Mercurial > repos > iuc > seurat
annotate seurat.xml @ 0:8d8412d35247 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit 24c0223b9baa6d59bba381ef94f7e77b1c204d80
| author | iuc |
|---|---|
| date | Sun, 26 Aug 2018 16:24:02 -0400 |
| parents | |
| children | 7319f83ae734 |
| rev | line source |
|---|---|
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8d8412d35247
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit 24c0223b9baa6d59bba381ef94f7e77b1c204d80
iuc
parents:
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changeset
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1 <tool id="seurat" name="Seurat" version="2.3.4"> |
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8d8412d35247
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit 24c0223b9baa6d59bba381ef94f7e77b1c204d80
iuc
parents:
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2 <description>- toolkit for exploration of single-cell RNA-seq data</description> |
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8d8412d35247
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit 24c0223b9baa6d59bba381ef94f7e77b1c204d80
iuc
parents:
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changeset
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3 <requirements> |
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8d8412d35247
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit 24c0223b9baa6d59bba381ef94f7e77b1c204d80
iuc
parents:
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4 <requirement type="package" version="3.4.1">r-base</requirement> |
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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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5 <requirement type="package" version="2.3.4">r-seurat</requirement> |
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8d8412d35247
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit 24c0223b9baa6d59bba381ef94f7e77b1c204d80
iuc
parents:
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6 <requirement type="package" version="1.0.0">bioconductor-singlecellexperiment</requirement> |
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8d8412d35247
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit 24c0223b9baa6d59bba381ef94f7e77b1c204d80
iuc
parents:
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7 <requirement type="package" version="1.6.0">r-optparse</requirement> |
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8d8412d35247
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit 24c0223b9baa6d59bba381ef94f7e77b1c204d80
iuc
parents:
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8 </requirements> |
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8d8412d35247
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit 24c0223b9baa6d59bba381ef94f7e77b1c204d80
iuc
parents:
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9 <version_command><![CDATA[ |
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8d8412d35247
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit 24c0223b9baa6d59bba381ef94f7e77b1c204d80
iuc
parents:
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10 echo $(R --version | grep version | grep -v GNU)", seurat version" $(R --vanilla --slave -e "library(seurat); cat(sessionInfo()\$otherPkgs\$seurat\$Version)" 2> /dev/null | grep -v -i "WARNING: ")", SingleCellExperiment version" $(R --vanilla --slave -e "library(SingleCellExperiment); cat(sessionInfo()\$otherPkgs\$SingleCellExperiment\$Version)" 2> /dev/null | grep -v -i "WARNING: ")", optparse version" $(R --vanilla --slave -e "library(optparse); cat(sessionInfo()\$otherPkgs\$optparse\$Version)" 2> /dev/null | grep -v -i "WARNING: ") |
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8d8412d35247
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit 24c0223b9baa6d59bba381ef94f7e77b1c204d80
iuc
parents:
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11 ]]></version_command> |
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8d8412d35247
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit 24c0223b9baa6d59bba381ef94f7e77b1c204d80
iuc
parents:
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12 <command detect_errors="exit_code"><![CDATA[ |
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8d8412d35247
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit 24c0223b9baa6d59bba381ef94f7e77b1c204d80
iuc
parents:
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13 |
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8d8412d35247
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit 24c0223b9baa6d59bba381ef94f7e77b1c204d80
iuc
parents:
diff
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14 #if $rscript: |
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8d8412d35247
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit 24c0223b9baa6d59bba381ef94f7e77b1c204d80
iuc
parents:
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15 cp '$__tool_directory__/seurat.R' '$out_rscript' && |
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8d8412d35247
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit 24c0223b9baa6d59bba381ef94f7e77b1c204d80
iuc
parents:
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16 #end if |
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8d8412d35247
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit 24c0223b9baa6d59bba381ef94f7e77b1c204d80
iuc
parents:
diff
changeset
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17 |
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8d8412d35247
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit 24c0223b9baa6d59bba381ef94f7e77b1c204d80
iuc
parents:
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18 Rscript '$__tool_directory__/seurat.R' |
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8d8412d35247
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit 24c0223b9baa6d59bba381ef94f7e77b1c204d80
iuc
parents:
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19 |
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8d8412d35247
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit 24c0223b9baa6d59bba381ef94f7e77b1c204d80
iuc
parents:
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20 --counts '$counts' |
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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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21 --numPCs $adv.num_PCs |
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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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22 --min.cells $adv.min_cells |
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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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23 --min.genes $adv.min_genes |
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8d8412d35247
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit 24c0223b9baa6d59bba381ef94f7e77b1c204d80
iuc
parents:
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changeset
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24 |
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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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25 #if $adv.low_thresholds: |
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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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26 --low.thresholds $adv.low_thresholds |
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8d8412d35247
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit 24c0223b9baa6d59bba381ef94f7e77b1c204d80
iuc
parents:
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27 #end if |
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8d8412d35247
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit 24c0223b9baa6d59bba381ef94f7e77b1c204d80
iuc
parents:
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28 #if $adv.high_thresholds: |
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8d8412d35247
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit 24c0223b9baa6d59bba381ef94f7e77b1c204d80
iuc
parents:
diff
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29 --high.thresholds $adv.high_thresholds |
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8d8412d35247
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit 24c0223b9baa6d59bba381ef94f7e77b1c204d80
iuc
parents:
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30 #end if |
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8d8412d35247
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit 24c0223b9baa6d59bba381ef94f7e77b1c204d80
iuc
parents:
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31 #if $adv.x_low_cutoff: |
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8d8412d35247
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit 24c0223b9baa6d59bba381ef94f7e77b1c204d80
iuc
parents:
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32 --x.low.cutoff $adv.x_low_cutoff |
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8d8412d35247
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit 24c0223b9baa6d59bba381ef94f7e77b1c204d80
iuc
parents:
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33 #end if |
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8d8412d35247
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit 24c0223b9baa6d59bba381ef94f7e77b1c204d80
iuc
parents:
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34 #if $adv.x_high_cutoff: |
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8d8412d35247
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit 24c0223b9baa6d59bba381ef94f7e77b1c204d80
iuc
parents:
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35 --x.high.cutoff $adv.x_high_cutoff |
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8d8412d35247
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit 24c0223b9baa6d59bba381ef94f7e77b1c204d80
iuc
parents:
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36 #end if |
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8d8412d35247
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit 24c0223b9baa6d59bba381ef94f7e77b1c204d80
iuc
parents:
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37 #if $adv.y_cutoff: |
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8d8412d35247
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit 24c0223b9baa6d59bba381ef94f7e77b1c204d80
iuc
parents:
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38 --y.cutoff $adv.y_cutoff |
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8d8412d35247
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit 24c0223b9baa6d59bba381ef94f7e77b1c204d80
iuc
parents:
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39 #end if |
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8d8412d35247
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit 24c0223b9baa6d59bba381ef94f7e77b1c204d80
iuc
parents:
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40 #if $adv.cells_use: |
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8d8412d35247
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit 24c0223b9baa6d59bba381ef94f7e77b1c204d80
iuc
parents:
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41 --cells.use $adv.cells_use |
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8d8412d35247
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit 24c0223b9baa6d59bba381ef94f7e77b1c204d80
iuc
parents:
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42 #end if |
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8d8412d35247
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit 24c0223b9baa6d59bba381ef94f7e77b1c204d80
iuc
parents:
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43 #if $adv.resolution: |
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8d8412d35247
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit 24c0223b9baa6d59bba381ef94f7e77b1c204d80
iuc
parents:
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44 --resolution $adv.resolution |
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8d8412d35247
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit 24c0223b9baa6d59bba381ef94f7e77b1c204d80
iuc
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45 #end if |
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8d8412d35247
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit 24c0223b9baa6d59bba381ef94f7e77b1c204d80
iuc
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46 #if $adv.min_pct: |
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8d8412d35247
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit 24c0223b9baa6d59bba381ef94f7e77b1c204d80
iuc
parents:
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47 --min.pct $adv.min_pct |
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8d8412d35247
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit 24c0223b9baa6d59bba381ef94f7e77b1c204d80
iuc
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48 #end if |
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8d8412d35247
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit 24c0223b9baa6d59bba381ef94f7e77b1c204d80
iuc
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49 #if $adv.logfc_threshold: |
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8d8412d35247
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit 24c0223b9baa6d59bba381ef94f7e77b1c204d80
iuc
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50 --logfc.threshold $adv.logfc_threshold |
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8d8412d35247
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit 24c0223b9baa6d59bba381ef94f7e77b1c204d80
iuc
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51 #end if |
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8d8412d35247
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit 24c0223b9baa6d59bba381ef94f7e77b1c204d80
iuc
parents:
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52 |
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8d8412d35247
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit 24c0223b9baa6d59bba381ef94f7e77b1c204d80
iuc
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53 #if $rds: |
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8d8412d35247
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit 24c0223b9baa6d59bba381ef94f7e77b1c204d80
iuc
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54 --rds '$rds' |
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8d8412d35247
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit 24c0223b9baa6d59bba381ef94f7e77b1c204d80
iuc
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55 #end if |
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8d8412d35247
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit 24c0223b9baa6d59bba381ef94f7e77b1c204d80
iuc
parents:
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56 |
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8d8412d35247
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit 24c0223b9baa6d59bba381ef94f7e77b1c204d80
iuc
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57 ]]></command> |
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8d8412d35247
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit 24c0223b9baa6d59bba381ef94f7e77b1c204d80
iuc
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58 |
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8d8412d35247
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit 24c0223b9baa6d59bba381ef94f7e77b1c204d80
iuc
parents:
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59 <inputs> |
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8d8412d35247
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit 24c0223b9baa6d59bba381ef94f7e77b1c204d80
iuc
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60 <param name="counts" type="data" format="tabular" 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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8d8412d35247
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit 24c0223b9baa6d59bba381ef94f7e77b1c204d80
iuc
parents:
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61 <param name="rscript" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="False" label="Output Rscript?" help="If this option is set to Yes, the Rscript used by this tool will be provided as a text file in the output. Default: No" /> |
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8d8412d35247
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit 24c0223b9baa6d59bba381ef94f7e77b1c204d80
iuc
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62 <param name="rds" type="boolean" truevalue="True" falsevalue="False" checked="False" label="Output Seurat RDS object?" |
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8d8412d35247
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit 24c0223b9baa6d59bba381ef94f7e77b1c204d80
iuc
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63 help="Output the Seurat RDS object, can be loaded into R. Default: No"> |
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8d8412d35247
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit 24c0223b9baa6d59bba381ef94f7e77b1c204d80
iuc
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64 </param> |
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8d8412d35247
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit 24c0223b9baa6d59bba381ef94f7e77b1c204d80
iuc
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65 <section name="adv" title="Advanced Options"> |
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8d8412d35247
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit 24c0223b9baa6d59bba381ef94f7e77b1c204d80
iuc
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66 <param argument="--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. Default: 10" /> |
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8d8412d35247
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit 24c0223b9baa6d59bba381ef94f7e77b1c204d80
iuc
parents:
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67 <param argument="--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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8d8412d35247
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit 24c0223b9baa6d59bba381ef94f7e77b1c204d80
iuc
parents:
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68 <param argument="--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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8d8412d35247
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit 24c0223b9baa6d59bba381ef94f7e77b1c204d80
iuc
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69 <param argument="--low_thresholds" type="float" optional="True" label="Low threshold for filtering cells" /> |
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8d8412d35247
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit 24c0223b9baa6d59bba381ef94f7e77b1c204d80
iuc
parents:
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70 <param argument="--high_thresholds" type="float" optional="True" label="High threshold for filtering cells" /> |
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8d8412d35247
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit 24c0223b9baa6d59bba381ef94f7e77b1c204d80
iuc
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71 <param argument="--x_low_cutoff" type="float" optional="True" label="X-axis low cutoff for variable genes" help="Bottom cutoff on x-axis for identifying variable genes" /> |
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8d8412d35247
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit 24c0223b9baa6d59bba381ef94f7e77b1c204d80
iuc
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72 <param argument="--x_high_cutoff" type="float" optional="True" label="X-axis high cutoff for variable genes" help="Top cutoff on x-axis for identifying variable genes" /> |
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8d8412d35247
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit 24c0223b9baa6d59bba381ef94f7e77b1c204d80
iuc
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73 <param argument="--y_cutoff" type="float" optional="True" label="Y-axis cutoff for variable genes" help="Bottom cutoff on y-axis for identifying variable genes" /> |
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8d8412d35247
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit 24c0223b9baa6d59bba381ef94f7e77b1c204d80
iuc
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74 <param argument="--cells_use" type="integer" min="0" optional="True" 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" /> |
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75 <param argument="--resolution" type="float" optional="True" 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." /> |
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76 <param argument="--min_pct" type="float" optional="True" label="Minimum percent cells" help="With FindMarkers only test genes that are detected in a minimum fraction of min.pct cells in either of the two populations. Meant to speed up the function by not testing genes that are very infrequently expressed. Default is 0.1" /> |
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77 <param argument="--logfc_threshold" type="float" min="0" optional="True" label="LogFC threshold" |
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78 help="With FindMarkers, limit testing to genes which show, on average, at least X-fold difference (log-scale)between the two groups of cells. Default is 0.25 Increasing logfc.threshold speeds up the function, but can miss weaker signals." /> |
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79 </section> |
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80 </inputs> |
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81 |
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82 <outputs> |
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83 <data name="out_pdf" format="pdf" from_work_dir="out.pdf" label="${tool.name} on ${on_string}: Plots" /> |
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84 <data name="out_rscript" format="txt" from_work_dir="out_rscript.txt" label="${tool.name} on ${on_string}: Rscript"> |
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85 <filter>rscript</filter> |
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86 </data> |
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87 <data name="out_rds" format="rds" from_work_dir="Seurat.rds" label="${tool.name} on ${on_string}: RData file"> |
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88 <filter>rds</filter> |
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89 </data> |
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90 </outputs> |
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91 |
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92 <tests> |
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93 <!-- Ensure count matrix input works --> |
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94 <test> |
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95 <param name="counts" ftype="tabular" value="deng_small.tab.gz"/> |
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96 <param name="min_cells" value="3"/> |
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97 <param name="min_genes" value="200"/> |
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98 <param name="low_thresholds" value="1" /> |
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99 <param name="high_thresholds" value="20000000" /> |
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100 <param name="x_low_cutoff" value="0.0125" /> |
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101 <param name="x_high_cutoff" value="3" /> |
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102 <param name="y_cutoff" value="0.5" /> |
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103 <param name="numPCs" value="10" /> |
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104 <param name="cells_use" value="500"/> |
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105 <param name="resolution" value="0.6" /> |
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106 <param name="min_pct" value="0.25" /> |
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107 <param name="logfc_threshold" value="0.25" /> |
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108 <output name="out_pdf" ftype="pdf" value="out.pdf" compare="sim_size"/> |
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109 </test> |
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110 </tests> |
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111 <help><![CDATA[ |
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112 .. class:: infomark |
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113 |
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114 **What it does** |
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115 |
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116 Seurat_ is a toolkit for quality control, analysis, and exploration of single cell RNA sequencing data. |
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117 It is developed and maintained by the `Satija Lab`_ at NYGC. Seurat aims to enable users to identify and |
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118 interpret sources of heterogeneity from single cell transcriptomic measurements, and to integrate diverse |
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119 types of single cell data. See the `Seurat Guided Clustering tutorial`_ for more information. |
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120 |
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121 ----- |
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122 |
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123 **Inputs** |
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124 |
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125 * Gene count matrix in TAB-separated format |
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126 |
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127 ----- |
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128 |
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129 **Outputs** |
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130 |
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131 * PDF of plots |
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132 |
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133 Optionally you can choose to output |
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134 |
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135 * Seurat RDS object (can use within R) |
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136 * Rscript |
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137 |
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138 .. _Seurat: https://www.nature.com/articles/nbt.4096 |
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139 .. _Satija Lab: https://satijalab.org/seurat/ |
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140 .. _Seurat Guided Clustering tutorial: https://satijalab.org/seurat/pbmc3k_tutorial.html |
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141 |
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142 ]]></help> |
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143 <citations> |
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144 <citation type="doi">10.1038/nbt.4096</citation> |
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145 </citations> |
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146 </tool> |