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<tool id="micrornas_v1" name="microRNA" veision="1.0.0">
  <description>Program for plant microRNA analysis(miRNA only) </description>

  <requirements>
	<requirement type="package" version="0.0.13">fastx_toolkit </requirement>
    <requirement type="package" version="0.12.7">bowtie</requirement>
    <requirement type="set_environment">SCRIPT_PATH</requirement>
    <!--requirement type="package" version="3.0.1">R</requirement!-->
	<requirement type="package" version="2.59">SVG</requirement>
	<requirement type="package" version="2.1.8">ViennaRNA</requirement>
  </requirements>

  <!--command interpreter="perl">miPlant.pl -i $input -format $format -gfa $gfa -idx $index -pre $pre -mat $mat -rfam $rfam -idx2 $idx2 -D $D -a $a -M $M -min $min -max $max -mis $mis -e $e -f $f -v $v -r $r -dis $dis -flank $flank -mfe $mfe -t $t -o $output</command-->

  <command interpreter="perl">microRNA.pl 
   ## Change this to accommodate the number of threads you have available.
        -t \${GALAXY_SLOTS:-4}
	-path \$SCRIPT_PATH


   ## Do or not annotate known microRNAs
    #if $mirbase.known_microRNA == "yes":
	-pre $mirbase.pre -mat $mirbase.mat 
	#end if

        ## prepare bowtie index
        #set index_path = ''
        #if str($reference_genome.source) == "history":
           ### bowtie-build "$reference_genome.own_file" genome; ln -s "$reference_genome.own_file" genome.fa;
            #set index_path = $reference_genome.own_file
			-gfa $index_path
        #else:
            #set index_path = $reference_genome.index.fields.path
			-gfa ${index_path}.fa -idx $index_path
		#end if


     -mis $mismatch  -i $config -fa $reads -e $e -f $f -r $r -dis $dis -flank $flank -mfe $mfe  > run.log
  </command>

  <inputs>
	<param name="config" type="data" label="Raw data configs file" />
	<param name="reads" type="data" label="Input Fasta. file of candidate microRNA sequence" />

	        <!-- reference genome -->
        <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">
            <option value="indexed">Use a built-in index</option>
            <option value="history">Use one from the history</option>
          </param>
          <when value="indexed">
            <param name="index" type="select" label="Select a reference genome" help="If your genome of interest is not listed, contact the Galaxy team">
              <options from_data_table="bowtie_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 the reference genome" />
          </when>
        </conditional>

	<conditional name="mirbase">
		<param name="known_microRNA" type="select" label="Analysis known microRNAs(eg. from mirbase)">
		  <option value="yes" selected="true">yes</option>
		  <option value="no">no</option>
		 </param>
		 <when value="yes">
			<param name="mat" type="data" label="mature microRNA sequence file" />
			<param name="pre" type="data" label="precursor microRNA sequence fie" />
		 </when>
    </conditional> <!-- params -->



	<param name="mismatch" type="integer" value="0" label="number of allowed mismatches when mapping reads to genome" />
	<param name="e" type="integer" value="2" label="number of nucleotides upstream of the mature sequence to consider" />
	<param name="f" type="integer" value="5" label="number of nucleotides downstream of the mature sequence to consider" />
	<param name="r" type="integer" value="25" label="a read is allowed to map up to this number of positions in the genome" />
	<param name="dis" type="integer" value="200" label="Maximal space between miRNA and miRNA*" />
	<param name="flank" type="integer" value="10" label="Flank sequence length of miRNA precursor" />
	<param name="mfe" type="float" value="-30" label="Maximal free energy allowed for a miRNA precursor" />

  </inputs>

  <outputs>
   <data format="txt" name="known microRNA express list" from_work_dir="miRNA_out/known_microRNA_express.txt" label="${tool.name} on ${on_string}: known microRNA express list">
   <filter>(mirbase['known_microRNA'] == 'yes')</filter>
   </data>
   <data format="txt" name="known microRNA express alignment" from_work_dir="miRNA_out/known_microRNA_express.aln" label="${tool.name} on ${on_string}: known microRNA express alignment">
   <filter>(mirbase['known_microRNA'] == 'yes')</filter>
   </data>
   <data format="txt" name="known microRNA moRs result" from_work_dir="miRNA_out/known_microRNA_express.moRs" label="${tool.name} on ${on_string}: known microRNA moRs result">
   <filter>(mirbase['known_microRNA'] == 'yes')</filter>
   </data>
   <data format="fasta" name="known microRNA precursor file" from_work_dir="miRNA_out/known_microRNA_precursor.fa" label="${tool.name} on ${on_string}: known microRNA precursor file">
   <filter>(mirbase['known_microRNA'] == 'yes')</filter>
   </data>
   <data format="fasta" name="known microRNA mature file" from_work_dir="miRNA_out/known_microRNA_mature.fa" label="${tool.name} on ${on_string}: known microRNA mature file">
   <filter>(mirbase['known_microRNA'] == 'yes')</filter>
   </data>
   <data format="txt" name="novel microRNA express list" from_work_dir="miRNA_out/novel_microRNA_express.txt" label="${tool.name} on ${on_string}: novel microRNA express list"/>
   <data format="fasta" name="novel microRNA precursor file" from_work_dir="miRNA_out/novel_microRNA_precursor.fa" label="${tool.name} on ${on_string}: novel microRNA precursor file"/>
   <data format="fasta" name="novel microRNA mature sequence file" from_work_dir="miRNA_out/novel_microRNA_mature.fa" label="${tool.name} on ${on_string}: novel microRNA mature sequence file"/>
   <data format="fasta" name="non-microRNA sequence FASTA file" from_work_dir="miRNA_out/non_microRNA_sequence.fa" label="${tool.name} on ${on_string}: Sequence FASTA file of non-microRNA tags"/>

  </outputs>

 <help>

 </help>
 </tool>