<tool id="ArmDB" name="ArmDB: Generation of Pre-miRNA arm reference DB (5p and 3p arms)" version="0.1.0">
  <requirements>
    <requirement type="package" version="2.28.0">Bedtools</requirement>
     <requirement type="package" version="3.7.4">python</requirement>
  </requirements>
  <command>
    #if $mir_input.analysis == "1":
     #set path=$mir_input.genome1.fields.dbkey
     python $__tool_directory__/armdb_mirbase.py -pos $positions -tool_dir $__tool_directory__ -gff3 "$path" -gen $mir_input.genome1.fields.value
    #end if    
    #if $mir_input.analysis == "2":
     #set path=$mir_input.genome2.fields.value
     python $__tool_directory__/armdb_mirgene.py -pos $positions -tool_dir $__tool_directory__ -sym "$path"
    #end if
  </command>
  <inputs>
   <conditional name="mir_input">
    <param name="analysis" type="select" label="Choose reference Mir database" help="Choose which database prefer to be used.">
      <option value="1" selected="true">MirBase</option>
      <option value="2">MirGene</option>
    </param>
    <when value="1">
        <param name="genome1" type="select" label="Choose organism" help="If your genome coordinates of interest is not listed, contact the Galaxy team">
          <options from_data_table="mirbase" />
        </param> 
    </when>
    <when value="2">
      <param name="genome2" type="select" label="Choose organism" help="If your genome coordinates of interest is not listed, contact the" >
        <options from_data_table="mirgene" />
      </param>
    </when>
   </conditional>
   <param name="positions" type="integer" min="0" max="8" value="1" label="Custom Arm length" help="Choose how many nucleotides you want to extend the 5p and 3p mature sequences to create the refernce arms" />
  </inputs>
  <outputs>
    <data name="shifted_gff1" format="txt" label="Custom Bed file" from_work_dir="$__tool_directory__/shifted_mirnas.bed">
         <filter>mir_input['analysis']== "1" </filter>
    </data>
    <data name="normal_gff1" format="fasta" label="Official Bed file" from_work_dir="$__tool_directory__/original_mirnas.bed" >
       	 <filter>mir_input['analysis']== "1" </filter>
    </data>
    <data name="custom reference genome1" format="fasta" label="Custom reference arms" from_work_dir="$__tool_directory__/new_ref.fa" >
       	 <filter>mir_input['analysis']== "1" </filter>
    </data>

    <data name="shifted_gff" format="txt" label="Mature and star miRNA sequences" from_work_dir="$__tool_directory__/shifted_mirnas.bed">
       	 <filter>mir_input['analysis']== "2" </filter>
    </data>
    <data name="normal_gff" format="fasta" label="Primary transcripts with flanks" from_work_dir="$__tool_directory__/original_mirnas.bed" >
         <filter>mir_input['analysis']== "2" </filter>
    </data>
    <data name="custom reference genome" format="fasta" label="Custom reference arms" from_work_dir="$__tool_directory__/new_ref.fa" >
    	 <filter>mir_input['analysis']== "2" </filter>
    </data>

  </outputs>
  <help>

  </help>
</tool>