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1 <tool id="r-sleuth" name="r-sleuth" version="0.29.0">
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2 <description>Sleuth is an R library for analysis of RNA-Seq experiments for which transcript abundances have been quantified with kallisto.</description>
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3 <requirements>
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4 <requirement type="package" version="1.20.0">r-getopt</requirement>
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5 <requirement type="package" version="0.29.0">r-sleuth</requirement>
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6 <requirement type="package" version="2.34.0">bioconductor-biomart</requirement>
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7 </requirements>
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8 <version_command>
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9 <![CDATA[
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10 echo $(R --version | grep version | grep -v GNU)", r-sleuth version" $(R --vanilla --slave -e "library(sleuth); cat(sessionInfo()\$otherPkgs\$sleuth\$Version)" 2> /dev/null | grep -v -i "WARNING: ")
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11 ]]>
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12 </version_command>
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13 <command detect_errors="aggressive">
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14 <![CDATA[
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15 #import re
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16 ## create symlinks to input datasets
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17 #for $file in $input_files
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18 #set $sname = re.sub('\.h5$', '', str($file.element_identifier))
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19 mkdir -p 'data/${sname}/kallisto' &&
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20 ln -s '$file' 'data/${sname}/kallisto/abundance.h5' &&
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21 #end for
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22
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23 Rscript '${__tool_directory__}/r-sleuth.R'
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24 --indir 'data'
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25 --metadata '$metadata'
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26 --full_model '~${full_model}'
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27 --reduced_model '~${reduced_model}'
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28 --gene_anno_name 'hsapiens_gene_ensembl' &&
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29 tar zcvf sleuth_shiny.tar.gz data/app.R data/so.rds
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30 ]]>
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31 </command>
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32 <inputs>
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33 <param name="input_files" type="data" format="h5" label="Select Abundance(HDF5) Datasets" min="2" multiple="True"/>
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34 <param name="metadata" type="data" format="txt,tsv,tabular" label="Metadata file"/>
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35 <param name="full_model" type="text" value="condition" label="Full model"/>
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36 <param name="reduced_model" type="text" value="1" label="Reduced model"/>
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37 <param name="gene_anno_name" type="select" label="BioMart dataset">
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38 <option value="hsapiens_gene_ensembl" selected="true">homo_sapiens</option>
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39 </param>
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40 </inputs>
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41 <outputs>
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42 <data name="output" format="tar" label="${tool.name} on ${on_string}: R Shiny app" from_work_dir="sleuth_shiny.tar.gz"/>
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43 </outputs>
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44 <tests>
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45 <test>
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46 <param name="input_files" value="SRR1867792.h5,SRR1909613.h5,SRR1909637.h5"/>
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47 <param name="metadata" value="metadata.txt"/>
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48 <output name="output" file="sleuth_shiny.tar.gz" ftype="tar"/>
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49 </test>
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50 </tests>
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51 <help>
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52 <![CDATA[
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53 This is a Galaxy wrapper for the Sleuth package.
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54
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55 **Input file format of metadata**
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56
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57 sample condition
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58 ---------------------
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59 SRR1867792 ESC
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60 SRR1909613 BM-MSC
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61 SRR1909637 BM-MSC
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62
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63 **Output**
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64
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65 This wrapper script generates Shiny web application files for RStudio.
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66 Unzip sleuth_shiny.tar.gz file, then run app.R file in RStudio.
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67 ]]>
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68 </help>
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69 <citations>
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70 <citation type="bibtex">
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71 @misc{githubsleuth,
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72 title = {sleuth},
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73 publisher = {GitHub},
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74 journal = {GitHub repository},
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75 url = {https://pachterlab.github.io/sleuth/},
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76 }
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77 </citation>
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78 </citations>
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79 </tool>
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