Mercurial > repos > iuc > seurat_integrate

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

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
author iuc
date Wed, 11 Sep 2024 10:20:51 +0000
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4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
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1 <macros>
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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2 <token name="@TOOL_VERSION@">5.0</token>
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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3 <token name="@VERSION_SUFFIX@">0</token>
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4 <token name="@PROFILE@">23.0</token>
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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5 <xml name="requirements">
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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6 <requirements>
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7 <requirement type="package" version="@TOOL_VERSION@">r-seurat</requirement>
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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8 <requirement type="package" version="1.2.1">fit-sne</requirement>
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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9 <requirement type="package" version="3.58.1">bioconductor-limma</requirement>
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10 <requirement type="package" version="1.28.0">bioconductor-mast</requirement>
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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11 <requirement type="package" version="1.42.0">bioconductor-deseq2</requirement>
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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12 <requirement type="package" version="2.1.3">r-svglite</requirement>
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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13 <requirement type="package" version="1.1">r-metap</requirement>
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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14 <requirement type="package" version="1.14.0">bioconductor-glmGamPoi</requirement>
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15 <requirement type="package" version="0.5.3">umap-learn</requirement> <!-- https://github.com/satijalab/seurat/issues/8283 -->
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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16 <requirement type="package" version="0.10.2">leidenalg</requirement>
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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17 <requirement type="package" version="1.2.0">r-harmony</requirement>
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18 <requirement type="package" version="1.18.0">bioconductor-batchelor</requirement>
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19 <requirement type="package" version="2.0.0">numpy</requirement>
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20 <requirement type="package" version="2.2.2">pandas</requirement>
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21 </requirements>
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22 </xml>
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23 <xml name="citations">
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24 <citations>
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25 <citation type="doi">10.1038/s41587-023-01767-y</citation>
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26 </citations>
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27 </xml>
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28 <xml name="sanitize_query" token_validinitial="string.printable">
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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29 <sanitizer>
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30 <valid initial="@VALIDINITIAL@">
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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31 <remove value="&apos;" />
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32 </valid>
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33 </sanitizer>
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34 </xml>
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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35 <xml name="sanitize_vectors" token_validinitial="string.digits">
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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36 <sanitizer>
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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37 <valid initial="@VALIDINITIAL@">
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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38 <add value=","/>
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39 </valid>
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40 </sanitizer>
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41 </xml>
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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42 <xml name="version_command">
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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43 <version_command><![CDATA[
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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44 echo $(R --version | grep version | grep -v GNU)", Seurat version" $(R --vanilla --slave -e "library(Seurat); cat(sessionInfo()\$otherPkgs\$DESeq2\$Version)" 2> /dev/null | grep -v -i "WARNING: ")
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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45 ]]></version_command>
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46 </xml>
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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47
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48 <token name="@CMD_imports@"><![CDATA[
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49 library(Seurat)
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50 ]]>
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51 </token>
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52 <token name="@reticulate_hack@"><![CDATA[
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53 library(reticulate)
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54 ## HACK: CI biocontainers do not contain a useable conda binary, just the env.
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55 ## see: https://github.com/galaxyproject/tools-iuc/issues/5585#issuecomment-1803773923
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56 is_biocontainer = grepl("^# cmd: /opt/conda/bin/",
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57 paste0(reticulate:::python_info_condaenv_find("/usr/local/"),
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58 "-none"))
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59 if (is_biocontainer) {
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60 ## conda detection false positive
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61 assignInNamespace("is_conda_python", function(x) FALSE, ns="reticulate")
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62 use_python("/usr/local/bin/python")
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63 } else {
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64 conda_path = Sys.getenv("CONDA_PREFIX")
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65 if (conda_path != "") {
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66 ## Active conda env found
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67 use_python(file.path(conda_path, "bin", "python3"))
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68 } else {
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69 ## Not biocontainer or conda, assume system python
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70 use_python("/usr/bin/python3")
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71 }
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72 }]]>
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73 </token>
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74 <xml name="input_rds">
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75 <param name="seurat_rds" type="data" format="rds" label="Input file with the Seurat object"/>
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76 </xml>
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77 <token name="@CMD_read_inputs@"><![CDATA[
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78 seurat_obj = readRDS('seurat.rds')
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79 ]]>
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80 </token>
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81 <token name="@CMD_read_expression_matrix@"><![CDATA[
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82 counts<-read.table("matrix.tab", header=TRUE, row.names=1, sep="\t")
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
83 ]]>]
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
84 </token>
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
85 <token name="@CMD@"><![CDATA[
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
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diff changeset
86 cp '$seurat_rds' seurat.rds &&
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
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diff changeset
87 cat '$script_file' > $hidden_output &&
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
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diff changeset
88 Rscript '$script_file' >> $hidden_output
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
89 ]]>
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
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90 </token>
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
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diff changeset
91 <xml name="inputs_common_advanced">
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
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diff changeset
92 <section name="advanced_common" title="Advanced Output" expanded="false">
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
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diff changeset
93 <param name="show_log" type="boolean" checked="false" label="Output Log?" />
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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94 </section>
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
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diff changeset
95 </xml>
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
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96 <xml name="outputs_common_advanced">
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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97 <data name="hidden_output" format="txt" label="Log file" >
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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98 <filter>advanced_common['show_log']</filter>
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
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99 </data>
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
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100 </xml>
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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101 <xml name="seurat_outputs">
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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102 <data name="rds_out" format="rds" from_work_dir="seurat.rds" label="${tool.name} (${method.method}) on ${on_string}: RDS">
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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103 <filter>method['method'] != 'Inspect'</filter>
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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104 </data>
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
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105 <expand macro="outputs_common_advanced"/>
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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106 </xml>
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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107 <token name="@CMD_rds_write_outputs@"><![CDATA[
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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108 saveRDS(seurat_obj, 'seurat.rds')
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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109 ]]>
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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110 </token>
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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111 <xml name="variable_out">
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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112 <data name="variable_tabular" format="txt" from_work_dir="variable_out.txt" label="${tool.name} (${method.method}) on ${on_string}: Top variable features list">
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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113 <filter>method['method'] == 'FindVariableFeatures' or method['method'] == 'SCTransform'</filter>
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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114 <filter>method['output_topN']['output_topN'] == 'true'</filter>
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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115 </data>
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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116 </xml>
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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117 <token name="@CMD_write_variable_tab@"><![CDATA[
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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118 write.table(top_N, 'variable_out.txt', sep= "\t", col.names = FALSE, quote = FALSE)
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
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119 ]]>
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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120 </token>
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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121 <xml name="markers_out">
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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122 <data name="markers_tabular" format="csv" from_work_dir="markers_out.csv" label="${tool.name} (${method.method}) on ${on_string}: Markers list">
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
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diff changeset
123 <filter>method['method'] == 'FindAllMarkers' or method['method'] == 'FindMarkers' or method['method'] == 'FindConservedMarkers'</filter>
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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124 </data>
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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125 </xml>
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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126 <token name="@CMD_write_markers_tab@"><![CDATA[
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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127 write.csv(seurat_obj, 'markers_out.csv', quote = FALSE)
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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128 ]]>
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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129 </token>
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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130 <xml name="print_top_pcs">
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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131 <data name="top_pcs" format="txt" from_work_dir="print_pcs.txt" label="${tool.name} Print PCs on ${on_string}">
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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diff changeset
132 <filter>method['method'] == 'RunPCA' and method['print_pcs']['print_pcs'] == 'true'</filter>
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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133 </data>
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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134 </xml>
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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135 <xml name="inspect_out">
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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136 <data name="inspect_tabular" format="tabular" from_work_dir="inspect_out.tab" label="${tool.name} Inspect (${method.inspect.inspect}) on ${on_string}">
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
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diff changeset
137 <filter>method['method'] == 'Inspect' and method['inspect']['inspect'] != 'General'</filter>
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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138 </data>
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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diff changeset
139 <data name="inspect_general" format="txt" from_work_dir="inspect.txt" label="${tool.name} Inspect General on ${on_string}">
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
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diff changeset
140 <filter>method['method'] == 'Inspect' and method['inspect']['inspect'] == 'General'</filter>
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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141 </data>
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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142 </xml>
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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143 <token name="@CMD_inspect_rds_outputs@"><![CDATA[
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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diff changeset
144 write.table(inspect, 'inspect_out.tab', sep="\t", col.names = col.names, row.names = row.names, quote = FALSE)
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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145 ]]>
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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146 </token>
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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147 <xml name="plot_out">
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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148 <data name="plot_out_png" format="png" from_work_dir="plot.png" label="${tool.name} (${method.method}) on ${on_string}: png plot">
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
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149 <filter>plot_format == 'png'</filter>
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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150 </data>
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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diff changeset
151 <data name="plot_out_pdf" format="pdf" from_work_dir="plot.pdf" label="${tool.name} (${method.method}) on ${on_string}: pdf plot">
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
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diff changeset
152 <filter>plot_format == 'pdf'</filter>
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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153 </data>
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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154 <data name="plot_out_svg" format="svg" from_work_dir="plot.svg" label="${tool.name} (${method.method}) on ${on_string}: svg plot">
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
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155 <filter>plot_format == 'svg'</filter>
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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156 </data>
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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157 <data name="plot_out_jpeg" format="jpeg" from_work_dir="plot.jpeg" label="${tool.name} (${method.method}) on ${on_string}: jpeg plot">
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
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diff changeset
158 <filter>plot_format == 'jpeg'</filter>
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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159 </data>
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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diff changeset
160 <data name="plot_out_tex" format="tex" from_work_dir="plot.tex" label="${tool.name} (${method.method}) on ${on_string}: tex plot">
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
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diff changeset
161 <filter>plot_format == 'tex'</filter>
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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162 </data>
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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diff changeset
163 <data name="plot_out_tiff" format="tiff" from_work_dir="plot.tiff" label="${tool.name} (${method.method}) on ${on_string}: tiff plot">
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
164 <filter>plot_format == 'tiff'</filter>
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
165 </data>
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
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diff changeset
166 <data name="plot_out_eps" format="eps" from_work_dir="plot.eps" label="${tool.name} (${method.method}) on ${on_string}: eps plot">
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
167 <filter>plot_format == 'eps'</filter>
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
168 </data>
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
169 </xml>
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
170 <xml name="param_eps" tokens="eps_value">
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
171 <param argument="eps" type="float" value="@EPS_VALUE@" label="Small number to avoid numerical errors"/>
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
172 </xml>
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
173 <xml name="valid_name">
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
174 <validator type="regex" message="Please only use letters, numbers, or _ - .">^[\w\-.]+$</validator>
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
175 </xml>
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
176 <xml name="valid_reduction_key">
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
177 <validator type="regex" message="Please only use letters and _">^[A-Za-z_]+$</validator>
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
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diff changeset
178 </xml>
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
179 <xml name="valid_list">
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
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diff changeset
180 <validator type="regex" message="Please only use letters, numbers, or _ - . ,">^[\w\-., ]+$</validator>
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
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181 </xml>
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
182 <xml name="valid_cell_name">
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
183 <validator type="regex" message="Please only use letters, numbers, or punctuation marks">^[\w[:punct:]]+$</validator>
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
184 </xml>
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
185 <xml name="valid_cell_list">
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
186 <validator type="regex" message="Please only use letters, numbers, or punctuation marks">^[\w[:punct:]]+$</validator>
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
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diff changeset
187 </xml>
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
188 <xml name="select_assay">
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
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189 <param argument="assay" type="text" optional="true" value="" label="Name of assay to use" help="leave blank to use default assay">
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
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diff changeset
190 <expand macro="valid_name"/>
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
191 </param>
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
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diff changeset
192 </xml>
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
193 <xml name="select_assay_RNA">
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
194 <param argument="assay" type="text" value="RNA" label="Name of assay to use">
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
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diff changeset
195 <expand macro="valid_name"/>
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
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diff changeset
196 </param>
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
197 </xml>
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
198 <xml name="select_slot_data">
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
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diff changeset
199 <param argument="slot" type="select" label="Slot to pull data from">
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
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200 <option value="counts">counts</option>
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
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diff changeset
201 <option value="data" selected="true">data</option>
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
202 <option value="scale.data">scale.data</option>
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
203 <option value="raw.data">raw.data</option>
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
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diff changeset
204 </param>
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
205 </xml>
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
206 <xml name="select_slot_scale">
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
207 <param argument="slot" type="select" label="Slot to pull data from">
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
208 <option value="counts">counts</option>
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
209 <option value="data">data</option>
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
210 <option value="scale.data" selected="true">scale.data</option>
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
211 <option value="raw.data">raw.data</option>
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
212 </param>
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
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diff changeset
213 </xml>
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
214 <xml name="select_slot_counts">
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
215 <param argument="slot" type="select" label="Slot to pull data from">
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
216 <option value="counts" selected="true">counts</option>
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
217 <option value="data">data</option>
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
218 <option value="scale.data">scale.data</option>
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
219 <option value="raw.data">raw.data</option>
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
220 </param>
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
221 </xml>
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
222 <xml name="select_layer">
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
223 <param argument="layer" type="text" optional="true" value="" label="Layer to pull data from" help="leave blank to use default">
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
224 <expand macro="valid_name"/>
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
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diff changeset
225 </param>
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
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diff changeset
226 </xml>
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
227 <xml name="select_reduction_pca">
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
228 <param argument="reduction" type="text" value="pca" label="Name of reduction to use" help="default is pca">
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
229 <expand macro="valid_name"/>
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
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diff changeset
230 </param>
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
231 </xml>
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
232 <xml name="select_reduction_umap">
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
233 <param argument="reduction" type="text" value="umap" label="Name of reduction to use" help="first defaults to umap, then tsne, then pca">
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
234 <expand macro="valid_name"/>
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
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diff changeset
235 </param>
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
236 </xml>
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
237 <xml name="set_topN">
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
238 <param name="topN" type="integer" value="10" label="Number to show"/>
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
239 </xml>
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
240 <xml name="set_dims">
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
241 <param argument="dims" type="integer" optional="true" value="10" label="Number of dimensions from reduction to use as input"/>
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
242 </xml>
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
243 <xml name="normalize">
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
244 <conditional name="normalization_method">
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
245 <param name="normalization_method" type="select" label="Method for normalization" help="(normalization.method)">
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
246 <option value="LogNormalize" selected="true">LogNormalize</option>
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
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247 <option value="CLR">CLR</option>
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248 <option value="RC">RC</option>
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249 </param>
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
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250 <when value="LogNormalize"></when>
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
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diff changeset
251 <when value="CLR">
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
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252 <param argument="margin" type="select" checked="true" label="Normalize across features (1) or cells (2)">
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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253 <option value="1" selected="true">features</option>
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
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254 <option value="2">cells</option>
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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255 </param>
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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256 </when>
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
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257 <when value="RC"></when>
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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258 </conditional>
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
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259 <param name="scale_factor" type="integer" value="10000" label="Set scale factor for normalization" help="(scale.factor)"/>
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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260 <param name="block_size" type="integer" optional="true" value="" label="Number of cells to run in each block" help="(block.size)"/>
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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261 </xml>
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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262 <xml name="integration_inputs">
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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263 <param argument="dims" type="integer" value="30" label="Number of dimensions from reduction to use for integration"/>
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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264 <param name="dims_to_integrate" type="integer" optional="true" value="" label="Number of dimensions to return integrated values for" help="(dims.to.integrate)"/>
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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265 <param name="k_weight" type="integer" value="100" label="Number of neighbors to consider when weighting anchors" help="(k.weight)"/>
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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266 <param name="weight_reduction" type="text" optional="true" value="" label="Name of reduction(s) to use for calculating anchor weights" help="leave blank to use full corrected space (weight.reduction)">
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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267 <expand macro="valid_list"/>
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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268 </param>
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269 <param name="sd_weight" type="float" value="1" label="Controls bandwidth of Gaussian kernel for weighting"/>
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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270 <param name="preserve_order" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="false" label="Preserve order" help="do not reorder objects based on size for each pairwise integration (preserve.order)"/>
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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271 </xml>
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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272 <xml name="markers_inputs">
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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273 <param argument="features" type="data" format="txt,tabular" optional="true" value="" label="Features to test" help="text file with one feature on each line, leave empty to use all genes"/>
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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274 <param name="logfc_threshold" type="float" value="0.1" label="Minimum log-fold difference to test" help="(logfc.threshold)"/>
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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275 <conditional name="test_use">
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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276 <param name="test_use" type="select" label="Select test to run" help="(test.use)">
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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277 <option value="wilcox" selected="true">wilcox</option>
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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278 <option value="wilcox_limma">wilcox_limma</option>
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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279 <option value="bimod">bimod</option>
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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280 <option value="roc">roc</option>
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
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281 <option value="t">t</option>
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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282 <option value="negbinom">negbinom</option>
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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283 <option value="poisson">poisson</option>
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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284 <option value="LR">LR</option>
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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285 <option value="MAST">MAST</option>
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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286 <option value="DESeq2">DESeq2</option>
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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287 </param>
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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288 <when value="wilcox">
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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289 <expand macro="select_slot_data"/>
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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290 </when>
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
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291 <when value="wilcox_limma">
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
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292 <expand macro="select_slot_data"/>
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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293 </when>
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
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294 <when value="bimod">
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
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295 <expand macro="select_slot_data"/>
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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296 </when>
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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297 <when value="roc">
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
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298 <expand macro="select_slot_data"/>
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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299 <param name="return_thresh" type="float" value="0.01" min="0.0" max="1.0" label="Only return markers with a p-value below or power above this threshold" help="(return.thresh)"/>
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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300 </when>
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
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diff changeset
301 <when value="t">
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
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302 <expand macro="select_slot_data"/>
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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303 </when>
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
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304 <when value="negbinom">
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
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305 <expand macro="select_slot_counts"/>
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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306 <param name="latent_vars" type="text" optional="true" value="" label="Select variables to test" help="(latent.vars)"/>
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
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307 <param name="min_cells_feature" type="integer" value="3" label="Minimum number of cells expressing the feature in at least one cluster" help="(min.cells.feature)"/>
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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308 </when>
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
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diff changeset
309 <when value="poisson">
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
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310 <expand macro="select_slot_counts"/>
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
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diff changeset
311 <param name="latent_vars" type="text" optional="true" value="" label="Select variables to test" help="(latent.vars)"/>
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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312 <param name="min_cells_feature" type="integer" value="3" label="Minimum number of cells expressing the feature in at least one cluster" help="(min.cells.feature)"/>
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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313 </when>
4341b8ff2a46 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="LR">
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
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315 <expand macro="select_slot_data"/>
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
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316 <param name="latent_vars" type="text" optional="true" value="" label="Select variables to test" help="(latent.vars)"/>
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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317 </when>
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
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318 <when value="MAST">
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
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319 <expand macro="select_slot_data"/>
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
320 <param name="latent_vars" type="text" optional="true" value="" label="Select variables to test" help="(latent.vars)"/>
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
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321 </when>
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
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322 <when value="DESeq2">
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
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323 <expand macro="select_slot_counts"/>
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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324 </when>
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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325 </conditional>
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
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326 </xml>
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
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327 <xml name="advanced_markers_inputs">
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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328 <expand macro="select_assay"/>
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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diff changeset
329 <param name="fc_name" type="text" optional="true" value="" label="Choose a name for the fold change, average difference, or custom function column" help="(fc.name)">
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
330 <expand macro="valid_name"/>
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
331 </param>
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
332 <param name="min_pct" type="float" value="0.01" min="0" max="100" label="Minimum percentage of cells genes must be present in to be tested" help="(min.pct)"/>
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
333 <param name="min_diff_pct" type="float" optional="true" value="" label="Minimum difference in percentage of expression between groups for genes to be tested" help="defaults to -Inf (min.diff.pct)"/>
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
334 <param name="only_pos" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="false" label="Only return positive markers" help="(only.pos)"/>
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
335 <param name="max_cells_per_ident" type="integer" optional="true" value="" label="Downsample each identity class to a max number of cells" help="defaults to Inf for no downsampling (max.cells.per.ident)"/>
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
336 <param name="random_seed" type="integer" optional = "true" value="1" label="Set a random seed for downsampling" help="(random.seed)"/>
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
337 <param name="min_cells_group" type="integer" value="3" label="Minimum number of cells in one group" help="(min.cells.group)"/>
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
338 <param argument="densify" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="false" label="Convert to dense matrix before running DE test"/>
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
339 </xml>
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
340 <xml name="plot_types">
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
341 <param name="plot_format" type="select" label="Format of plot to produce">
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
342 <option value="png">png</option>
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
343 <option value="pdf">pdf</option>
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
344 <option value="svg">svg</option>
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
345 <option value="jpeg">jpeg</option>
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
346 <option value="tex">tex</option>
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
347 <option value="tiff">tiff</option>
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
348 <option value="eps">eps</option>
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
349 </param>
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
350 </xml>
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
351 <xml name="plot_sizes">
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
352 <conditional name="resize">
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
353 <param name="resize" type="select" label="Change size of plot">
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
354 <option value="false" selected="true">No</option>
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
355 <option value="true">Yes</option>
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
356 </param>
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
357 <when value="false"></when>
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
358 <when value="true">
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
359 <param argument="width" type="integer" value="2100" label="Width of plot in pixels"/>
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
360 <param argument="height" type="integer" value="2100" label="Height of plot in pixels"/>
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
361 </when>
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
362 </conditional>
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
363 </xml>
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
364 <xml name="plot_cols">
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
365 <param argument="cols" type="text" optional="true" value="" label="Colours to use for plotting" help="comma separated list">
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
366 <expand macro="valid_list"/>
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
367 </param>
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
368 </xml>
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
369 <xml name="plot_log_scale">
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
370 <param argument="log" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="false" label="Plot on a log scale"/>
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
371 </xml>
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
372 <xml name="plot_2_dims">
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
373 <param name="dims_1" type="integer" value="1" label="Dimension to plot on x axis"/>
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
374 <param name="dims_2" type="integer" value="2" label="Dimension to plot on y axis"/>
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
375 </xml>
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
376 <xml name="plot_projected_and_balanced">
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
377 <param argument="projected" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="false" label="Use reduction values for full dataset" help="i.e. projected dimensional reduction values"/>
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
378 <param argument="balanced" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="false" label="Return an equal number of genes with + and - scores"/>
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
379 </xml>
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
380 <xml name="plot_disp_min_max">
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
381 <param name="disp_min" type="float" optional="true" value="-2.5" label="Minimum display value" help="all values below are clipped (disp.min)"/>
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
382 <param name="disp_max" type="float" optional="true" value="" label="Maximum display value" help="all values above are clipped. Defaults to 2.5 if slot is scale.data, otherwise defaults to 6 (disp.max)"/>
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
383 </xml>
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
384 <xml name="plot_shuffle_and_seed">
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
385 <conditional name="shuffle">
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
386 <param argument="shuffle" type="select" label="Randomly shuffle order of points" help="can help with crowded plots if points of interest are hidden">
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
387 <option value="TRUE">Yes</option>
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
388 <option value="FALSE" selected="true">No</option>
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
389 </param>
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
390 <when value="TRUE">
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
391 <param argument="seed" type="integer" value="1" label="Set random seed for shuffling"/>
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
392 </when>
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
393 <when value="FALSE"></when>
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
394 </conditional>
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
395 </xml>
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
396 <xml name="plot_order">
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
397 <param argument="order" type="text" optional="true" value="" label="Specify the order of plotting for the idents" help="a full comma-separated list or the ident to be plotted last on the top">
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
398 <expand macro="valid_list"/>
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
399 </param>
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
400 </xml>
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
401 <xml name="plot_group_by">
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
402 <param name="group_by" type="text" optional="true" value="" label="Factor to group cells by" help="(group.by)"/>
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
403 </xml>
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
404 <xml name="plot_split_by">
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
405 <param name="split_by" type="text" optional="true" value="" label="Factor or identity to split the plot by" help="(split.by)"/>
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
406 </xml>
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
407 <xml name="plot_alpha">
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
408 <param argument="alpha" type="integer" value="1" label="Alpha value for points"/>
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
409 </xml>
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
410 <xml name="plot_pt_size">
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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411 <param name="pt_size" type="float" optional="true" value="" label="Point size for plot" help="(pt.size)"/>
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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412 </xml>
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
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413 <xml name="plot_smooth">
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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414 <param argument="smooth" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="false" label="Smooth the graph"/>
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
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415 </xml>
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
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416 <xml name="plot_ncol">
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
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417 <param argument="ncol" type="integer" optional="true" value="" label="Number of columns to display"/>
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
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418 </xml>
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
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419 <xml name="raster_select">
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
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420 <conditional name="raster">
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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421 <param argument="raster" type="select" label="Convert points to raster format" help="NULL will automatically use raster if more than 100,000 points plotted">
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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422 <option value="NULL" selected="true">NULL</option>
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
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423 <option value="TRUE">TRUE</option>
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
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424 <option value="FALSE">FALSE</option>
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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425 </param>
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
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426 <when value="NULL"></when>
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
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427 <when value="TRUE">
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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428 <param name="raster_x" type="integer" value="512" label="Horizontal length of raster plot (pixels)"/>
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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429 <param name="raster_y" type="integer" value="512" label="Vertical height of raster plot (pixels)"/>
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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430 </when>
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
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431 <when value="FALSE"></when>
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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432 </conditional>
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
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433 </xml>
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
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434 <xml name="raster_boolean">
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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435 <param argument="raster" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="true" label="Convert to raster format"/>
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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436 </xml>
4341b8ff2a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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437 </macros>