <conditional name="method">
d0c26c9430f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
404 <param name="method" value="Add_QC_Metrics"/>
d0c26c9430f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
405 <conditional name="match">
d0c26c9430f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
406 <param name="match" value="pattern"/>
d0c26c9430f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
407 <param name="pattern" value="^Rp"/>
d0c26c9430f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
408 </conditional>
d0c26c9430f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
409 <param name="col_name" value="percent.ribo"/>
d0c26c9430f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
410 </conditional>
d0c26c9430f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
411 <section name="advanced_common">
d0c26c9430f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
412 <param name="show_log" value="true"/>
d0c26c9430f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
413 </section>
d0c26c9430f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
414 <output name="hidden_output">
d0c26c9430f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
415 <assert_contents>
d0c26c9430f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
416 <has_text_matching expression="PercentageFeatureSet"/>
d0c26c9430f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
417 <has_text_matching expression="percent.ribo"/>
d0c26c9430f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
418 </assert_contents>
d0c26c9430f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
419 </output>
d0c26c9430f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
420 <output name="rds_out" location="https://zenodo.org/records/13732784/files/ribodata.rds" ftype="rds"/>
d0c26c9430f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
421 </test>
d0c26c9430f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
422 <test expect_num_outputs="2">
d0c26c9430f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
423 <!-- test5: FilterCells -->
d0c26c9430f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
424 <param name="seurat_rds" location="https://zenodo.org/records/13732784/files/ribodata.rds"/>
d0c26c9430f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
425 <conditional name="method">
d0c26c9430f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
426 <param name="method" value="FilterCells"/>
d0c26c9430f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
427 <param name="minimum_nCount_RNA" value="1"/>
d0c26c9430f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
428 <param name="maximum_nCount_RNA" value="20000000"/>
d0c26c9430f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
429 <conditional name="other">
d0c26c9430f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
430 <param name="other" value="true"/>
d0c26c9430f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
431 <param name="other_variable" value="percent.mt"/>
d0c26c9430f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
432 <param name="maximum" value="2"/>
d0c26c9430f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
433 </conditional>
d0c26c9430f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
434 </conditional>
d0c26c9430f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
435 <section name="advanced_common">
d0c26c9430f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
436 <param name="show_log" value="true"/>
d0c26c9430f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
437 </section>
d0c26c9430f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
438 <output name="hidden_output">
d0c26c9430f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
439 <assert_contents>
d0c26c9430f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
440 <has_text_matching expression="subset"/>
d0c26c9430f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
441 </assert_contents>
d0c26c9430f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
442 </output>
d0c26c9430f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
443 <output name="rds_out" location="https://zenodo.org/records/13732784/files/filtered.rds" ftype="rds"/>
d0c26c9430f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
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diff changeset
444 </test>
d0c26c9430f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
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diff changeset
445 </tests>
d0c26c9430f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
446 <help><![CDATA[
d0c26c9430f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
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diff changeset
447 Seurat
d0c26c9430f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
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diff changeset
448 ======
d0c26c9430f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
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diff changeset
449
1
a7af4acac32c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit 566984b588e88225f0b3f2dae88c6fd084315e7c
iuc
parents: 0
diff changeset
450 Seurat is an R package designed for QC, analysis, and exploration of single-cell RNA-seq data.
0
d0c26c9430f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
451
d0c26c9430f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
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diff changeset
452 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.
d0c26c9430f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
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diff changeset
453
1
a7af4acac32c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit 566984b588e88225f0b3f2dae88c6fd084315e7c
iuc
parents: 0
diff changeset
454 Creating a Seurat Object
0
d0c26c9430f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
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diff changeset
455 ========================
d0c26c9430f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
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diff changeset
456
1
a7af4acac32c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit 566984b588e88225f0b3f2dae88c6fd084315e7c
iuc
parents: 0
diff changeset
457 Seurat objects can be created from single cell data in matrix market or tab-delimited table formats, using the Read10X or read.table functions followed by CreateSeuratObject.
0
d0c26c9430f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
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diff changeset
458 The input should be a single cell matrix with cells as rows and genes as columns.
d0c26c9430f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
459
d0c26c9430f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
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diff changeset
460 Both RNA-seq and combined RNA and CITE-seq data can be used as inputs.
d0c26c9430f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
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diff changeset
461
1
a7af4acac32c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit 566984b588e88225f0b3f2dae88c6fd084315e7c
iuc
parents: 0
diff changeset
462 Read10X
0
d0c26c9430f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
463 ========
d0c26c9430f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
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diff changeset
464
d0c26c9430f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
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diff changeset
465 Load sparse data matrices provided by 10X genomics.
d0c26c9430f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
466
d0c26c9430f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
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diff changeset
467 More details on the `seurat documentation
d0c26c9430f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
468 <https://satijalab.org/seurat/reference/read10x>`__
d0c26c9430f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
469
d0c26c9430f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
470 read.table
d0c26c9430f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
471 ==========
d0c26c9430f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
472
1
a7af4acac32c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit 566984b588e88225f0b3f2dae88c6fd084315e7c
iuc
parents: 0
diff changeset
473 Read a tab-delimited tsv or tabular file into an RDS file as a table.
0
d0c26c9430f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
474
d0c26c9430f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
475 More details on the `R documentation
d0c26c9430f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
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diff changeset
476 <https://www.rdocumentation.org/packages/utils/versions/3.6.2/topics/read.table>`__
d0c26c9430f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
477
d0c26c9430f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
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diff changeset
478 CreateSeuratObject
d0c26c9430f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
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diff changeset
479 ==================
d0c26c9430f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
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diff changeset
480
1
a7af4acac32c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit 566984b588e88225f0b3f2dae88c6fd084315e7c
iuc
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diff changeset
481 Create a Seurat Object from raw data in RDS format.
0
d0c26c9430f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
482
d0c26c9430f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
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diff changeset
483 names.field
d0c26c9430f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
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diff changeset
484
1
a7af4acac32c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit 566984b588e88225f0b3f2dae88c6fd084315e7c
iuc
parents: 0
diff changeset
485 For the initial identity class for each cell, choose this field from the cell's name.
0
d0c26c9430f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
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diff changeset
486 E.g. If your cells are named as BARCODE_CLUSTER_CELLTYPE in the input matrix, set names.field to 3 to set the initial identities to CELLTYPE.
d0c26c9430f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
487
d0c26c9430f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
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diff changeset
488 names.delim
d0c26c9430f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
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diff changeset
489
1
a7af4acac32c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit 566984b588e88225f0b3f2dae88c6fd084315e7c
iuc
parents: 0
diff changeset
490 For the initial identity class for each cell, choose this delimiter from the cell's column name.
0
d0c26c9430f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
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diff changeset
491 E.g. If your cells are named as BARCODE-CLUSTER-CELLTYPE, set this to “-” to separate the cell name into its component parts for picking the relevant field.
d0c26c9430f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
492
d0c26c9430f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
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diff changeset
493 meta.data
d0c26c9430f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
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diff changeset
494
1
a7af4acac32c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit 566984b588e88225f0b3f2dae88c6fd084315e7c
iuc
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diff changeset
495 Additional cell-level metadata to add to the Seurat object. Should be a data.frame where the rows are cell names and the columns are additional metadata fields.
0
d0c26c9430f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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diff changeset
496 Row names in the metadata need to match the column names of the counts matrix.
d0c26c9430f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
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diff changeset
497
d0c26c9430f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
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diff changeset
498 Filtering can also be performed on:
d0c26c9430f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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diff changeset
499
1
a7af4acac32c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit 566984b588e88225f0b3f2dae88c6fd084315e7c
iuc
parents: 0
diff changeset
500 min.cells = only include features/genes detected in at least this many cells
0
d0c26c9430f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
501
1
a7af4acac32c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit 566984b588e88225f0b3f2dae88c6fd084315e7c
iuc
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diff changeset
502 min.features = only include cells where at least this many features are detected
0
d0c26c9430f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
503
d0c26c9430f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
504 Some QC metrics are added when creating a Seurat Object (nCount_RNA and nFeature_RNA).
d0c26c9430f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
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diff changeset
505 Mito percentage can optionally be calculated - it will be based on gene names starting with "MT-". If this pattern does not work for your gene names then you can use the separate 'Calculate QC Metrics' function instead.
d0c26c9430f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
506
d0c26c9430f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
507 More details on the `seurat documentation
d0c26c9430f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
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diff changeset
508 <https://satijalab.github.io/seurat-object/reference/CreateSeuratObject.html>`__
d0c26c9430f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
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509
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510 Calculate QC Metrics
d0c26c9430f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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511 ====================
d0c26c9430f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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512
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513 Calculate the percentage of all the counts belonging to a subset of the possible features for each cell. This is useful when trying to compute the percentage of transcripts that map to mitochondrial genes for example.
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514 The calculation here is simply the column sum of the matrix present in the counts slot for features belonging to the set divided by the column sum for all features times 100.
d0c26c9430f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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515
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516 Feature sets can be defined by entering a list of genes or using a shared pattern in the gene names, such as "^MT-" or "^RP[LS]" for human mitochondrial or ribosomal genes.
d0c26c9430f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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517
d0c26c9430f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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518 More details on the `seurat documentation
d0c26c9430f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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519 <https://satijalab.org/seurat/reference/percentagefeatureset>`__
d0c26c9430f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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520
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521 Filter Cells
d0c26c9430f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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522 ============
d0c26c9430f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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523
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524 Filter cells based on QC metrics.
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525
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526 nFeature_RNA = number of unique genes identified in the cell
d0c26c9430f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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527
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528 ncounts_RNA = total number of RNAs found in the cell
d0c26c9430f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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529
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530 percent.mt = percentage of mitochondrial genes in the cell
d0c26c9430f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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531
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532 More details on the `R documentation
d0c26c9430f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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533 <https://rdrr.io/r/base/subset.html>`__
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534
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535
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536 ]]></help>
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537 <expand macro="citations"/>
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538 </tool>