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<tool id="sleuth" name="sleuth" version="0.30.0">
  <description>Sleuth is an R library for analysis of RNA-Seq experiments for which transcript abundances have been quantified with kallisto.</description>
  <requirements>
    <container type="docker">youyuh48/sleuth:0.30.0</container>
  </requirements>
  <version_command>
    <![CDATA[
      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: ")
    ]]>
  </version_command>
  <command detect_errors="aggressive">
    <![CDATA[
      #import re
      ## create symlinks to input datasets
      #for $file in $input_files
        #set $sname = re.sub('\.h5$', '', str($file.element_identifier))
        mkdir -p 'data/${sname}/kallisto' &&
        ln -s '$file' 'data/${sname}/kallisto/abundance.h5' &&
      #end for

      Rscript '${__tool_directory__}/sleuth.R'
        --indir 'data'
        --metadata '$metadata'
        --full_model '~${full_model}'
        --reduced_model '~${reduced_model}'
        #if $anno.biomart == "Yes"
        --gene_anno_name '$anno.gene_anno_name'
        #end if
      && tar zcvf sleuth_shiny.tar.gz data/app.R data/so.rds
    ]]>
  </command>
  <inputs>
    <param name="input_files" type="data" format="h5" label="Select Abundance(HDF5) Datasets" min="2" multiple="True"/>
    <param name="metadata" type="data" format="txt,tsv,tabular" label="Metadata file"/>
    <param name="full_model" type="text" value="condition" label="Full model"/>
    <param name="reduced_model" type="text" value="1" label="Reduced model"/>
    <conditional name="anno">
      <param name="biomart" type="select" label="Use BioMart?" help="">
        <option value="Yes">Yes</option>
        <option value="No">No</option>
      </param>
      <when value="Yes">
        <param name="gene_anno_name" type="select" label="BioMart dataset">
          <option value="hsapiens_gene_ensembl" selected="true">homo_sapiens</option>
        </param>
      </when>
      <when value="No"></when>
    </conditional>
  </inputs>
  <outputs>
    <data name="output" format="tar" label="${tool.name} on ${on_string}: R Shiny app" from_work_dir="sleuth_shiny.tar.gz"/>
  </outputs>
  <tests>
    <test>
      <param name="input_files" value="SRR1867792.h5,SRR1909613.h5,SRR1909637.h5"/>
      <param name="metadata" value="metadata.txt"/>
      <output name="output" file="sleuth_shiny.tar.gz" ftype="tar"/>
    </test>
  </tests>
  <help>
    <![CDATA[
This is a Galaxy wrapper for the Sleuth package.

**Input file format of metadata**

sample      condition
---------------------
SRR1867792  ESC
SRR1909613  BM-MSC
SRR1909637  BM-MSC

**Output**

This wrapper script generates Shiny web application files for RStudio.
Unzip sleuth_shiny.tar.gz file, then run app.R file in RStudio.
]]>
  </help>
  <citations>
    <citation type="bibtex">
      @misc{githubsleuth, title = {sleuth}, publisher = {GitHub}, journal = {GitHub repository}, url = {https://pachterlab.github.io/sleuth/}, }
    </citation>
  </citations>
</tool>