Mercurial > repos > ebi-gxa > seurat_run_tsne

annotate seurat_run_tsne.xml @ 0:3aea769deab1 draft

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planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 9bf9a6e46a330890be932f60d1d996dd166426c4
author ebi-gxa
date Wed, 03 Apr 2019 11:19:13 -0400
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3aea769deab1 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 9bf9a6e46a330890be932f60d1d996dd166426c4
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1 <tool id="seurat_run_tsne" name="Seurat RunTSNE" version="2.3.1+galaxy1">
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2 <description>run t-SNE dimensionality reduction</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 seurat-run-tsne.R
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11 --input-object-file '$input'
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13 #if $genes_use:
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14 --genes-use '$genes_use'
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15 #end if
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17 #if str($adv.dims_use):
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18 --dims-use \$(seq -s , 1 '$adv.dims_use')
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19 #else
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20 --dims-use 1,10
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21 #end if
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23 #if not $adv.do_fast:
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24 --do-fast '$adv.do_fast'
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25 #end if
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27 --output-object-file '$output'
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28 --output-embeddings-file output_embed
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29 ]]></command>
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31 <inputs>
3aea769deab1 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 9bf9a6e46a330890be932f60d1d996dd166426c4
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32 <param name="input" argument="--input-obj-file" type="data" format="rdata" label="Seurat RDS object" help="The RDS/Rdata result of Seurat FindClusters."/>
3aea769deab1 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 9bf9a6e46a330890be932f60d1d996dd166426c4
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33 <expand macro="genes-use-input"/>
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34 <section name="adv" title="Advanced Options">
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35 <expand macro="dims-use-input"/>
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36 <param name="do_fast" label="Faster execution" argument="--do-fast" checked="true" type="boolean" truevalue="" falsevalue="FALSE" help="If TRUE, uses the Barnes-hut implementation, which runs faster, but is less flexible. TRUE by default."/>
3aea769deab1 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 9bf9a6e46a330890be932f60d1d996dd166426c4
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37 </section>
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38 </inputs>
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39
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40 <outputs>
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41 <data name="output" format="rdata" from_work_dir="*.rds" label="${tool.name} on ${on_string}: Seurat RDS"/>
3aea769deab1 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 9bf9a6e46a330890be932f60d1d996dd166426c4
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42 <data name="output_embed" format="csv" from_work_dir="output_embed" label="${tool.name} on ${on_string}: Seurat Embeddings"/>
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43 </outputs>
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44
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45 <tests>
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46 <test>
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47 <param name="input" ftype="rdata" value="out_findclust.rds"/>
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48 <output name="output" ftype="rdata" value="out_runtsne.rds" compare="sim_size"/>
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49 </test>
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50 </tests>
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51 <help><![CDATA[
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52 .. class:: infomark
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53
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54 **What it does**
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55
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56 Seurat_ is a toolkit for quality control, analysis, and exploration of single cell RNA sequencing data.
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57 It is developed and maintained by the `Satija Lab`_ at NYGC. Seurat aims to enable users to identify and
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58 interpret sources of heterogeneity from single cell transcriptomic measurements, and to integrate diverse
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59 types of single cell data.
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60
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61 Run t-SNE dimensionality reduction on selected features. Has the option of
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62 running in a reduced dimensional space (i.e. spectral tSNE, recommended),
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63 or running based on a set of genes. For details about stored TSNE calculation
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64 parameters, see standard output of the tool.
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65
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66 -----
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67
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68 **Inputs**
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69
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70 * RDS object
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71
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72 -----
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73
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74 **Outputs**
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75
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76 * Seurat RDS object
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77
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78 .. _Seurat: https://www.nature.com/articles/nbt.4096
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79 .. _Satija Lab: https://satijalab.org/seurat/
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80
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81 @VERSION_HISTORY@
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82 ]]></help>
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83 <expand macro="citations" />
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84 </tool>