Mercurial > repos > ebi-gxa > seurat_export_cellbrowser

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planemo upload commit 34c30124158749b9eef51d5f323b608a503e7940
author ebi-gxa
date Sun, 01 Oct 2023 09:06:07 +0000
parents 6e876c9925c5
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1 <tool id="seurat_export_cellbrowser" name="Seurat Export2CellBrowser" profile="18.01" version="@SEURAT_VERSION@+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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12
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13 seurat-export-cellbrowser.R
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14 @INPUT_OBJECT@
0
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16 #if $markers_file:
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17 -m markers.csv
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18 #end if
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20 -o output_html;
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22 cd output_html && tar -cf '$output' *;
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23 ]]></command>
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25 <inputs>
2
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26 <expand macro="input_object_params"/>
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27 <param name="markers_file" type="data" optional="True" format="txt" label="Marker genes file from Seurat" />
0
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28 </inputs>
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30 <outputs>
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31 <data name="output" format="tar" label="${tool.name} on ${on_string}: UCSC CellBrowser bundle"/>
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32 </outputs>
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34 <tests>
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35 <test>
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36 <param name="rds_seurat_file" ftype="rdata" value="E-MTAB-6077-3k_features_90_cells-tsne.rds"/>
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37 <param name="markers_file" ftype="txt" value="E-MTAB-6077-3k_features_90_cells-markers.csv"/>
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38 <output name="output" >
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39 <assert_contents>
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40 <has_size value="2182656" delta="200000"/>
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41 </assert_contents>
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42 </output>
0
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43 </test>
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44 </tests>
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45 <help><![CDATA[
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46 .. class:: infomark
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48 **What it does**
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49
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50 This tool converts a Seurat object (hopefully with t-SNE results) and its
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51 accompanying marker genes file (optional) to a tar that can be feed to the
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52 UCSC CellBrowser tool.
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54 @SEURAT_INTRO@
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55
0
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56 -----
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58 **Inputs**
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60 * RDS object
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62 -----
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64 **Outputs**
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66 * Text file
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68 .. _Seurat: https://www.nature.com/articles/nbt.4096
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69 .. _Satija Lab: https://satijalab.org/seurat/
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70
1
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71 @VERSION_HISTORY@
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72
0
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73 ]]></help>
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74 <expand macro="citations" />
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75 </tool>