<tool id="plant_sirna_v1" name="siRNA" veision="1.0.0">
  <description>tool for plant siRNA analisis</description>

  <requirements>
    <requirement type="set_environment">SCRIPT_PATH</requirement>
    <requirement type="package" version="0.12.7">bowtie</requirement>
    <requirement type="package" version="3.0.1">R</requirement>
    <requirement type="package" version="1.20.0">degseq</requirement>
	<requirement type="package" version="0.0.13">fastx_toolkit </requirement>
	<requirement type="package" version="1.96">threads</requirement>
	<requirement type="package" version="1.06">Parallel-ForkManager</requirement>
	<requirement type="package" version="2.59">SVG</requirement>
	<requirement type="package" version="1.4_001">Boost-Graph</requirement>
  </requirements>

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

	-path \$SCRIPT_PATH

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

   ## Do or not annotate siRNAs by function
    #if $params.function_anno == "yes":
     -nat $params.nat -repeat $params.repeat
	#end if
   
   ## Do or not DEG
    #if $degseq.degseq_analysis == "yes" :
    -deg $degseq.deg
    #end if

  -format $format -g $genome -f $gff -mis $mis -rfam $rfam -v $v -a $a -n $mapnt -d $d -p $p -l $l  -cen $cen -span $span > run.log

  </command>

  <inputs>

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

	<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="genome"  type="data" label="genome sequence fasta file"/>
	<!--param type="data" name="index" label="genome sequence bowtie index"/-->
	<param name="gff" type="data" label="gff file" />
	<param name="mis" type="integer" value="0" label="number of allowed mismatches when mapping reads to genome" />
	<param name="rfam" type="data" label="rfam sequence file" />
	<param name="v" type="integer" value="0" label="report end-to-end hits less than v mismatches"/>
	<param name="a" type="text" value="ATCTCGTATG" label="3' adapter sequence" />
	<param name="mapnt" type="integer" value="25" label="a read is allowed to map up to this number of positions in the genome" />
	<param name="d" type="integer" value="100" label="distance of tag to merged a cluster" />

	<param name="p" type="select" lable="cluster method" multiple="false">
	  <option value="F">conventional</option>
	  <option value="T">NIBLES</option>
	</param>
	<param name="l" type="integer" value="1000" label="the length of the upstream and downstream,used in position annotate" />


	<conditional name="params">
		<param name="function_anno" type="select" label="Do or not annotate siRNAs by function">
		  <option value="no" selected="true">no</option>
		  <option value="yes">yes</option>
		 </param>
		 <when value="yes">
			<param name="nat" type="data" label="atural antisense transcripts file" />
			<param name="repeat" type="data" label="repeat information file out of Repeatmasker" />
		 </when>
    </conditional> <!-- params -->
	
	<param name="cen" type="data" label="centromere file input" />
	<param name="span" type="integer" value="50000" label="plot span" />
	
    <conditional name="degseq">
       <param name="degseq_analysis" type="select" label="Do or not identify Difference Expression Clusters">
		  <option value="no" selected="true">no</option>
		  <option value="yes">yes</option>
       </param>
       <when value="yes">
			<param name="deg" type="data" label="file config of de sample" />
        </when>
    </conditional>
    
  </inputs>

  <outputs>
   <data format="txt" name="siRNA cluster" from_work_dir="cluster_runs/total.result" label="${tool.name} on ${on_string}: siRNA cluster"/>
   <data format="html" name="analysis result" from_work_dir="cluster_runs/result.html" label="${tool.name} on ${on_string}: analysis result"/>

  </outputs>

 <help>

 </help>
 </tool>