<tool id="sRNAPipe" name="sRNAPipe" version="0.0.1">
  <description>In-depth study of small RNA</description>
  <command interpreter="perl">

    ./bin/sRNAPipe.pl

    --fastq ${first_input}
    --fastq_n ${first_input.name}
    #for $input_file in $input_files:
    --fastq ${input_file.additional_input}
    --fastq_n ${input_file.additional_input.name}
    #end for

    #if $Genome.refGenomeSource == "history":
    --ref "${Genome.ownFile}"
    --build_index
    #else:
    --ref "${Genome.indices.fields.path}"
    #end if

    #if $tRNAs.refGenomeSource == "history":
    --tRNAs "${tRNAs.ownFile}"
    --build_tRNAs
    #elif $tRNAs.refGenomeSource == "none":
    --tRNAs "None"
    #else:
    --tRNAs "${tRNAs.indices.fields.path}"
    #end if

    #if $snRNAs.refGenomeSource == "history":
    --snRNAs "${snRNAs.ownFile}"
    --build_snRNAs
    #elif $snRNAs.refGenomeSource == "none":
    --snRNAs "None"
    #else:
    --snRNAs "${snRNAs.indices.fields.path}"
    #end if

    #if $rRNAs.refGenomeSource == "history":
    --rRNAs "${rRNAs.ownFile}"
    --build_rRNAs
    #elif $rRNAs.refGenomeSource == "none":
    --rRNAs "None"
    #else:
    --rRNAs "${rRNAs.indices.fields.path}"
    #end if

    #if $miRNAs.refGenomeSource == "history":
    --miRNAs "${miRNAs.ownFile}"
    --build_miRNAs
    #else:
    --miRNAs "${miRNAs.indices.fields.path}"
    #end if

    #if $transcripts.refGenomeSource == "history":
    --transcripts "${transcripts.ownFile}"
    --build_transcripts
    #else:
    --transcripts "${transcripts.indices.fields.path}"
    #end if

    #if $TE.refGenomeSource == "history":
    --TE "${TE.ownFile}"
    --build_TE
    #else:
    --TE "${TE.indices.fields.path}"
    #end if

    --si_min $si_min
    --si_max $si_max
    --pi_min $pi_min
    --pi_max $pi_max
    --min $min
    --max $max

    --mis  $mis
    --misTE $misTE
    --dir $html_out.files_path
    --html $html_out
    --PPPon $PPPon
  </command>

  <requirements> 
    <requirement type="package" version="0.7.12">bwa</requirement>
    <requirement type="package" version="2.24">bedtools</requirement>
    <requirement type="package" version="1.2">samtools</requirement>
    <requirement type="package" version="3.3.2">r-base</requirement>
    <requirement type="package" version="5.20.3.1">perl</requirement>
    <requirement type="package" version="2.50">perl-getopt-long</requirement>
    <requirement type="package" version="1.19">perl-parallel-forkmanager</requirement>
    <requirement type="package" version="0.34" >perl-statistics-r</requirement>
    <requirement type="package" version="0.29">perl-string-random</requirement>
    <requirement type="package" version="3.6">r-plotrix</requirement>
    <requirement type="package" version="1.14.0">bioconductor-sushi</requirement>
    <requirement type="package" version="1.1_2">r-colorbrewer</requirement>
    <requirement type="package" version="1.0.1">r-ggplot2</requirement>
  </requirements> 

  <inputs>
    <param format="fastqsanger" name="first_input" type="data" label="fastqsanger (Q33)" help=""/>
    <repeat name="input_files" title="Additional Fastq Files">
      <param format="fastqsanger" name="additional_input" type="data" label="fastqsanger (Q33)" help=""/>
    </repeat>
    <conditional name="Genome">
      <param name="refGenomeSource" type="select" label="Will you select a reference genome from your history or use a built-in index?">
        <option value="indexed">Use a built-in index</option>
        <option value="history">Use one from the history</option>
      </param>
      <when value="indexed">
        <param name="indices" type="select" label="Select a reference genome">
          <options from_data_table="bwa_indexes">
            <filter type="sort_by" column="2" />
            <validator type="no_options" message="No indexes are available" />
          </options>
        </param>
      </when>
      <when value="history">
        <param name="ownFile" type="data" format="fasta" metadata_name="dbkey" label="Select a reference from history" />
      </when>
    </conditional>
    <conditional name="transcripts">
      <param name="refGenomeSource" type="select" label="Will you select transcripts database from your history or use a built-in index?">
        <option value="indexed">Use a built-in index</option>
        <option value="history">Use one from the history</option>
      </param>
      <when value="indexed">
        <param name="indices" type="select" label="Select a transcripts reference">
          <options from_data_table="bwa_indexes">
            <filter type="sort_by" column="2" />
            <validator type="no_options" message="No indexes are available" />
          </options>
        </param>
      </when>
      <when value="history">
        <param name="ownFile" type="data" format="fasta" metadata_name="dbkey" label="Select a reference from history" />
      </when>
    </conditional>
    <conditional name="TE">
      <param name="refGenomeSource" type="select" label="Will you select TE database from your history or use a built-in index?">
        <option value="indexed">Use a built-in index</option>
        <option value="history">Use one from the history</option>
      </param>
      <when value="indexed">
        <param name="indices" type="select" label="Select a TE reference">
          <options from_data_table="bwa_indexes">
            <filter type="sort_by" column="2" />
            <validator type="no_options" message="No indexes are available" />
          </options>
        </param>
      </when>
      <when value="history">
        <param name="ownFile" type="data" format="fasta" metadata_name="dbkey" label="Select a reference from history" />
      </when>
    </conditional>
    <conditional name="miRNAs">
      <param name="refGenomeSource" type="select" label="Will you select miRNA database from your history or use a built-in index?">
        <option value="indexed">Use a built-in index</option>
        <option value="history">Use one from the history</option>
      </param>
      <when value="indexed">
        <param name="indices" type="select" label="Select a miRNA reference">
          <options from_data_table="bwa_indexes">
            <filter type="sort_by" column="2" />
            <validator type="no_options" message="No indexes are available" />
          </options>
        </param>
      </when>
      <when value="history">
        <param name="ownFile" type="data" format="fasta" metadata_name="dbkey" label="Select a reference from history" />
      </when>
    </conditional>
    <conditional name="snRNAs">
      <param name="refGenomeSource" type="select" label="Will you select snRNA database from your history or use a built-in index?">
        <option value="indexed">Use a built-in index</option>
        <option value="history">Use one from the history</option>
        <option value="none">None</option>
      </param>
      <when value="indexed">
        <param name="indices" type="select" label="Select a snRNAs reference">
          <options from_data_table="bwa_indexes">
            <filter type="sort_by" column="2" />
            <validator type="no_options" message="No indexes are available" />
          </options>
        </param>
      </when>
      <when value="history">
        <param name="ownFile" type="data" format="fasta" metadata_name="dbkey" label="Select a reference from history" />
      </when>
    </conditional>
    <conditional name="rRNAs">
      <param name="refGenomeSource" type="select" label="Will you select rRNAs database from your history or use a built-in index?">
        <option value="indexed">Use a built-in index</option>
        <option value="history">Use one from the history</option>
        <option value="none">None</option>
      </param>
      <when value="indexed">
        <param name="indices" type="select" label="Select a rRNAs reference">
          <options from_data_table="bwa_indexes">
            <filter type="sort_by" column="2" />
            <validator type="no_options" message="No indexes are available" />
          </options>
        </param>
      </when>
      <when value="history">
        <param name="ownFile" type="data" format="fasta" metadata_name="dbkey" label="Select a reference from history" />
      </when>
    </conditional>
    <conditional name="tRNAs">
      <param name="refGenomeSource" type="select" label="Will you select tRNA database from your history or use a built-in index?">
        <option value="indexed">Use a built-in index</option>
        <option value="history">Use one from the history</option>
        <option value="none">None</option>
      </param>
      <when value="indexed">
        <param name="indices" type="select" label="Select a tRNA reference">
          <options from_data_table="bwa_indexes">
            <filter type="sort_by" column="2" />
            <validator type="no_options" message="No indexes are available" />
          </options>
        </param>
      </when>
      <when value="history">
        <param name="ownFile" type="data" format="fasta" metadata_name="dbkey" label="Select a reference from history" />
      </when>
    </conditional>

    <param name="min" type="integer" value="18" label="minimum read size"/>
    <param name="max" type="integer" value="29" label="maximum read size"/>
    <param name="si_min" type="integer" value="21" label="lower bound of siRNA range"/>  
    <param name="si_max" type="integer" value="21" label="higher bound of siRNA range"/>
    <param name="pi_min" type="integer" value="23" label="lower bound of piRNA range"/>
    <param name="pi_max" type="integer" value="29" label="higher bound of piRNA range"/>

    <param name="mis" type="integer" value="0" label="maximal genome mismatches"/>
    <param name="misTE" type="integer" value="3" label="maximal TE mismatches"/>
    <param name="PPPon" type="boolean" checked="true" label="PPPartners"/>
  </inputs>
  <outputs>
    <data  format="html" name="html_out" label="${tool.name}_${first_input.name}_${on_string}"/>

       <collection format ="fastqsanger" type="list" label="${tool.name}_fastq_outputs" name="output_fastqsanger">
            <discover_datasets format ="fastqsanger" pattern="(?P&lt;name&gt;.*)" directory="fastq_dir" />
        </collection>

  </outputs>
  <help>
 	**User manual**
 	"https://github.com/brassetjensen/sRNAPipe/blob/master/sRNAPipe_User_Manual.pdf"
  </help>
</tool>