Mercurial > repos > ebi-gxa > seurat_export_cellbrowser

annotate seurat_export_cellbrowser.xml @ 0:29112eeaf521 draft

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planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit fc12e1e90bdc675bd81cf50528afd64ff3dc5c08
author ebi-gxa
date Mon, 04 Mar 2019 12:08:58 -0500
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children 45d02a754a7d
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29112eeaf521 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit fc12e1e90bdc675bd81cf50528afd64ff3dc5c08
ebi-gxa
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1 <tool id="seurat_export_cellbrowser" name="Seurat Export2CellBrowser" version="2.3.1+galaxy0">
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2 <description>produces files for UCSC CellBrowser import.</description>
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3 <macros>
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4 <import>seurat_macros.xml</import>
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5 </macros>
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6 <expand macro="requirements" />
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7 <expand macro="version" />
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8 <command detect_errors="exit_code"><![CDATA[
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9 #if $markers_file:
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10 cp '$markers_file' markers.csv;
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11 #end if
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13 seurat-export-cellbrowser.R -i '$rds_input'
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29112eeaf521 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit fc12e1e90bdc675bd81cf50528afd64ff3dc5c08
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15 #if $markers_file:
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16 -m markers.csv
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17 #end if
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19 -o output_html;
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21 cd output_html && tar -cf '$output' *;
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22 ]]></command>
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24 <inputs>
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25 <param name="rds_input" type="data" format="rdata" label="Seurat RDS object" />
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26 <param name="markers_file" type="data" format="txt" label="Marker genes file from Seurat" />
29112eeaf521 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit fc12e1e90bdc675bd81cf50528afd64ff3dc5c08
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27 </inputs>
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28
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29 <outputs>
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30 <data name="output" format="tar" label="${tool.name} on ${on_string}: UCSC CellBrowser bundle"/>
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31 </outputs>
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32
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33 <tests>
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34 <test>
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35 <param name="rds_input" ftype="rdata" value="out_runtsne.rds"/>
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36 <param name="markers_file" ftype="txt" value="out_markers.csv"/>
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37 <output name="output" ftype="tar" value="out_cellbrowser_bundle.tar"/>
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38 </test>
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39 </tests>
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40 <help><![CDATA[
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41 .. class:: infomark
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42
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43 **What it does**
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44
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45 Seurat_ is a toolkit for quality control, analysis, and exploration of single cell RNA sequencing data.
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46 It is developed and maintained by the `Satija Lab`_ at NYGC. Seurat aims to enable users to identify and
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47 interpret sources of heterogeneity from single cell transcriptomic measurements, and to integrate diverse
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48 types of single cell data.
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49
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50 This tool converts a Seurat object (hopefully with t-SNE results) and its accompanying marker genes file (optional)
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51 to a tar that can be feed to the UCSC CellBrowser tool.
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52 -----
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53
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54 **Inputs**
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55
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56 * RDS object
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57
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58 -----
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59
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60 **Outputs**
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61
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62 * Text file
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63
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64 .. _Seurat: https://www.nature.com/articles/nbt.4096
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65 .. _Satija Lab: https://satijalab.org/seurat/
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66
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67 ]]></help>
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68 <expand macro="citations" />
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69 </tool>