Mercurial > repos > iuc > seurat
annotate seurat.xml @ 10:bb9732cfcdbe draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit c7b2b60384d54bf3ab5deca109cccba6d30b5c2e"
author | iuc |
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date | Mon, 20 Dec 2021 10:09:33 +0000 |
parents | c4db6ec33fec |
children | b72d84f6941d |
rev | line source |
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7
4c139a9415d7
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit 8f89414ecee8120447febc2902ff1ddbbd71e638"
iuc
parents:
6
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changeset
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1 <tool id="seurat" name="Seurat" version="@TOOL_VERSION@+galaxy0"> |
0
8d8412d35247
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit 24c0223b9baa6d59bba381ef94f7e77b1c204d80
iuc
parents:
diff
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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> |
10
bb9732cfcdbe
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit c7b2b60384d54bf3ab5deca109cccba6d30b5c2e"
iuc
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4 <token name="@TOOL_VERSION@">4.0.6</token> |
2
321bdd834266
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit 3cf715ec11e2c9944f46572e324e5b2db5aa151f"
iuc
parents:
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5 </macros> |
0
8d8412d35247
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit 24c0223b9baa6d59bba381ef94f7e77b1c204d80
iuc
parents:
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6 <requirements> |
2
321bdd834266
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit 3cf715ec11e2c9944f46572e324e5b2db5aa151f"
iuc
parents:
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7 <requirement type="package" version="@TOOL_VERSION@">r-seurat</requirement> |
9
c4db6ec33fec
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit 7681c9101062f58ac4eb296a98b1644d4ed2340a"
iuc
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8
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8 <requirement type="package" version="2.11">r-rmarkdown</requirement> |
0
8d8412d35247
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit 24c0223b9baa6d59bba381ef94f7e77b1c204d80
iuc
parents:
diff
changeset
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9 </requirements> |
8d8412d35247
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit 24c0223b9baa6d59bba381ef94f7e77b1c204d80
iuc
parents:
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10 <command detect_errors="exit_code"><![CDATA[ |
1
7319f83ae734
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit 88cf23c767023f71b4ea1e72aac568cc694cc34a"
iuc
parents:
0
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11 #if "vln" in $meta.plots: |
7319f83ae734
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit 88cf23c767023f71b4ea1e72aac568cc694cc34a"
iuc
parents:
0
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12 #set $vln = 'T' |
7319f83ae734
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit 88cf23c767023f71b4ea1e72aac568cc694cc34a"
iuc
parents:
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13 #else |
7319f83ae734
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit 88cf23c767023f71b4ea1e72aac568cc694cc34a"
iuc
parents:
0
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14 #set $vln = 'F' |
7319f83ae734
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit 88cf23c767023f71b4ea1e72aac568cc694cc34a"
iuc
parents:
0
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15 #end if |
7319f83ae734
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit 88cf23c767023f71b4ea1e72aac568cc694cc34a"
iuc
parents:
0
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changeset
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16 #if "feat" in $meta.plots: |
7319f83ae734
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit 88cf23c767023f71b4ea1e72aac568cc694cc34a"
iuc
parents:
0
diff
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17 #set $feat = 'T' |
7319f83ae734
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit 88cf23c767023f71b4ea1e72aac568cc694cc34a"
iuc
parents:
0
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18 #else |
7319f83ae734
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit 88cf23c767023f71b4ea1e72aac568cc694cc34a"
iuc
parents:
0
diff
changeset
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19 #set $feat = 'F' |
0
8d8412d35247
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit 24c0223b9baa6d59bba381ef94f7e77b1c204d80
iuc
parents:
diff
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20 #end if |
1
7319f83ae734
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit 88cf23c767023f71b4ea1e72aac568cc694cc34a"
iuc
parents:
0
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21 #if "PCs" in $meta.plots: |
7319f83ae734
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit 88cf23c767023f71b4ea1e72aac568cc694cc34a"
iuc
parents:
0
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22 #set $PCs = 'T' |
7319f83ae734
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit 88cf23c767023f71b4ea1e72aac568cc694cc34a"
iuc
parents:
0
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23 #else |
7319f83ae734
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit 88cf23c767023f71b4ea1e72aac568cc694cc34a"
iuc
parents:
0
diff
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24 #set $PCs = 'F' |
0
8d8412d35247
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit 24c0223b9baa6d59bba381ef94f7e77b1c204d80
iuc
parents:
diff
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25 #end if |
1
7319f83ae734
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit 88cf23c767023f71b4ea1e72aac568cc694cc34a"
iuc
parents:
0
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26 #if "tsne" in $meta.plots: |
7319f83ae734
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit 88cf23c767023f71b4ea1e72aac568cc694cc34a"
iuc
parents:
0
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27 #set $tsne = 'T' |
7319f83ae734
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit 88cf23c767023f71b4ea1e72aac568cc694cc34a"
iuc
parents:
0
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28 #else |
7319f83ae734
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit 88cf23c767023f71b4ea1e72aac568cc694cc34a"
iuc
parents:
0
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29 #set $tsne = 'F' |
0
8d8412d35247
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit 24c0223b9baa6d59bba381ef94f7e77b1c204d80
iuc
parents:
diff
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30 #end if |
1
7319f83ae734
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit 88cf23c767023f71b4ea1e72aac568cc694cc34a"
iuc
parents:
0
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31 #if "heat" in $meta.plots: |
7319f83ae734
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit 88cf23c767023f71b4ea1e72aac568cc694cc34a"
iuc
parents:
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32 #set $heatmaps = 'T' |
7319f83ae734
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit 88cf23c767023f71b4ea1e72aac568cc694cc34a"
iuc
parents:
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33 #else |
7319f83ae734
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit 88cf23c767023f71b4ea1e72aac568cc694cc34a"
iuc
parents:
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34 #set $heatmaps = 'F' |
0
8d8412d35247
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit 24c0223b9baa6d59bba381ef94f7e77b1c204d80
iuc
parents:
diff
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35 #end if |
6
764f076e9d52
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit e8eeff2efea68e1e5bc697d0ff6a5808cd978db2"
iuc
parents:
5
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36 #if not str($adv.perplexity): |
764f076e9d52
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit e8eeff2efea68e1e5bc697d0ff6a5808cd978db2"
iuc
parents:
5
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37 #set $adv_perplexity = -1 |
764f076e9d52
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit e8eeff2efea68e1e5bc697d0ff6a5808cd978db2"
iuc
parents:
5
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38 #else: |
764f076e9d52
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit e8eeff2efea68e1e5bc697d0ff6a5808cd978db2"
iuc
parents:
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39 #set $adv_perplexity = $adv.perplexity |
764f076e9d52
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit e8eeff2efea68e1e5bc697d0ff6a5808cd978db2"
iuc
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5
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40 #end if |
1
7319f83ae734
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit 88cf23c767023f71b4ea1e72aac568cc694cc34a"
iuc
parents:
0
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41 Rscript -e "library(\"rmarkdown\"); render(\"$__tool_directory__/Seurat.R\", |
7319f83ae734
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit 88cf23c767023f71b4ea1e72aac568cc694cc34a"
iuc
parents:
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42 params = list(counts = \"${counts}\", |
7319f83ae734
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit 88cf23c767023f71b4ea1e72aac568cc694cc34a"
iuc
parents:
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43 min_cells = \"${adv.min_cells}\", |
7319f83ae734
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit 88cf23c767023f71b4ea1e72aac568cc694cc34a"
iuc
parents:
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44 min_genes = \"${adv.min_genes}\", |
7319f83ae734
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit 88cf23c767023f71b4ea1e72aac568cc694cc34a"
iuc
parents:
0
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45 low_thresholds = \"${adv.low_thresholds}\", |
7319f83ae734
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit 88cf23c767023f71b4ea1e72aac568cc694cc34a"
iuc
parents:
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46 high_thresholds = \"${adv.high_thresholds}\", |
7319f83ae734
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit 88cf23c767023f71b4ea1e72aac568cc694cc34a"
iuc
parents:
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47 numPCs = \"${adv.num_PCs}\", |
7319f83ae734
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit 88cf23c767023f71b4ea1e72aac568cc694cc34a"
iuc
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48 cells_use = \"${adv.cells_use}\", |
7319f83ae734
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit 88cf23c767023f71b4ea1e72aac568cc694cc34a"
iuc
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49 resolution = \"${adv.resolution}\", |
6
764f076e9d52
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit e8eeff2efea68e1e5bc697d0ff6a5808cd978db2"
iuc
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50 perplexity = \"${adv_perplexity}\", |
1
7319f83ae734
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit 88cf23c767023f71b4ea1e72aac568cc694cc34a"
iuc
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51 min_pct = \"${adv.min_pct}\", |
7319f83ae734
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit 88cf23c767023f71b4ea1e72aac568cc694cc34a"
iuc
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52 logfc_threshold = \"${adv.logfc_threshold}\", |
7319f83ae734
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit 88cf23c767023f71b4ea1e72aac568cc694cc34a"
iuc
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53 warn = \"${meta.warn}\", |
7319f83ae734
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit 88cf23c767023f71b4ea1e72aac568cc694cc34a"
iuc
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54 varstate = \"${meta.varstate}\", |
7319f83ae734
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit 88cf23c767023f71b4ea1e72aac568cc694cc34a"
iuc
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55 showcode = \"${meta.showcode}\", |
7319f83ae734
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit 88cf23c767023f71b4ea1e72aac568cc694cc34a"
iuc
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56 vlnfeat = \"$vln\", |
7319f83ae734
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit 88cf23c767023f71b4ea1e72aac568cc694cc34a"
iuc
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57 featplot = \"$feat\", |
7319f83ae734
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit 88cf23c767023f71b4ea1e72aac568cc694cc34a"
iuc
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58 PCplots = \"$PCs\", |
7319f83ae734
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit 88cf23c767023f71b4ea1e72aac568cc694cc34a"
iuc
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59 tsne = \"$tsne\", |
7319f83ae734
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit 88cf23c767023f71b4ea1e72aac568cc694cc34a"
iuc
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60 heatmaps = \"$heatmaps\"), |
7319f83ae734
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit 88cf23c767023f71b4ea1e72aac568cc694cc34a"
iuc
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61 intermediates_dir = \".\", |
7319f83ae734
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit 88cf23c767023f71b4ea1e72aac568cc694cc34a"
iuc
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62 output_format = html_document(), |
7319f83ae734
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit 88cf23c767023f71b4ea1e72aac568cc694cc34a"
iuc
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63 output_dir = \".\", |
7319f83ae734
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit 88cf23c767023f71b4ea1e72aac568cc694cc34a"
iuc
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64 output_file = \"out.html\")" |
7319f83ae734
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit 88cf23c767023f71b4ea1e72aac568cc694cc34a"
iuc
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65 ]]></command> |
0
8d8412d35247
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit 24c0223b9baa6d59bba381ef94f7e77b1c204d80
iuc
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66 <inputs> |
1
7319f83ae734
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit 88cf23c767023f71b4ea1e72aac568cc694cc34a"
iuc
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67 <param name="counts" 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"/> |
7319f83ae734
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit 88cf23c767023f71b4ea1e72aac568cc694cc34a"
iuc
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68 <section name="adv" title="Advanced Options" expanded="true"> |
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c4db6ec33fec
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit 7681c9101062f58ac4eb296a98b1644d4ed2340a"
iuc
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69 <param name="num_PCs" type="integer" min="0" value="10" label="Number of PCs to use in plots" help="Uses this number of PCs in PCHEatmap, JackStrawPlot, FindClusters, RunTSNE" /> |
c4db6ec33fec
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit 7681c9101062f58ac4eb296a98b1644d4ed2340a"
iuc
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70 <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" /> |
c4db6ec33fec
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit 7681c9101062f58ac4eb296a98b1644d4ed2340a"
iuc
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71 <param name="min_genes" type="integer" min="0" value="0" label="Minimum genes" help="Include cells where at least this many genes are detected" /> |
1
7319f83ae734
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit 88cf23c767023f71b4ea1e72aac568cc694cc34a"
iuc
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72 <param name="low_thresholds" type="integer" value="1" label="Low threshold for filtering cells" /> |
7319f83ae734
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit 88cf23c767023f71b4ea1e72aac568cc694cc34a"
iuc
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73 <param name="high_thresholds" type="integer" value="20000000" label="High threshold for filtering cells" /> |
7319f83ae734
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit 88cf23c767023f71b4ea1e72aac568cc694cc34a"
iuc
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74 <param name="cells_use" type="integer" min="1" value="500" label="Cells to use for PCHeatmap" help="Plots this number of top ‘extreme’ cells on both ends of the spectrum, which dramatically speeds plotting for large datasets" /> |
9
c4db6ec33fec
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit 7681c9101062f58ac4eb296a98b1644d4ed2340a"
iuc
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75 <param name="resolution" type="float" value="0.6" label="Resolution parameter" help="Value of the resolution parameter used in FindClusters, use a value above (below) 1.0 if you want to obtain a larger (smaller) number of communities" /> |
6
764f076e9d52
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit e8eeff2efea68e1e5bc697d0ff6a5808cd978db2"
iuc
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76 <param name="perplexity" type="integer" value="" optional="true" label="Perplexity parameter" help="Parameter for the tSNE dimensionality reduction" /> |
9
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit 7681c9101062f58ac4eb296a98b1644d4ed2340a"
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77 <param name="min_pct" type="float" value="0.1" label="Minimum percent cells" help="With FindMarkers, only test genes that are detected in at least this percentage of cells in either of the two populations. Meant to speed up the function by not testing genes that are very infrequently expressed" /> |
c4db6ec33fec
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit 7681c9101062f58ac4eb296a98b1644d4ed2340a"
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78 <param name="logfc_threshold" type="float" min="0" value="0.25" label="Log fold change threshold" |
c4db6ec33fec
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit 7681c9101062f58ac4eb296a98b1644d4ed2340a"
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79 help="With FindMarkers, limit testing to genes which show, on average, at least X-fold difference (log-scale) between the two groups of cells. Increasing this parameter speeds up the function, but can miss weaker signals" /> |
0
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit 24c0223b9baa6d59bba381ef94f7e77b1c204d80
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80 </section> |
1
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit 88cf23c767023f71b4ea1e72aac568cc694cc34a"
iuc
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81 <section name="meta" title="Output options" expanded="true"> |
7319f83ae734
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit 88cf23c767023f71b4ea1e72aac568cc694cc34a"
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82 <param name="showcode" type="boolean" truevalue="T" falsevalue="F" checked="false" label="Show code alongside outputs?"/> |
7319f83ae734
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit 88cf23c767023f71b4ea1e72aac568cc694cc34a"
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83 <param name="warn" type="boolean" truevalue="T" falsevalue="F" checked="false" label="Include warnings in the output file (Yes) or pipe to stdout (No)"/> |
7319f83ae734
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit 88cf23c767023f71b4ea1e72aac568cc694cc34a"
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84 <param name="varstate" type="boolean" truevalue="T" falsevalue="F" checked="false" label="Display variable values used in code at the beginning of output file?"/> |
7319f83ae734
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit 88cf23c767023f71b4ea1e72aac568cc694cc34a"
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85 <param name="plots" type="select" optional="true" multiple="true" display="checkboxes" label="Which plots should be output?"> |
7319f83ae734
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit 88cf23c767023f71b4ea1e72aac568cc694cc34a"
iuc
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86 <option value="vln" selected="true">Violin and Scatter plots</option> |
7319f83ae734
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit 88cf23c767023f71b4ea1e72aac568cc694cc34a"
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87 <option value="feat" selected="true">Feature counts plots</option> |
7319f83ae734
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit 88cf23c767023f71b4ea1e72aac568cc694cc34a"
iuc
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88 <option value="PCs" selected="true">PC plots</option> |
7319f83ae734
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit 88cf23c767023f71b4ea1e72aac568cc694cc34a"
iuc
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89 <option value="tsne" selected="true">tSNE plots</option> |
7319f83ae734
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit 88cf23c767023f71b4ea1e72aac568cc694cc34a"
iuc
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90 <option value="heat" selected="true">Heatmap plots</option> |
7319f83ae734
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit 88cf23c767023f71b4ea1e72aac568cc694cc34a"
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91 </param> |
7319f83ae734
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit 88cf23c767023f71b4ea1e72aac568cc694cc34a"
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92 </section> |
0
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit 24c0223b9baa6d59bba381ef94f7e77b1c204d80
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93 </inputs> |
8d8412d35247
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit 24c0223b9baa6d59bba381ef94f7e77b1c204d80
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94 <outputs> |
1
7319f83ae734
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit 88cf23c767023f71b4ea1e72aac568cc694cc34a"
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95 <data name="out_html" format="html" from_work_dir="out.html" label="${tool.name} on ${on_string}" /> |
0
8d8412d35247
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit 24c0223b9baa6d59bba381ef94f7e77b1c204d80
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96 </outputs> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit 24c0223b9baa6d59bba381ef94f7e77b1c204d80
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97 |
8d8412d35247
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98 <tests> |
8d8412d35247
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit 24c0223b9baa6d59bba381ef94f7e77b1c204d80
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99 <test> |
1
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit 88cf23c767023f71b4ea1e72aac568cc694cc34a"
iuc
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100 <param name="counts" ftype="tabular" value="counts.tab.gz"/> |
7319f83ae734
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit 88cf23c767023f71b4ea1e72aac568cc694cc34a"
iuc
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101 <section name="adv"> |
7319f83ae734
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit 88cf23c767023f71b4ea1e72aac568cc694cc34a"
iuc
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102 <param name="numPCs" value="10" /> |
7319f83ae734
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit 88cf23c767023f71b4ea1e72aac568cc694cc34a"
iuc
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103 <param name="min_cells" value="3"/> |
7319f83ae734
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit 88cf23c767023f71b4ea1e72aac568cc694cc34a"
iuc
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104 <param name="min_genes" value="200"/> |
7319f83ae734
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit 88cf23c767023f71b4ea1e72aac568cc694cc34a"
iuc
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105 <param name="low_thresholds" value="1" /> |
7319f83ae734
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit 88cf23c767023f71b4ea1e72aac568cc694cc34a"
iuc
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106 <param name="high_thresholds" value="20000000" /> |
7319f83ae734
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit 88cf23c767023f71b4ea1e72aac568cc694cc34a"
iuc
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107 <param name="cells_use" value="500"/> |
7319f83ae734
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit 88cf23c767023f71b4ea1e72aac568cc694cc34a"
iuc
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108 <param name="resolution" value="0.6" /> |
7319f83ae734
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit 88cf23c767023f71b4ea1e72aac568cc694cc34a"
iuc
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109 <param name="min_pct" value="0.25" /> |
7319f83ae734
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit 88cf23c767023f71b4ea1e72aac568cc694cc34a"
iuc
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110 <param name="logfc_threshold" value="0.25" /> |
7319f83ae734
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit 88cf23c767023f71b4ea1e72aac568cc694cc34a"
iuc
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111 </section> |
7319f83ae734
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit 88cf23c767023f71b4ea1e72aac568cc694cc34a"
iuc
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112 <section name="meta"> |
7319f83ae734
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit 88cf23c767023f71b4ea1e72aac568cc694cc34a"
iuc
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113 <param name="showcode" value="T"/> |
7319f83ae734
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit 88cf23c767023f71b4ea1e72aac568cc694cc34a"
iuc
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114 <param name="warn" value="F"/> |
7319f83ae734
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit 88cf23c767023f71b4ea1e72aac568cc694cc34a"
iuc
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115 <param name="varstate" value="F"/> |
7319f83ae734
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit 88cf23c767023f71b4ea1e72aac568cc694cc34a"
iuc
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116 <param name="plots" value="feat"/> |
7319f83ae734
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit 88cf23c767023f71b4ea1e72aac568cc694cc34a"
iuc
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117 </section> |
9
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit 7681c9101062f58ac4eb296a98b1644d4ed2340a"
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118 <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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119 <assert_contents> |
c4db6ec33fec
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit 7681c9101062f58ac4eb296a98b1644d4ed2340a"
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120 <has_text text="Seurat Analysis" /> |
c4db6ec33fec
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit 7681c9101062f58ac4eb296a98b1644d4ed2340a"
iuc
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121 <has_text text="Performed using Galaxy" /> |
c4db6ec33fec
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit 7681c9101062f58ac4eb296a98b1644d4ed2340a"
iuc
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122 <has_text text="img src="data:image/png;base64" /> |
c4db6ec33fec
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit 7681c9101062f58ac4eb296a98b1644d4ed2340a"
iuc
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123 </assert_contents> |
c4db6ec33fec
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit 7681c9101062f58ac4eb296a98b1644d4ed2340a"
iuc
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124 </output> |
0
8d8412d35247
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit 24c0223b9baa6d59bba381ef94f7e77b1c204d80
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125 </test> |
6
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit e8eeff2efea68e1e5bc697d0ff6a5808cd978db2"
iuc
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126 <test> <!-- perplexity test --> |
764f076e9d52
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit e8eeff2efea68e1e5bc697d0ff6a5808cd978db2"
iuc
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127 <param name="counts" ftype="tabular" value="counts.tab.gz"/> |
764f076e9d52
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit e8eeff2efea68e1e5bc697d0ff6a5808cd978db2"
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128 <section name="adv"> |
764f076e9d52
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit e8eeff2efea68e1e5bc697d0ff6a5808cd978db2"
iuc
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129 <param name="numPCs" value="10" /> |
764f076e9d52
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit e8eeff2efea68e1e5bc697d0ff6a5808cd978db2"
iuc
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130 <param name="min_cells" value="3"/> |
764f076e9d52
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit e8eeff2efea68e1e5bc697d0ff6a5808cd978db2"
iuc
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131 <param name="min_genes" value="200"/> |
764f076e9d52
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit e8eeff2efea68e1e5bc697d0ff6a5808cd978db2"
iuc
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132 <param name="low_thresholds" value="1" /> |
764f076e9d52
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit e8eeff2efea68e1e5bc697d0ff6a5808cd978db2"
iuc
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133 <param name="high_thresholds" value="20000000" /> |
764f076e9d52
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit e8eeff2efea68e1e5bc697d0ff6a5808cd978db2"
iuc
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134 <param name="cells_use" value="500"/> |
764f076e9d52
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit e8eeff2efea68e1e5bc697d0ff6a5808cd978db2"
iuc
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135 <param name="resolution" value="0.6" /> |
764f076e9d52
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit e8eeff2efea68e1e5bc697d0ff6a5808cd978db2"
iuc
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136 <param name="perplexity" value="16" /> |
764f076e9d52
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit e8eeff2efea68e1e5bc697d0ff6a5808cd978db2"
iuc
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137 <param name="min_pct" value="0.25" /> |
764f076e9d52
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit e8eeff2efea68e1e5bc697d0ff6a5808cd978db2"
iuc
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138 <param name="logfc_threshold" value="0.25" /> |
764f076e9d52
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit e8eeff2efea68e1e5bc697d0ff6a5808cd978db2"
iuc
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139 </section> |
764f076e9d52
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit e8eeff2efea68e1e5bc697d0ff6a5808cd978db2"
iuc
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140 <section name="meta"> |
764f076e9d52
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit e8eeff2efea68e1e5bc697d0ff6a5808cd978db2"
iuc
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141 <param name="showcode" value="T"/> |
764f076e9d52
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit e8eeff2efea68e1e5bc697d0ff6a5808cd978db2"
iuc
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142 <param name="warn" value="F"/> |
764f076e9d52
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit e8eeff2efea68e1e5bc697d0ff6a5808cd978db2"
iuc
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143 <param name="varstate" value="F"/> |
764f076e9d52
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit e8eeff2efea68e1e5bc697d0ff6a5808cd978db2"
iuc
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144 <param name="plots" value="feat"/> |
764f076e9d52
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit e8eeff2efea68e1e5bc697d0ff6a5808cd978db2"
iuc
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145 </section> |
9
c4db6ec33fec
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit 7681c9101062f58ac4eb296a98b1644d4ed2340a"
iuc
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146 <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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147 <assert_contents> |
c4db6ec33fec
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit 7681c9101062f58ac4eb296a98b1644d4ed2340a"
iuc
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148 <has_text text="Seurat Analysis" /> |
c4db6ec33fec
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit 7681c9101062f58ac4eb296a98b1644d4ed2340a"
iuc
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149 <has_text text="Performed using Galaxy" /> |
c4db6ec33fec
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit 7681c9101062f58ac4eb296a98b1644d4ed2340a"
iuc
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150 <has_text text="img src="data:image/png;base64" /> |
c4db6ec33fec
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit 7681c9101062f58ac4eb296a98b1644d4ed2340a"
iuc
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151 </assert_contents> |
c4db6ec33fec
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit 7681c9101062f58ac4eb296a98b1644d4ed2340a"
iuc
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152 </output> |
6
764f076e9d52
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit e8eeff2efea68e1e5bc697d0ff6a5808cd978db2"
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153 </test> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit 24c0223b9baa6d59bba381ef94f7e77b1c204d80
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154 </tests> |
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155 <help><![CDATA[ |
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156 .. class:: infomark |
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157 |
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158 **What it does** |
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159 |
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160 Seurat_ is a toolkit for quality control, analysis, and exploration of single cell RNA sequencing data. |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit 24c0223b9baa6d59bba381ef94f7e77b1c204d80
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161 It is developed and maintained by the `Satija Lab`_ at NYGC. Seurat aims to enable users to identify and |
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162 interpret sources of heterogeneity from single cell transcriptomic measurements, and to integrate diverse |
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163 types of single cell data. See the `Seurat Guided Clustering tutorial`_ for more information. |
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164 |
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165 ----- |
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166 |
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167 **Inputs** |
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168 |
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169 * Gene count matrix in TAB-separated format |
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170 |
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171 ----- |
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172 |
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173 **Outputs** |
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174 |
1
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175 * HTML of plots |
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176 |
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177 Optionally you can choose to output |
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178 |
8
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179 * R commands used to generate plots printed alongside figures |
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180 |
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181 .. _Seurat: https://www.nature.com/articles/nbt.4096 |
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182 .. _Satija Lab: https://satijalab.org/seurat/ |
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183 .. _Seurat Guided Clustering tutorial: https://satijalab.org/seurat/pbmc3k_tutorial.html |
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184 |
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185 ]]></help> |
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186 <citations> |
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187 <citation type="doi">10.1038/nbt.4096</citation> |
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188 </citations> |
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189 </tool> |