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annotate seurat.xml @ 15:fab6ff46e019 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit b437a46efb50e543b6d7c9988f954efe2caa9046
author iuc
date Fri, 07 Jul 2023 01:43:02 +0000
parents c0fd285eb553
children
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rev   line source
15
fab6ff46e019 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit b437a46efb50e543b6d7c9988f954efe2caa9046
iuc
parents: 14
diff changeset
1 <tool id="seurat" name="Seurat" version="@TOOL_VERSION@+galaxy1">
0
8d8412d35247 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit 24c0223b9baa6d59bba381ef94f7e77b1c204d80
iuc
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2 <description>- toolkit for exploration of single-cell RNA-seq data</description>
2
321bdd834266 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit 3cf715ec11e2c9944f46572e324e5b2db5aa151f"
iuc
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3 <macros>
15
fab6ff46e019 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit b437a46efb50e543b6d7c9988f954efe2caa9046
iuc
parents: 14
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4 <import>macros.xml</import>
2
321bdd834266 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit 3cf715ec11e2c9944f46572e324e5b2db5aa151f"
iuc
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5 </macros>
15
fab6ff46e019 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit b437a46efb50e543b6d7c9988f954efe2caa9046
iuc
parents: 14
diff changeset
6 <expand macro="requirements"/>
0
8d8412d35247 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit 24c0223b9baa6d59bba381ef94f7e77b1c204d80
iuc
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7 <command detect_errors="exit_code"><![CDATA[
15
fab6ff46e019 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit b437a46efb50e543b6d7c9988f954efe2caa9046
iuc
parents: 14
diff changeset
8 #if $function.function_select == "base":
fab6ff46e019 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit b437a46efb50e543b6d7c9988f954efe2caa9046
iuc
parents: 14
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9 Rscript -e "library(\"rmarkdown\"); render(\"$__tool_directory__/Seurat.R\",
fab6ff46e019 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit b437a46efb50e543b6d7c9988f954efe2caa9046
iuc
parents: 14
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10 params = list(counts = \"${function.input}\",
fab6ff46e019 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit b437a46efb50e543b6d7c9988f954efe2caa9046
iuc
parents: 14
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11 min_cells = \"${function.min_cells}\",
fab6ff46e019 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit b437a46efb50e543b6d7c9988f954efe2caa9046
iuc
parents: 14
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12 min_genes = \"${function.min_genes}\",
fab6ff46e019 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit b437a46efb50e543b6d7c9988f954efe2caa9046
iuc
parents: 14
diff changeset
13 low_thresholds = \"${function.low_thresholds}\",
fab6ff46e019 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit b437a46efb50e543b6d7c9988f954efe2caa9046
iuc
parents: 14
diff changeset
14 high_thresholds = \"${function.high_thresholds}\",
fab6ff46e019 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit b437a46efb50e543b6d7c9988f954efe2caa9046
iuc
parents: 14
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15 vlnfeat = \"${function.vlnfeat}\",
fab6ff46e019 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit b437a46efb50e543b6d7c9988f954efe2caa9046
iuc
parents: 14
diff changeset
16 norm_out = \"${function.norm_file}\",
fab6ff46e019 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit b437a46efb50e543b6d7c9988f954efe2caa9046
iuc
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17 #if $function.variable_continue.variable_continue == "yes":
fab6ff46e019 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit b437a46efb50e543b6d7c9988f954efe2caa9046
iuc
parents: 14
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18 featplot = \"${function.variable_continue.featplot}\",
fab6ff46e019 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit b437a46efb50e543b6d7c9988f954efe2caa9046
iuc
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diff changeset
19 variable_out = \"${function.variable_continue.var_file}\",
fab6ff46e019 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit b437a46efb50e543b6d7c9988f954efe2caa9046
iuc
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20 #if $function.variable_continue.pca_continue.pca_continue == "yes":
fab6ff46e019 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit b437a46efb50e543b6d7c9988f954efe2caa9046
iuc
parents: 14
diff changeset
21 numPCs = \"${function.variable_continue.pca_continue.num_PCs}\",
fab6ff46e019 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit b437a46efb50e543b6d7c9988f954efe2caa9046
iuc
parents: 14
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22 PCplots = \"${function.variable_continue.pca_continue.pc_plots}\",
fab6ff46e019 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit b437a46efb50e543b6d7c9988f954efe2caa9046
iuc
parents: 14
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23 pca_out = \"${function.variable_continue.pca_continue.pca_file}\",
fab6ff46e019 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit b437a46efb50e543b6d7c9988f954efe2caa9046
iuc
parents: 14
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24 #if $function.variable_continue.pca_continue.clusters_continue.clusters_continue == "yes":
fab6ff46e019 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit b437a46efb50e543b6d7c9988f954efe2caa9046
iuc
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25 perplexity = \"${function.variable_continue.pca_continue.clusters_continue.perplexity}\",
fab6ff46e019 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit b437a46efb50e543b6d7c9988f954efe2caa9046
iuc
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26 resolution = \"${function.variable_continue.pca_continue.clusters_continue.resolution}\",
fab6ff46e019 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit b437a46efb50e543b6d7c9988f954efe2caa9046
iuc
parents: 14
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27 nmds = \"${function.variable_continue.pca_continue.clusters_continue.nmds}\",
fab6ff46e019 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit b437a46efb50e543b6d7c9988f954efe2caa9046
iuc
parents: 14
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28 clusters_out = \"${function.variable_continue.pca_continue.clusters_continue.clusters_file}\",
fab6ff46e019 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit b437a46efb50e543b6d7c9988f954efe2caa9046
iuc
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29 #if $function.variable_continue.pca_continue.clusters_continue.markers_continue.markers_continue == "yes":
fab6ff46e019 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit b437a46efb50e543b6d7c9988f954efe2caa9046
iuc
parents: 14
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30 min_pct = \"${function.variable_continue.pca_continue.clusters_continue.markers_continue.min_pct}\",
fab6ff46e019 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit b437a46efb50e543b6d7c9988f954efe2caa9046
iuc
parents: 14
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31 logfc_threshold = \"${function.variable_continue.pca_continue.clusters_continue.markers_continue.logfc_threshold}\",
fab6ff46e019 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit b437a46efb50e543b6d7c9988f954efe2caa9046
iuc
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32 heatmaps = \"${function.variable_continue.pca_continue.clusters_continue.markers_continue.heatmaps}\",
fab6ff46e019 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit b437a46efb50e543b6d7c9988f954efe2caa9046
iuc
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33 markers_out = \"${function.variable_continue.pca_continue.clusters_continue.markers_continue.markers_file}\",
fab6ff46e019 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit b437a46efb50e543b6d7c9988f954efe2caa9046
iuc
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34 end_step="\"5"\",
fab6ff46e019 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit b437a46efb50e543b6d7c9988f954efe2caa9046
iuc
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35 #else:
fab6ff46e019 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit b437a46efb50e543b6d7c9988f954efe2caa9046
iuc
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36 end_step="\"4"\",
fab6ff46e019 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit b437a46efb50e543b6d7c9988f954efe2caa9046
iuc
parents: 14
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37 #end if
fab6ff46e019 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit b437a46efb50e543b6d7c9988f954efe2caa9046
iuc
parents: 14
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38 #else:
fab6ff46e019 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit b437a46efb50e543b6d7c9988f954efe2caa9046
iuc
parents: 14
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39 end_step="\"3"\",
fab6ff46e019 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit b437a46efb50e543b6d7c9988f954efe2caa9046
iuc
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40 #end if
fab6ff46e019 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit b437a46efb50e543b6d7c9988f954efe2caa9046
iuc
parents: 14
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41 #else:
fab6ff46e019 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit b437a46efb50e543b6d7c9988f954efe2caa9046
iuc
parents: 14
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42 end_step="\"2"\",
fab6ff46e019 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit b437a46efb50e543b6d7c9988f954efe2caa9046
iuc
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43 #end if
fab6ff46e019 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit b437a46efb50e543b6d7c9988f954efe2caa9046
iuc
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44 #else:
fab6ff46e019 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit b437a46efb50e543b6d7c9988f954efe2caa9046
iuc
parents: 14
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45 end_step="\"1"\",
fab6ff46e019 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit b437a46efb50e543b6d7c9988f954efe2caa9046
iuc
parents: 14
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46 #end if
fab6ff46e019 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit b437a46efb50e543b6d7c9988f954efe2caa9046
iuc
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47 varstate = \"${meta.varstate}\",
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48 warn = \"${meta.warn}\",
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fab6ff46e019 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit b437a46efb50e543b6d7c9988f954efe2caa9046
iuc
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49 showcode = \"${meta.showcode}\"),
fab6ff46e019 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit b437a46efb50e543b6d7c9988f954efe2caa9046
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50 intermediates_dir = \".\",
fab6ff46e019 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit b437a46efb50e543b6d7c9988f954efe2caa9046
iuc
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51 output_format = html_document(),
fab6ff46e019 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit b437a46efb50e543b6d7c9988f954efe2caa9046
iuc
parents: 14
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52 output_dir = \".\",
fab6ff46e019 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit b437a46efb50e543b6d7c9988f954efe2caa9046
iuc
parents: 14
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53 output_file = \"out.html\")"
fab6ff46e019 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit b437a46efb50e543b6d7c9988f954efe2caa9046
iuc
parents: 14
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54 #else:
fab6ff46e019 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit b437a46efb50e543b6d7c9988f954efe2caa9046
iuc
parents: 14
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55 Rscript -e "library(\"rmarkdown\"); render(\"$__tool_directory__/citeseq_Seurat.R\",
fab6ff46e019 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit b437a46efb50e543b6d7c9988f954efe2caa9046
iuc
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56 params = list(rna = \"${function.rna}\",
fab6ff46e019 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit b437a46efb50e543b6d7c9988f954efe2caa9046
iuc
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57 prot = \"${function.prot}\",
fab6ff46e019 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit b437a46efb50e543b6d7c9988f954efe2caa9046
iuc
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58 cite_markers = \"${function.cite_markers}\",
fab6ff46e019 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit b437a46efb50e543b6d7c9988f954efe2caa9046
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59
fab6ff46e019 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit b437a46efb50e543b6d7c9988f954efe2caa9046
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60
fab6ff46e019 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit b437a46efb50e543b6d7c9988f954efe2caa9046
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61 #if $function.comparison.comparison == "yes"
fab6ff46e019 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit b437a46efb50e543b6d7c9988f954efe2caa9046
iuc
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62 comparison="\"T"\",
fab6ff46e019 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit b437a46efb50e543b6d7c9988f954efe2caa9046
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63 feat_comp=\"${function.comparison.feat_comp}\",
fab6ff46e019 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit b437a46efb50e543b6d7c9988f954efe2caa9046
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64 #else:
fab6ff46e019 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit b437a46efb50e543b6d7c9988f954efe2caa9046
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65 comparison="\"F"\",
fab6ff46e019 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit b437a46efb50e543b6d7c9988f954efe2caa9046
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66 feat_comp="\""\",
fab6ff46e019 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit b437a46efb50e543b6d7c9988f954efe2caa9046
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67 #end if
fab6ff46e019 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit b437a46efb50e543b6d7c9988f954efe2caa9046
iuc
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68 #if $function.marker_compare.marker_compare == "yes"
fab6ff46e019 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit b437a46efb50e543b6d7c9988f954efe2caa9046
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69 marker_compare="\"T"\",
fab6ff46e019 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit b437a46efb50e543b6d7c9988f954efe2caa9046
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70 top_x=\"${function.marker_compare.top_x}\",
fab6ff46e019 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit b437a46efb50e543b6d7c9988f954efe2caa9046
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71 #else:
fab6ff46e019 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit b437a46efb50e543b6d7c9988f954efe2caa9046
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72 marker_compare="\"F"\",
fab6ff46e019 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit b437a46efb50e543b6d7c9988f954efe2caa9046
iuc
parents: 14
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73 top_x="\""\",
fab6ff46e019 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit b437a46efb50e543b6d7c9988f954efe2caa9046
iuc
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74 #end if
fab6ff46e019 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit b437a46efb50e543b6d7c9988f954efe2caa9046
iuc
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75 min_cells = \"${function.min_cells}\",
fab6ff46e019 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit b437a46efb50e543b6d7c9988f954efe2caa9046
iuc
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76 min_genes = \"${function.min_genes}\",
fab6ff46e019 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit b437a46efb50e543b6d7c9988f954efe2caa9046
iuc
parents: 14
diff changeset
77 low_thresholds = \"${function.low_thresholds}\",
fab6ff46e019 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit b437a46efb50e543b6d7c9988f954efe2caa9046
iuc
parents: 14
diff changeset
78 high_thresholds = \"${function.high_thresholds}\",
fab6ff46e019 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit b437a46efb50e543b6d7c9988f954efe2caa9046
iuc
parents: 14
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79 vlnfeat = \"${function.vlnfeat}\",
fab6ff46e019 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit b437a46efb50e543b6d7c9988f954efe2caa9046
iuc
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diff changeset
80 norm_out = \"${function.norm_file}\",
fab6ff46e019 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit b437a46efb50e543b6d7c9988f954efe2caa9046
iuc
parents: 14
diff changeset
81 featplot = \"${function.featplot}\",
fab6ff46e019 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit b437a46efb50e543b6d7c9988f954efe2caa9046
iuc
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diff changeset
82 variable_out = \"${function.var_file}\",
fab6ff46e019 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit b437a46efb50e543b6d7c9988f954efe2caa9046
iuc
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83 numPCs = \"${function.num_PCs}\",
fab6ff46e019 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit b437a46efb50e543b6d7c9988f954efe2caa9046
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84 PCplots = \"${function.pc_plots}\",
fab6ff46e019 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit b437a46efb50e543b6d7c9988f954efe2caa9046
iuc
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85 pca_out = \"${function.pca_file}\",
fab6ff46e019 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit b437a46efb50e543b6d7c9988f954efe2caa9046
iuc
parents: 14
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86 perplexity = \"${function.perplexity}\",
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87 resolution = \"${function.resolution}\",
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88 nmds = \"${function.nmds}\",
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89 clusters_out = \"${function.clusters_file}\",
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90 min_pct = \"${function.min_pct}\",
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91 logfc_threshold = \"${function.logfc_threshold}\",
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92 heatmaps = \"${function.heatmaps}\",
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93 markers_out = \"${function.markers_file}\",
1
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94 varstate = \"${meta.varstate}\",
15
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95 warn = \"${meta.warn}\",
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96 showcode = \"${meta.showcode}\"),
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97 intermediates_dir = \".\",
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98 output_format = html_document(),
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99 output_dir = \".\",
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100 output_file = \"out.html\")"
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101 #end if
1
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102 ]]></command>
0
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103 <inputs>
15
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104 <conditional name="function">
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105 <param name="function_select" type="select" label="Which Seurat method should be run?">
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106 <option value="base">Base</option>
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107 <option value="cite">Cite-seq</option>
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108 </param>
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109 <when value="base">
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110 <param name="input" type="data" format="tabular,tsv" label="Counts file" help="The should be a TAB-separated count matrix with gene identifers in the first column and a header row"/>
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111 <param name="min_cells" type="integer" min="0" value="0" label="Minimum cells" help="Include genes with detected expression in at least this many cells" />
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112 <param name="min_genes" type="integer" min="0" value="0" label="Minimum genes" help="Include cells where at least this many genes are detected"/>
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113 <expand macro="norm"/>
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114 <conditional name="variable_continue">
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115 <param name="variable_continue" type="select" label="Continue workflow after Normalization step?">
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116 <option value="yes">Yes</option>
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117 <option value="no" selected="true">No</option>
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118 </param>
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119 <when value="yes">
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120 <expand macro="variable"/>
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121 <conditional name="pca_continue">
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122 <param name="pca_continue" type="select" label="Continue workflow after scaling step?">
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123 <option value="yes">Yes</option>
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124 <option value="no" selected="true">No</option>
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125 </param>
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126 <when value="yes">
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127 <expand macro="pca"/>
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128 <conditional name="clusters_continue">
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129 <param name="clusters_continue" type="select" label="Continue workflow after PCA step?">
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130 <option value="yes">Yes</option>
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131 <option value="no" selected="true">No</option>
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132 </param>
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133 <when value="yes">
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134 <expand macro="clusters"/>
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135 <conditional name="markers_continue">
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iuc
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136 <param name="markers_continue" type="select" label="Continue workflow after TSNE and UMAP step?">
fab6ff46e019 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit b437a46efb50e543b6d7c9988f954efe2caa9046
iuc
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137 <option value="yes">Yes</option>
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138 <option value="no" selected="true">No</option>
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139 </param>
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140 <when value="yes">
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141 <expand macro="markers"/>
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142 </when>
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143 <when value="no"/>
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144 </conditional>
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145 </when>
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146 <when value="no"/>
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147 </conditional>
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148 </when>
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149 <when value="no"/>
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150 </conditional>
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151 </when>
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152 <when value="no"/>
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153 </conditional>
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154 </when>
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155 <when value="cite">
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156 <param name="rna" type="data" format="tabular,tsv" label="RNA counts file" help="The should be a TAB-separated count matrix with gene identifers in the first column and a header row"/>
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157 <param name="prot" type="data" format="tabular,tsv" label="Protein counts file" help="The should be a TAB-separated count matrix with gene identifers in the first column and a header row"/>
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158 <param name="min_cells" type="integer" min="0" value="0" label="Minimum cells" help="Include genes with detected expression in at least this many cells" />
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159 <param name="min_genes" type="integer" min="0" value="0" label="Minimum genes" help="Include cells where at least this many genes are detected"/>
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diff changeset
160 <expand macro="norm"/>
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diff changeset
161 <expand macro="variable"/>
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162 <expand macro="pca"/>
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163 <expand macro="clusters"/>
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164 <expand macro="markers"/>
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165 <expand macro="cite-seq"/>
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166 </when>
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167 </conditional>
1
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168 <section name="meta" title="Output options" expanded="true">
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169 <param name="showcode" type="boolean" truevalue="T" falsevalue="F" checked="false" label="Show code alongside outputs?"/>
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170 <param name="warn" type="boolean" truevalue="T" falsevalue="F" checked="false" label="Include warnings in the output file (Yes) or pipe to stdout (No)"/>
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171 <param name="varstate" type="boolean" truevalue="T" falsevalue="F" checked="false" label="Display variable values used in code at the beginning of output file?"/>
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172 </section>
0
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173 </inputs>
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174 <outputs>
1
7319f83ae734 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit 88cf23c767023f71b4ea1e72aac568cc694cc34a"
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175 <data name="out_html" format="html" from_work_dir="out.html" label="${tool.name} on ${on_string}" />
15
fab6ff46e019 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit b437a46efb50e543b6d7c9988f954efe2caa9046
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176 <data name="norm_out" format="rdata" from_work_dir="norm_out.rds" label="${tool.name} on ${on_string}: normalization intermediate output">
fab6ff46e019 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit b437a46efb50e543b6d7c9988f954efe2caa9046
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177 <filter>@FUNCTION_BASE@</filter>
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178 <filter>function['norm_file']</filter>
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179 </data>
fab6ff46e019 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit b437a46efb50e543b6d7c9988f954efe2caa9046
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180 <data name="var_out" format="rdata" from_work_dir="var_out.rds" label="${tool.name} on ${on_string}: normalization and scaling intermediate output">
fab6ff46e019 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit b437a46efb50e543b6d7c9988f954efe2caa9046
iuc
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181 <filter>@FUNCTION_BASE@</filter>
fab6ff46e019 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit b437a46efb50e543b6d7c9988f954efe2caa9046
iuc
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182 <filter>@VARIABLE_CONTINUE@</filter>
fab6ff46e019 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit b437a46efb50e543b6d7c9988f954efe2caa9046
iuc
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183 <filter>function['variable_continue']['var_file']</filter>
fab6ff46e019 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit b437a46efb50e543b6d7c9988f954efe2caa9046
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184 </data>
fab6ff46e019 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit b437a46efb50e543b6d7c9988f954efe2caa9046
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185 <data name="pca_out" format="rdata" from_work_dir="pca_out.rds" label="${tool.name} on ${on_string}: PCA embedding data">
fab6ff46e019 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit b437a46efb50e543b6d7c9988f954efe2caa9046
iuc
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186 <filter>@FUNCTION_BASE@</filter>
fab6ff46e019 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit b437a46efb50e543b6d7c9988f954efe2caa9046
iuc
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187 <filter>@VARIABLE_CONTINUE@</filter>
fab6ff46e019 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit b437a46efb50e543b6d7c9988f954efe2caa9046
iuc
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188 <filter>@PCA_CONTINUE@</filter>
fab6ff46e019 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit b437a46efb50e543b6d7c9988f954efe2caa9046
iuc
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189 <filter>function['variable_continue']['pca_continue']['pca_file']</filter>
fab6ff46e019 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit b437a46efb50e543b6d7c9988f954efe2caa9046
iuc
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190 </data>
fab6ff46e019 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit b437a46efb50e543b6d7c9988f954efe2caa9046
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191 <data name="cluters_out" format="rdata" from_work_dir="tsne_out.rds" label="${tool.name} on ${on_string}: TSNE embedding data">
fab6ff46e019 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit b437a46efb50e543b6d7c9988f954efe2caa9046
iuc
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192 <filter>@FUNCTION_BASE@</filter>
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iuc
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193 <filter>@VARIABLE_CONTINUE@</filter>
fab6ff46e019 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit b437a46efb50e543b6d7c9988f954efe2caa9046
iuc
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194 <filter>@PCA_CONTINUE@</filter>
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iuc
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195 <filter>@CLUSTERS_CONTINUE@</filter>
fab6ff46e019 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit b437a46efb50e543b6d7c9988f954efe2caa9046
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196 <filter>function['variable_continue']['pca_continue']['clusters_continue']['clusters_file']</filter>
fab6ff46e019 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit b437a46efb50e543b6d7c9988f954efe2caa9046
iuc
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197 </data>
fab6ff46e019 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit b437a46efb50e543b6d7c9988f954efe2caa9046
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198 <data name="umap_out" format="rdata" from_work_dir="umap_out.rds" label="${tool.name} on ${on_string}: UMAP embedding data">
fab6ff46e019 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit b437a46efb50e543b6d7c9988f954efe2caa9046
iuc
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199 <filter>@FUNCTION_BASE@</filter>
fab6ff46e019 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit b437a46efb50e543b6d7c9988f954efe2caa9046
iuc
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200 <filter>@VARIABLE_CONTINUE@</filter>
fab6ff46e019 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit b437a46efb50e543b6d7c9988f954efe2caa9046
iuc
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201 <filter>@PCA_CONTINUE@</filter>
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iuc
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202 <filter>@CLUSTERS_CONTINUE@</filter>
fab6ff46e019 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit b437a46efb50e543b6d7c9988f954efe2caa9046
iuc
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203 <filter>function['variable_continue']['pca_continue']['clusters_continue']['clusters_file']</filter>
fab6ff46e019 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit b437a46efb50e543b6d7c9988f954efe2caa9046
iuc
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204 </data>
fab6ff46e019 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit b437a46efb50e543b6d7c9988f954efe2caa9046
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205 <data name="markers_out" format="rdata" from_work_dir="markers_out.rds" label="${tool.name} on ${on_string}: Markers data">
fab6ff46e019 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit b437a46efb50e543b6d7c9988f954efe2caa9046
iuc
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206 <filter>@FUNCTION_BASE@</filter>
fab6ff46e019 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit b437a46efb50e543b6d7c9988f954efe2caa9046
iuc
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207 <filter>@VARIABLE_CONTINUE@</filter>
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iuc
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208 <filter>@PCA_CONTINUE@</filter>
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iuc
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209 <filter>@CLUSTERS_CONTINUE@</filter>
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iuc
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210 <filter>@MARKERS_CONTINUE@</filter>
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iuc
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211 <filter>function['variable_continue']['pca_continue']['clusters_continue']['markers_continue']['markers_file']</filter>
fab6ff46e019 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit b437a46efb50e543b6d7c9988f954efe2caa9046
iuc
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212 </data>
fab6ff46e019 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit b437a46efb50e543b6d7c9988f954efe2caa9046
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213 <data name="markers_tabular" format="tabular" from_work_dir="markers_out.tsv" label="${tool.name} on ${on_string}: Markers list">
fab6ff46e019 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit b437a46efb50e543b6d7c9988f954efe2caa9046
iuc
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214 <filter>@FUNCTION_BASE@</filter>
fab6ff46e019 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit b437a46efb50e543b6d7c9988f954efe2caa9046
iuc
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215 <filter>@VARIABLE_CONTINUE@</filter>
fab6ff46e019 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit b437a46efb50e543b6d7c9988f954efe2caa9046
iuc
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216 <filter>@PCA_CONTINUE@</filter>
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iuc
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217 <filter>@CLUSTERS_CONTINUE@</filter>
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iuc
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218 <filter>@MARKERS_CONTINUE@</filter>
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iuc
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219 <filter>function['variable_continue']['pca_continue']['clusters_continue']['markers_continue']['markers_file']</filter>
fab6ff46e019 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit b437a46efb50e543b6d7c9988f954efe2caa9046
iuc
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220 <actions>
fab6ff46e019 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit b437a46efb50e543b6d7c9988f954efe2caa9046
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221 <action name="column_names" type="metadata" default="\\,p_val,avg_log2FC,pct.1,pct.2,p_val_adj,cluster,gene" />
fab6ff46e019 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit b437a46efb50e543b6d7c9988f954efe2caa9046
iuc
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222 <action name="column_types" type="metadata" default="str,float,float,float,float,float,int,str" />
fab6ff46e019 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit b437a46efb50e543b6d7c9988f954efe2caa9046
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223 </actions>
fab6ff46e019 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit b437a46efb50e543b6d7c9988f954efe2caa9046
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224 </data>
fab6ff46e019 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit b437a46efb50e543b6d7c9988f954efe2caa9046
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225 <!-- cite-seq out -->
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226 <data name="protmarkerst" format="tabular" from_work_dir="protein_out.tsv" label="${tool.name} cite-seq on ${on_string}: Protein markers">
fab6ff46e019 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit b437a46efb50e543b6d7c9988f954efe2caa9046
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227 <filter>@FUNCTION_CITE@</filter>
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228 <filter>function['cite_markers']</filter>
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229 <actions>
fab6ff46e019 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit b437a46efb50e543b6d7c9988f954efe2caa9046
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230 <action name="column_names" type="metadata" default="\\,p_val,avg_log2FC,pct.1,pct.2,p_val_adj,cluster,gene" />
fab6ff46e019 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit b437a46efb50e543b6d7c9988f954efe2caa9046
iuc
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231 <action name="column_types" type="metadata" default="str,float,float,float,float,float,int,str" />
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232 </actions>
fab6ff46e019 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit b437a46efb50e543b6d7c9988f954efe2caa9046
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233 </data>
fab6ff46e019 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit b437a46efb50e543b6d7c9988f954efe2caa9046
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234 <data name="rnamarkerst" format="tabular" from_work_dir="rna_out.tsv" label="${tool.name} cite-seq on ${on_string}: RNA markers">
fab6ff46e019 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit b437a46efb50e543b6d7c9988f954efe2caa9046
iuc
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235 <filter>@FUNCTION_CITE@</filter>
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236 <filter>function['cite_markers']</filter>
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237 <actions>
fab6ff46e019 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit b437a46efb50e543b6d7c9988f954efe2caa9046
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238 <action name="column_names" type="metadata" default="\\,p_val,avg_log2FC,pct.1,pct.2,p_val_adj,cluster,gene" />
fab6ff46e019 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit b437a46efb50e543b6d7c9988f954efe2caa9046
iuc
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239 <action name="column_types" type="metadata" default="str,float,float,float,float,float,int,str" />
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240 </actions>
fab6ff46e019 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit b437a46efb50e543b6d7c9988f954efe2caa9046
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241 </data>
fab6ff46e019 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit b437a46efb50e543b6d7c9988f954efe2caa9046
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242 <data name="cite_graps" format="pdf" from_work_dir="citeseq_out.pdf" label="${tool.name} cite-seq on ${on_string}: Citeseq graphs">
fab6ff46e019 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit b437a46efb50e543b6d7c9988f954efe2caa9046
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243 <filter>@FUNCTION_CITE@</filter>
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iuc
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244 <filter>function['marker_compare']['marker_compare'] == "yes"</filter>
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245 </data>
fab6ff46e019 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit b437a46efb50e543b6d7c9988f954efe2caa9046
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246 <data name="norm_cite" format="rdata" from_work_dir="norm_out.rds" label="${tool.name} cite-seq on ${on_string}: normalization intermediate output">
fab6ff46e019 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit b437a46efb50e543b6d7c9988f954efe2caa9046
iuc
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247 <filter>@FUNCTION_CITE@</filter>
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248 <filter>function['norm_file']</filter>
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249 </data>
fab6ff46e019 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit b437a46efb50e543b6d7c9988f954efe2caa9046
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250 <data name="var_cite" format="rdata" from_work_dir="var_out.rds" label="${tool.name} cite-seq on ${on_string}: normalization and scaling intermediate output">
fab6ff46e019 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit b437a46efb50e543b6d7c9988f954efe2caa9046
iuc
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251 <filter>@FUNCTION_CITE@</filter>
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iuc
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252 <filter>function['var_file']</filter>
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253 </data>
fab6ff46e019 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit b437a46efb50e543b6d7c9988f954efe2caa9046
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254 <data name="pca_cite" format="rdata" from_work_dir="pca_out.rds" label="${tool.name} cite-seq on ${on_string}: PCA embedding data">
fab6ff46e019 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit b437a46efb50e543b6d7c9988f954efe2caa9046
iuc
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255 <filter>@FUNCTION_CITE@</filter>
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256 <filter>function['pca_file']</filter>
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257 </data>
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258 <data name="cluters_cite" format="rdata" from_work_dir="tsne_out.rds" label="${tool.name} cite-seq on ${on_string}: TSNE embedding data">
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259 <filter>@FUNCTION_CITE@</filter>
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260 <filter>function['clusters_file']</filter>
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261 </data>
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262 <data name="umap_cite" format="rdata" from_work_dir="umap_out.rds" label="${tool.name} cite-seq on ${on_string}: UMAP embedding data">
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263 <filter>@FUNCTION_CITE@</filter>
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264
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265 <filter>function['clusters_file']</filter>
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266 </data>
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267 <data name="markers_cite" format="rdata" from_work_dir="markers_out.rds" label="${tool.name} cite-seq on ${on_string}: Markers data">
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268 <filter>@FUNCTION_CITE@</filter>
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269 <filter>function['markers_file']</filter>
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270 </data>
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271 <data name="markers_cite_tabular" format="tabular" from_work_dir="markers_out.tsv" label="${tool.name} cite-seq on ${on_string}: Markers list">
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272 <filter>@FUNCTION_CITE@</filter>
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273 <filter>function['markers_file']</filter>
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274 <actions>
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275 <action name="column_names" type="metadata" default="\\,p_val,avg_log2FC,pct.1,pct.2,p_val_adj,cluster,gene" />
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276 <action name="column_types" type="metadata" default="str,float,float,float,float,float,int,str" />
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277 </actions>
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278 </data>
0
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279 </outputs>
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diff changeset
280 <tests>
15
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281 <test expect_num_outputs="8">
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282 <conditional name="function">
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283 <param name="function_select" value="base"/>
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284 <param name="input" ftype="tabular" value="counts.tab.gz"/>
1
7319f83ae734 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit 88cf23c767023f71b4ea1e72aac568cc694cc34a"
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285 <param name="min_cells" value="3"/>
7319f83ae734 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit 88cf23c767023f71b4ea1e72aac568cc694cc34a"
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286 <param name="min_genes" value="200"/>
7319f83ae734 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit 88cf23c767023f71b4ea1e72aac568cc694cc34a"
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287 <param name="low_thresholds" value="1" />
7319f83ae734 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit 88cf23c767023f71b4ea1e72aac568cc694cc34a"
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288 <param name="high_thresholds" value="20000000" />
15
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289 <param name="vlnfeat" value="T"/>
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290 <param name="norm_file" value="T"/>
fab6ff46e019 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit b437a46efb50e543b6d7c9988f954efe2caa9046
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291 <conditional name="variable_continue">
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292 <param name="variable_continue" value="yes"/>
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293 <param name="featplot" value="T"/>
fab6ff46e019 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit b437a46efb50e543b6d7c9988f954efe2caa9046
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294 <param name="var_file" value="T"/>
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295 <conditional name="pca_continue">
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296 <param name="pca_continue" value="yes"/>
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297 <param name="numPCs" value="10" />
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298 <param name="pc_plots" value="T"/>
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299 <param name="pca_file" value="T"/>
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300 <conditional name="clusters_continue">
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301 <param name="clusters_continue" value="yes"/>
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302 <param name="resolution" value="0.6" />
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303 <param name="nmds" value="T"/>
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304 <param name="clusters_file" value="T"/>
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305 <conditional name="markers_continue">
fab6ff46e019 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit b437a46efb50e543b6d7c9988f954efe2caa9046
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306 <param name="markers_continue" value="yes"/>
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307 <param name="min_pct" value="0.25" />
fab6ff46e019 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit b437a46efb50e543b6d7c9988f954efe2caa9046
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308 <param name="logfc_threshold" value="0.25" />
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309 <param name="heatmaps" value="T"/>
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310 <param name="markers_file" value="T"/>
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311 </conditional>
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312 </conditional>
fab6ff46e019 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit b437a46efb50e543b6d7c9988f954efe2caa9046
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313 </conditional>
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314 </conditional>
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315 </conditional>
1
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316 <section name="meta">
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317 <param name="showcode" value="T"/>
7319f83ae734 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit 88cf23c767023f71b4ea1e72aac568cc694cc34a"
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318 <param name="warn" value="F"/>
7319f83ae734 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit 88cf23c767023f71b4ea1e72aac568cc694cc34a"
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319 <param name="varstate" value="F"/>
7319f83ae734 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit 88cf23c767023f71b4ea1e72aac568cc694cc34a"
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320 </section>
9
c4db6ec33fec "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit 7681c9101062f58ac4eb296a98b1644d4ed2340a"
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321 <output name="out_html" ftype="html">
c4db6ec33fec "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit 7681c9101062f58ac4eb296a98b1644d4ed2340a"
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322 <assert_contents>
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323 <has_text text="Seurat Analysis" />
c4db6ec33fec "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit 7681c9101062f58ac4eb296a98b1644d4ed2340a"
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324 <has_text text="Performed using Galaxy" />
c4db6ec33fec "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit 7681c9101062f58ac4eb296a98b1644d4ed2340a"
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325 <has_text text="img src=&quot;data:image/png;base64" />
c4db6ec33fec "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit 7681c9101062f58ac4eb296a98b1644d4ed2340a"
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326 </assert_contents>
c4db6ec33fec "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit 7681c9101062f58ac4eb296a98b1644d4ed2340a"
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327 </output>
15
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328 <output name="markers_tabular" file="markers.tsv" compare="sim_size" delta="500"/>
0
8d8412d35247 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit 24c0223b9baa6d59bba381ef94f7e77b1c204d80
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329 </test>
15
fab6ff46e019 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit b437a46efb50e543b6d7c9988f954efe2caa9046
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diff changeset
330 <test expect_num_outputs="1">
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diff changeset
331 <!-- test perplexity and output filters -->
fab6ff46e019 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit b437a46efb50e543b6d7c9988f954efe2caa9046
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diff changeset
332 <conditional name="function">
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diff changeset
333 <param name="function_select" value="base"/>
fab6ff46e019 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit b437a46efb50e543b6d7c9988f954efe2caa9046
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diff changeset
334 <param name="input" ftype="tabular" value="counts.tab.gz"/>
6
764f076e9d52 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit e8eeff2efea68e1e5bc697d0ff6a5808cd978db2"
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diff changeset
335 <param name="min_cells" value="3"/>
764f076e9d52 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit e8eeff2efea68e1e5bc697d0ff6a5808cd978db2"
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336 <param name="min_genes" value="200"/>
764f076e9d52 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit e8eeff2efea68e1e5bc697d0ff6a5808cd978db2"
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337 <param name="low_thresholds" value="1" />
764f076e9d52 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit e8eeff2efea68e1e5bc697d0ff6a5808cd978db2"
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338 <param name="high_thresholds" value="20000000" />
15
fab6ff46e019 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit b437a46efb50e543b6d7c9988f954efe2caa9046
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diff changeset
339 <param name="vlnfeat" value="T"/>
fab6ff46e019 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit b437a46efb50e543b6d7c9988f954efe2caa9046
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diff changeset
340 <param name="norm_file" value="F"/>
fab6ff46e019 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit b437a46efb50e543b6d7c9988f954efe2caa9046
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diff changeset
341 <conditional name="variable_continue">
fab6ff46e019 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit b437a46efb50e543b6d7c9988f954efe2caa9046
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342 <param name="variable_continue" value="yes"/>
fab6ff46e019 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit b437a46efb50e543b6d7c9988f954efe2caa9046
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diff changeset
343 <param name="featplot" value="T"/>
fab6ff46e019 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit b437a46efb50e543b6d7c9988f954efe2caa9046
iuc
parents: 14
diff changeset
344 <param name="var_file" value="F"/>
fab6ff46e019 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit b437a46efb50e543b6d7c9988f954efe2caa9046
iuc
parents: 14
diff changeset
345 <conditional name="pca_continue">
fab6ff46e019 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit b437a46efb50e543b6d7c9988f954efe2caa9046
iuc
parents: 14
diff changeset
346 <param name="pca_continue" value="yes"/>
fab6ff46e019 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit b437a46efb50e543b6d7c9988f954efe2caa9046
iuc
parents: 14
diff changeset
347 <param name="numPCs" value="10" />
fab6ff46e019 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit b437a46efb50e543b6d7c9988f954efe2caa9046
iuc
parents: 14
diff changeset
348 <param name="pc_plots" value="T"/>
fab6ff46e019 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit b437a46efb50e543b6d7c9988f954efe2caa9046
iuc
parents: 14
diff changeset
349 <param name="pca_file" value="F"/>
fab6ff46e019 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit b437a46efb50e543b6d7c9988f954efe2caa9046
iuc
parents: 14
diff changeset
350 <conditional name="clusters_continue">
fab6ff46e019 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit b437a46efb50e543b6d7c9988f954efe2caa9046
iuc
parents: 14
diff changeset
351 <param name="clusters_continue" value="yes"/>
fab6ff46e019 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit b437a46efb50e543b6d7c9988f954efe2caa9046
iuc
parents: 14
diff changeset
352 <param name="perplexity" value="16"/>
fab6ff46e019 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit b437a46efb50e543b6d7c9988f954efe2caa9046
iuc
parents: 14
diff changeset
353 <param name="resolution" value="0.6" />
fab6ff46e019 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit b437a46efb50e543b6d7c9988f954efe2caa9046
iuc
parents: 14
diff changeset
354 <param name="nmds" value="T"/>
fab6ff46e019 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit b437a46efb50e543b6d7c9988f954efe2caa9046
iuc
parents: 14
diff changeset
355 <param name="clusters_file" value="F"/>
fab6ff46e019 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit b437a46efb50e543b6d7c9988f954efe2caa9046
iuc
parents: 14
diff changeset
356 <conditional name="markers_continue">
fab6ff46e019 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit b437a46efb50e543b6d7c9988f954efe2caa9046
iuc
parents: 14
diff changeset
357 <param name="markers_continue" value="yes"/>
fab6ff46e019 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit b437a46efb50e543b6d7c9988f954efe2caa9046
iuc
parents: 14
diff changeset
358 <param name="min_pct" value="0.25" />
fab6ff46e019 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit b437a46efb50e543b6d7c9988f954efe2caa9046
iuc
parents: 14
diff changeset
359 <param name="logfc_threshold" value="0.25" />
fab6ff46e019 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit b437a46efb50e543b6d7c9988f954efe2caa9046
iuc
parents: 14
diff changeset
360 <param name="heatmaps" value="T"/>
fab6ff46e019 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit b437a46efb50e543b6d7c9988f954efe2caa9046
iuc
parents: 14
diff changeset
361 <param name="markers_file" value="F"/>
fab6ff46e019 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit b437a46efb50e543b6d7c9988f954efe2caa9046
iuc
parents: 14
diff changeset
362 </conditional>
fab6ff46e019 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit b437a46efb50e543b6d7c9988f954efe2caa9046
iuc
parents: 14
diff changeset
363 </conditional>
fab6ff46e019 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit b437a46efb50e543b6d7c9988f954efe2caa9046
iuc
parents: 14
diff changeset
364 </conditional>
fab6ff46e019 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit b437a46efb50e543b6d7c9988f954efe2caa9046
iuc
parents: 14
diff changeset
365 </conditional>
fab6ff46e019 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit b437a46efb50e543b6d7c9988f954efe2caa9046
iuc
parents: 14
diff changeset
366 </conditional>
6
764f076e9d52 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit e8eeff2efea68e1e5bc697d0ff6a5808cd978db2"
iuc
parents: 5
diff changeset
367 <section name="meta">
764f076e9d52 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit e8eeff2efea68e1e5bc697d0ff6a5808cd978db2"
iuc
parents: 5
diff changeset
368 <param name="showcode" value="T"/>
764f076e9d52 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit e8eeff2efea68e1e5bc697d0ff6a5808cd978db2"
iuc
parents: 5
diff changeset
369 <param name="warn" value="F"/>
764f076e9d52 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit e8eeff2efea68e1e5bc697d0ff6a5808cd978db2"
iuc
parents: 5
diff changeset
370 <param name="varstate" value="F"/>
764f076e9d52 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit e8eeff2efea68e1e5bc697d0ff6a5808cd978db2"
iuc
parents: 5
diff changeset
371 </section>
9
c4db6ec33fec "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit 7681c9101062f58ac4eb296a98b1644d4ed2340a"
iuc
parents: 8
diff changeset
372 <output name="out_html" ftype="html">
c4db6ec33fec "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit 7681c9101062f58ac4eb296a98b1644d4ed2340a"
iuc
parents: 8
diff changeset
373 <assert_contents>
c4db6ec33fec "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit 7681c9101062f58ac4eb296a98b1644d4ed2340a"
iuc
parents: 8
diff changeset
374 <has_text text="Seurat Analysis" />
c4db6ec33fec "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit 7681c9101062f58ac4eb296a98b1644d4ed2340a"
iuc
parents: 8
diff changeset
375 <has_text text="Performed using Galaxy" />
c4db6ec33fec "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit 7681c9101062f58ac4eb296a98b1644d4ed2340a"
iuc
parents: 8
diff changeset
376 <has_text text="img src=&quot;data:image/png;base64" />
c4db6ec33fec "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit 7681c9101062f58ac4eb296a98b1644d4ed2340a"
iuc
parents: 8
diff changeset
377 </assert_contents>
c4db6ec33fec "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit 7681c9101062f58ac4eb296a98b1644d4ed2340a"
iuc
parents: 8
diff changeset
378 </output>
15
fab6ff46e019 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit b437a46efb50e543b6d7c9988f954efe2caa9046
iuc
parents: 14
diff changeset
379 </test>
fab6ff46e019 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit b437a46efb50e543b6d7c9988f954efe2caa9046
iuc
parents: 14
diff changeset
380 <test expect_num_outputs="4">
fab6ff46e019 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit b437a46efb50e543b6d7c9988f954efe2caa9046
iuc
parents: 14
diff changeset
381 <conditional name="function">
fab6ff46e019 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit b437a46efb50e543b6d7c9988f954efe2caa9046
iuc
parents: 14
diff changeset
382 <param name="function_select" value="cite"/>
fab6ff46e019 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit b437a46efb50e543b6d7c9988f954efe2caa9046
iuc
parents: 14
diff changeset
383 <param name="rna" ftype="tabular" value="rna.tab.gz"/>
fab6ff46e019 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit b437a46efb50e543b6d7c9988f954efe2caa9046
iuc
parents: 14
diff changeset
384 <param name="prot" ftype="tabular" value="adt.tab.gz"/>
fab6ff46e019 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit b437a46efb50e543b6d7c9988f954efe2caa9046
iuc
parents: 14
diff changeset
385 <param name="min_cells" value="0"/>
fab6ff46e019 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit b437a46efb50e543b6d7c9988f954efe2caa9046
iuc
parents: 14
diff changeset
386 <param name="min_genes" value="0"/>
fab6ff46e019 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit b437a46efb50e543b6d7c9988f954efe2caa9046
iuc
parents: 14
diff changeset
387 <param name="low_thresholds" value="1" />
fab6ff46e019 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit b437a46efb50e543b6d7c9988f954efe2caa9046
iuc
parents: 14
diff changeset
388 <param name="high_thresholds" value="20000000" />
fab6ff46e019 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit b437a46efb50e543b6d7c9988f954efe2caa9046
iuc
parents: 14
diff changeset
389 <param name="vlnfeat" value="F"/>
fab6ff46e019 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit b437a46efb50e543b6d7c9988f954efe2caa9046
iuc
parents: 14
diff changeset
390 <param name="norm_file" value="F"/>
fab6ff46e019 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit b437a46efb50e543b6d7c9988f954efe2caa9046
iuc
parents: 14
diff changeset
391 <param name="featplot" value="T"/>
fab6ff46e019 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit b437a46efb50e543b6d7c9988f954efe2caa9046
iuc
parents: 14
diff changeset
392 <param name="var_file" value="F"/>
fab6ff46e019 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit b437a46efb50e543b6d7c9988f954efe2caa9046
iuc
parents: 14
diff changeset
393 <param name="num_PCs" value="20" />
fab6ff46e019 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit b437a46efb50e543b6d7c9988f954efe2caa9046
iuc
parents: 14
diff changeset
394 <param name="pc_plots" value="T"/>
fab6ff46e019 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit b437a46efb50e543b6d7c9988f954efe2caa9046
iuc
parents: 14
diff changeset
395 <param name="pca_file" value="F"/>
fab6ff46e019 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit b437a46efb50e543b6d7c9988f954efe2caa9046
iuc
parents: 14
diff changeset
396 <param name="resolution" value="0.6" />
fab6ff46e019 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit b437a46efb50e543b6d7c9988f954efe2caa9046
iuc
parents: 14
diff changeset
397 <param name="nmds" value="F"/>
fab6ff46e019 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit b437a46efb50e543b6d7c9988f954efe2caa9046
iuc
parents: 14
diff changeset
398 <param name="clusters_file" value="F"/>
fab6ff46e019 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit b437a46efb50e543b6d7c9988f954efe2caa9046
iuc
parents: 14
diff changeset
399 <param name="min_pct" value="0.25" />
fab6ff46e019 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit b437a46efb50e543b6d7c9988f954efe2caa9046
iuc
parents: 14
diff changeset
400 <param name="logfc_threshold" value="0.25" />
fab6ff46e019 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit b437a46efb50e543b6d7c9988f954efe2caa9046
iuc
parents: 14
diff changeset
401 <param name="heatmaps" value="T"/>
fab6ff46e019 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit b437a46efb50e543b6d7c9988f954efe2caa9046
iuc
parents: 14
diff changeset
402 <param name="markers_file" value="F"/>
fab6ff46e019 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit b437a46efb50e543b6d7c9988f954efe2caa9046
iuc
parents: 14
diff changeset
403 <param name="cite_markers" value="T"/>
fab6ff46e019 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit b437a46efb50e543b6d7c9988f954efe2caa9046
iuc
parents: 14
diff changeset
404 <conditional name="comparison">
fab6ff46e019 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit b437a46efb50e543b6d7c9988f954efe2caa9046
iuc
parents: 14
diff changeset
405 <param name="comparison" value="yes"/>
fab6ff46e019 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit b437a46efb50e543b6d7c9988f954efe2caa9046
iuc
parents: 14
diff changeset
406 <param name="feat_comp" value="CD4,CD19"/>
fab6ff46e019 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit b437a46efb50e543b6d7c9988f954efe2caa9046
iuc
parents: 14
diff changeset
407 </conditional>
fab6ff46e019 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit b437a46efb50e543b6d7c9988f954efe2caa9046
iuc
parents: 14
diff changeset
408 <conditional name="marker_compare">
fab6ff46e019 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit b437a46efb50e543b6d7c9988f954efe2caa9046
iuc
parents: 14
diff changeset
409 <param name="marker_compare" value="yes"/>
fab6ff46e019 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit b437a46efb50e543b6d7c9988f954efe2caa9046
iuc
parents: 14
diff changeset
410 <param name="top_x" value="3"/>
fab6ff46e019 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit b437a46efb50e543b6d7c9988f954efe2caa9046
iuc
parents: 14
diff changeset
411 </conditional>
fab6ff46e019 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit b437a46efb50e543b6d7c9988f954efe2caa9046
iuc
parents: 14
diff changeset
412 </conditional>
fab6ff46e019 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit b437a46efb50e543b6d7c9988f954efe2caa9046
iuc
parents: 14
diff changeset
413 <section name="meta">
fab6ff46e019 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit b437a46efb50e543b6d7c9988f954efe2caa9046
iuc
parents: 14
diff changeset
414 <param name="showcode" value="T"/>
fab6ff46e019 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit b437a46efb50e543b6d7c9988f954efe2caa9046
iuc
parents: 14
diff changeset
415 <param name="warn" value="F"/>
fab6ff46e019 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit b437a46efb50e543b6d7c9988f954efe2caa9046
iuc
parents: 14
diff changeset
416 <param name="varstate" value="F"/>
fab6ff46e019 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit b437a46efb50e543b6d7c9988f954efe2caa9046
iuc
parents: 14
diff changeset
417 </section>
fab6ff46e019 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit b437a46efb50e543b6d7c9988f954efe2caa9046
iuc
parents: 14
diff changeset
418 <output name="rnamarkerst" ftype="tabular" file="rna_out.tsv" compare="sim_size" delta="500" />
fab6ff46e019 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit b437a46efb50e543b6d7c9988f954efe2caa9046
iuc
parents: 14
diff changeset
419 <output name="protmarkerst" ftype="tabular" file="protein_out.tsv" compare="sim_size" delta="500" />
fab6ff46e019 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit b437a46efb50e543b6d7c9988f954efe2caa9046
iuc
parents: 14
diff changeset
420 </test>
fab6ff46e019 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit b437a46efb50e543b6d7c9988f954efe2caa9046
iuc
parents: 14
diff changeset
421 <test expect_num_outputs="9">
fab6ff46e019 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit b437a46efb50e543b6d7c9988f954efe2caa9046
iuc
parents: 14
diff changeset
422 <conditional name="function">
fab6ff46e019 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit b437a46efb50e543b6d7c9988f954efe2caa9046
iuc
parents: 14
diff changeset
423 <param name="function_select" value="cite"/>
fab6ff46e019 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit b437a46efb50e543b6d7c9988f954efe2caa9046
iuc
parents: 14
diff changeset
424 <param name="rna" ftype="tabular" value="rna.tab.gz"/>
fab6ff46e019 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit b437a46efb50e543b6d7c9988f954efe2caa9046
iuc
parents: 14
diff changeset
425 <param name="prot" ftype="tabular" value="adt.tab.gz"/>
fab6ff46e019 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit b437a46efb50e543b6d7c9988f954efe2caa9046
iuc
parents: 14
diff changeset
426 <param name="min_cells" value="0"/>
fab6ff46e019 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit b437a46efb50e543b6d7c9988f954efe2caa9046
iuc
parents: 14
diff changeset
427 <param name="min_genes" value="0"/>
fab6ff46e019 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit b437a46efb50e543b6d7c9988f954efe2caa9046
iuc
parents: 14
diff changeset
428 <param name="low_thresholds" value="1" />
fab6ff46e019 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit b437a46efb50e543b6d7c9988f954efe2caa9046
iuc
parents: 14
diff changeset
429 <param name="high_thresholds" value="20000000" />
fab6ff46e019 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit b437a46efb50e543b6d7c9988f954efe2caa9046
iuc
parents: 14
diff changeset
430 <param name="vlnfeat" value="F"/>
fab6ff46e019 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit b437a46efb50e543b6d7c9988f954efe2caa9046
iuc
parents: 14
diff changeset
431 <param name="norm_file" value="T"/>
fab6ff46e019 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit b437a46efb50e543b6d7c9988f954efe2caa9046
iuc
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432 <param name="featplot" value="T"/>
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433 <param name="var_file" value="T"/>
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434 <param name="num_PCs" value="20" />
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435 <param name="pc_plots" value="T"/>
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436 <param name="pca_file" value="T"/>
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437 <param name="resolution" value="0.6" />
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438 <param name="nmds" value="T"/>
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439 <param name="clusters_file" value="T"/>
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440 <param name="min_pct" value="0.25" />
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441 <param name="logfc_threshold" value="0.25" />
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442 <param name="heatmaps" value="T"/>
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443 <param name="markers_file" value="T"/>
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444 <param name="cite_markers" value="F"/>
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445 <conditional name="comparison">
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446 <param name="comparison" value="yes"/>
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447 <param name="feat_comp" value="CD4,CD19"/>
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448 </conditional>
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449 <conditional name="marker_compare">
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450 <param name="marker_compare" value="yes"/>
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451 <param name="top_x" value="3"/>
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452 </conditional>
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453 </conditional>
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454 <section name="meta">
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455 <param name="showcode" value="T"/>
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456 <param name="warn" value="F"/>
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457 <param name="varstate" value="F"/>
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458 </section>
6
764f076e9d52 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit e8eeff2efea68e1e5bc697d0ff6a5808cd978db2"
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459 </test>
0
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460 </tests>
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461 <help><![CDATA[
8d8412d35247 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit 24c0223b9baa6d59bba381ef94f7e77b1c204d80
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462 .. class:: infomark
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463
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464 **What it does**
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465
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466 Seurat_ is a toolkit for quality control, analysis, and exploration of single cell RNA sequencing data.
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467 It is developed and maintained by the `Satija Lab`_ at NYGC. Seurat aims to enable users to identify and
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468 interpret sources of heterogeneity from single cell transcriptomic measurements, and to integrate diverse
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469 types of single cell data. See the `Seurat Guided Clustering tutorial`_ for more information.
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470
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471 -----
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472
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473 **Inputs**
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474
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475 * Gene count matrix in TAB-separated format
15
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476 or
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477 * RNA and Protein count matrices in TAB-separated formats
0
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478
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479 -----
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480
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481 **Outputs**
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482
1
7319f83ae734 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit 88cf23c767023f71b4ea1e72aac568cc694cc34a"
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483 * HTML of plots
0
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484
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485 Optionally you can choose to output
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486
8
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487 * R commands used to generate plots printed alongside figures
0
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488
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489 .. _Seurat: https://www.nature.com/articles/nbt.4096
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490 .. _Satija Lab: https://satijalab.org/seurat/
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491 .. _Seurat Guided Clustering tutorial: https://satijalab.org/seurat/pbmc3k_tutorial.html
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492
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493 ]]></help>
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494 <citations>
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495 <citation type="doi">10.1038/nbt.4096</citation>
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496 </citations>
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497 </tool>