ca_jp_STAR.xml

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<tool id="ca_jp_STAR" name="Run_STAR" version="2.7.3a">
  <description> STAR Quantification mode </description>
  <command interpreter="bash"><![CDATA[ca_jp_STAR.sh $genome_ref_fasta $genome_ref_gtf
  #if $pair_single_end.pair_end == "F":
      $pair_single_end.reads > $logs;
  #else:
    $pair_single_end.reads_1 $pair_single_end.reads_2 > $logs;
  #end if
  cat ReadsPerGene.out.tab>$output;
  ]]></command>

<inputs>
    <param format="fasta" name="genome_ref_fasta" type="data" label="Reference genome (fasta)" />
    <param format="gff" name="genome_ref_gtf" type="data" label="Reference genome (gtf)" />
  <conditional name="pair_single_end" >
    <param name="pair_end" type = "select" help = "Pair or single end sequencing ?" label = "Pair or single end sequencing ?" >
        <option value = "T"> Pair </option>
        <option value = "F"> Single </option>
    </param>
    <when value = "F"> 
        <param format="fastq" name="reads" type="data" label="Reads file"/>
    </when>
    <when value = "T">
        <param format="fastq" name="reads_1" type="data" label="Reads_1 file" />
        <param format="fastq" name="reads_2" type="data" label="Reads_2 file" />
    </when>
  </conditional>
</inputs>
  
<outputs>
  <data format="txt" name="logs" label ="Logs.txt" />
  <data format="tabular" name="output" label="ReadsPerGene.tab" />
</outputs>

<help>
  STAR build-in quantification for single or paired end reads. Following these steps :
  * Indexing the genome
  * Reads mapping
  * Quantification
</help>
 
</tool>