<tool id="plant_microRNA_v1" name="miRPlant" veision="1.0.0">
  <description>tool for plant microRNA analisis</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">miRPlant.pl 
   ## Change this to accommodate the number of threads you have available.
        -t \${GALAXY_SLOTS:-4}
   ## Do or not delet rfam mapped tags
    #if $params.delet_rfam == "yes":
	-D 
	#end if
	-path \$SCRIPT_PATH

    #for $j, $s in enumerate( $series )
    ##rank_of_series=$j
    -i ${s.input}
    -tag ${s.tag}
    #end for

    -format $format -gfa $gfa -pre $pre -mat $mat -rfam $rfam  -a $a -M $mapnt -min $min -max $max -mis $mismatch -e $e -f $f -v $v -r $r -dis $dis -flank $flank -mfe $mfe > run.log
  </command>

  <inputs>

   <repeat name="series" title="Series">
     <param name="input" type="data" label="Raw data"/>
     <param name="tag" type="text" data_ref="input" label="Sample name of raw data"/>
   </repeat>

	<conditional name="params">
		<param name="delet_rfam" type="select" label="delet rfam mapped reads">
		  <option value="yes" selected="true">yes</option>
		  <option value="no">no</option>
		 </param>
    </conditional> <!-- params -->

	<!--param name="input" format="tabular"  type="data" label="input config file" /-->
	
	<param name="format" type="select" lable="raw data format" multiple="false">
	  <option value="fastq">Raw data is fastq. format</option>
	  <option value="fasta">Raw data is fasta. format</option>
	</param>
	
	<param name="gfa"  type="data" label="genome sequence fasta file"/>
	<!--param type="data" name="index" label="genome sequence bowtie index"/-->
	<param name="mat" type="data" label="mature microRNA sequence file" />
	<param name="pre" type="data" label="precursor microRNA sequence fie" />
	<param name="rfam" type="data" label="rfam sequence file" />
	<!--param type="data" name="idx2" label="rfam sequence bowtie index " -->
	<param name="a" type="text" value="ATCTCGTATG" label="3' adapter sequence" />
	<param name="mapnt" type="integer" value="8" label="minimum adapter map nts" />
	<param name="min" type="integer" value="19" label="minimum microRNA length" />
	<param name="max" type="integer" value="28" label="maximum microRNA length" />
	<param name="mismatch" type="integer" value="0" label="number of allowed mismatches when mapping reads to precursors" />
	<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="v" type="integer" value="0" label="report end-to-end hits less than v mismatches"/>
	<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="miRPlant_out/known_microRNA_express.txt" label="${tool.name} on ${on_string}: known microRNA express list"/>
   <data format="txt" name="known microRNA express alignment" from_work_dir="miRPlant_out/known_microRNA_express.aln" label="${tool.name} on ${on_string}: known microRNA express alignment"/>
   <data format="txt" name="known microRNA moRs result" from_work_dir="miRPlant_out/known_microRNA_express.moRs" label="${tool.name} on ${on_string}: known microRNA moRs result"/>
   <data format="txt" name="known microRNA precursor file" from_work_dir="miRPlant_out/known_microRNA_precursor.fa" label="${tool.name} on ${on_string}: known microRNA precursor file"/>
   <data format="txt" name="known microRNA mature file" from_work_dir="miRPlant_out/known_microRNA_mature.fa" label="${tool.name} on ${on_string}: known microRNA mature file"/>
   <data format="txt" name="novel microRNA express list" from_work_dir="miRPlant_out/novel_microRNA_express.txt" label="${tool.name} on ${on_string}: novel microRNA express list"/>
   <data format="txt" name="novel microRNA precursor file" from_work_dir="miRPlant_out/novel_microRNA_precursor.fa" label="${tool.name} on ${on_string}: novel microRNA precursor file"/>
   <data format="txt" name="novel microRNA mature sequence file" from_work_dir="miRPlant_out/novel_microRNA_mature.fa" label="${tool.name} on ${on_string}: novel microRNA mature sequence file"/>
   <data format="html" name="analysis result" from_work_dir="miRPlant_out/result.html" label="${tool.name} on ${on_string}: analysis result"/>
  </outputs>

 <help>

 </help>
 </tool>