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annotate sleuth.xml @ 3:172091d47f5a draft default tip

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planemo upload for repository https://github.com/youyuh48/galaxy-sleuth/tree/master/ commit 8d9ff6181e933951e015e67f1719588bab2b3ab5-dirty
author youyuh48
date Tue, 12 Jun 2018 17:58:47 -0400
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3
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1 <tool id="sleuth" name="sleuth" version="0.30.0">
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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 <container type="docker">youyuh48/sleuth:0.30.0</container>
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5 </requirements>
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6 <version_command>
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7 <![CDATA[
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8 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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9 ]]>
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10 </version_command>
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11 <command detect_errors="aggressive">
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12 <![CDATA[
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13 #import re
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14 ## create symlinks to input datasets
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15 #for $file in $input_files
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16 #set $sname = re.sub('\.h5$', '', str($file.element_identifier))
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17 mkdir -p 'data/${sname}/kallisto' &&
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18 ln -s '$file' 'data/${sname}/kallisto/abundance.h5' &&
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19 #end for
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20
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21 Rscript '${__tool_directory__}/sleuth.R'
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22 --indir 'data'
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23 --metadata '$metadata'
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24 --full_model '~${full_model}'
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25 --reduced_model '~${reduced_model}'
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26 #if $anno.biomart == "Yes"
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27 --gene_anno_name '$anno.gene_anno_name'
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28 #end if
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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 <conditional name="anno">
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38 <param name="biomart" type="select" label="Use BioMart?" help="">
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39 <option value="Yes">Yes</option>
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40 <option value="No">No</option>
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41 </param>
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42 <when value="Yes">
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43 <param name="gene_anno_name" type="select" label="BioMart dataset">
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44 <option value="hsapiens_gene_ensembl" selected="true">homo_sapiens</option>
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45 </param>
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46 </when>
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47 <when value="No"></when>
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48 </conditional>
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49 </inputs>
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50 <outputs>
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51 <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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52 </outputs>
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53 <tests>
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54 <test>
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55 <param name="input_files" value="SRR1867792.h5,SRR1909613.h5,SRR1909637.h5"/>
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56 <param name="metadata" value="metadata.txt"/>
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57 <output name="output" file="sleuth_shiny.tar.gz" ftype="tar"/>
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58 </test>
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59 </tests>
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60 <help>
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61 <![CDATA[
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62 This is a Galaxy wrapper for the Sleuth package.
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63
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64 **Input file format of metadata**
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65
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66 sample condition
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67 ---------------------
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68 SRR1867792 ESC
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69 SRR1909613 BM-MSC
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70 SRR1909637 BM-MSC
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71
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72 **Output**
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73
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74 This wrapper script generates Shiny web application files for RStudio.
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75 Unzip sleuth_shiny.tar.gz file, then run app.R file in RStudio.
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76 ]]>
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77 </help>
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78 <citations>
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79 <citation type="bibtex">
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80 @misc{githubsleuth, title = {sleuth}, publisher = {GitHub}, journal = {GitHub repository}, url = {https://pachterlab.github.io/sleuth/}, }
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81 </citation>
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82 </citations>
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83 </tool>