<?xml version="1.0"?>
<tool id="SoftSearch" name="SoftSearch">
  <description>for structure variation</description>
  <command> #if $source.index_source=="history" 
	        samtools index $bam_file ; samtools faidx $source.history_fasta_file ; $inc | ~/2.4/src/SoftSearch.pl -l $min_length_soft_clip -q $min_map_quality -r $min_depth_soft_clip_loc -m $min_no_discordant_read -s $no_sd_consider_discordant -b $bam_file -f $source.history_fasta_file -o $out_file1
	    #else
		samtools index $bam_file ; samtools faidx $source.ref_fasta.fields.path ; $inc | ~/2.4/src/SoftSearch.pl -l $min_length_soft_clip -q $min_map_quality -r $min_depth_soft_clip_loc -m $min_no_discordant_read -s $no_sd_consider_discordant -b $bam_file -f $source.ref_fasta.fields.path -o $out_file1
	    #end if		
 </command>
  <inputs>
      <param name="bam_file" type="data"   format="bam" label="BAM Files" />
	 <conditional name="source">
            <param name="index_source" type="select" label="Choose the source for the reference list">
                <option value="cached">Locally cached</option>
                <option value="history">History</option>
            </param>
            <when value="history">
                <param format="fasta" name="history_fasta_file" type="data" label="Fasta file from history."/>
            </when>
            <when value="cached">
                  <param name="ref_fasta" type="select" >
                    <options from_data_table="fasta_indexes">
                    <validator type="no_options" message="No Fasta file is available" />
                    </options>
                  </param>
            </when>
        </conditional>
      <param name="inc" type="hidden" value="n=$RANDOM" />
     	<param name="min_length_soft_clip" type="integer" value="10" label="-l Minimum length of soft-clipped segment [5]" /> 
        <param name="min_map_quality" type="integer" value="20" label="-q Minimum mapping quality [20]" /> 	
	<param name="min_depth_soft_clip_loc" type="integer" value="10" label="-r Minimum depth of soft-clipped reads at position [5]" /> 
	<param name="min_no_discordant_read" type="integer" value="10" label="-m Minimum number of discordant read pairs [5]" /> 
	<param name="no_sd_consider_discordant" type="integer" value="4" label="-s Number of sd away from mean to be considered discordant" />       
  </inputs>
  <outputs>
      <data format="vcf" name="out_file1" />
  </outputs>
  <help>
  </help>
</tool>