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<tool id="download_align" name="Download and align" version="0.0.1">
  <description> Downloads fastq.gz, unzips, trims with cutadapt and alignes to reference</description>
  <requirements>
      <requirement type="package" version="1.8">cutadapt</requirement>
      <requirement type="package" version="2.2.4">bowtie2</requirement>
      <requirement type="package" version="0.1.18">samtools</requirement>
  </requirements>
  <command>
  #set index_path = ''
  #if str($reference_genome.source) == "history":
    bowtie2-build "$reference_genome.own_file" genome &amp;&amp;
    ln -s "$reference_genome.own_file" genome.fa &amp;&amp;
    #set index_path = 'genome'
  #else:
    #set index_path = $reference_genome.index.fields.path
  #end if
  wget -O - $file | gunzip -c | cutadapt   -q 20 -m 20 - | bowtie2  -q 
  ## index file path
  -x $index_path 
  -U - | samtools view -bS - > $output
  </command>
  <stdio>
    <exit_code range="1:" level="fatal" description="Tool exception" />
  </stdio>
  <inputs>
    <param format="text" name="file" type="text" label="URL for fastq.gz"/>
    <conditional name="reference_genome">
          <param name="source" type="select" label="Will you select a reference genome from your history or use a built-in index?" help="Built-ins were indexed using default options. See `Indexes` section of help below">
            <option value="indexed">Use a built-in genome index</option>
            <option value="history">Use a genome from the history and build index</option>
          </param>
          <when value="indexed">
            <param name="index" type="select" label="Select reference genome" help="If your genome of interest is not listed, contact the Galaxy team">
              <options from_data_table="bowtie2_indexes">
                <filter type="sort_by" column="2"/>
                <validator type="no_options" message="No indexes are available for the selected input dataset"/>
              </options>
            </param>
          </when>
          <when value="history">
            <param name="own_file" type="data" format="fasta" metadata_name="dbkey" label="Select reference genome" />
          </when>
    </conditional>
  </inputs> 
  <outputs> 
      <data format="bam" name="output" label="${tool.name} on ${on_string}: aligned reads (sorted BAM)" />
  </outputs>
  <help>
    This tool extracts reads from sra, runs cutdapt and bowtie and outputs a bam file. 

    Contact Eduardo Alves at [e-mail] for support and bug reports.
  </help>
</tool>