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<?xml version="1.0"?>
<tool id="blast_parser_using_awk" name="BLAST OUTPUT PARSER" version="0.0.1">

<description>parses Blast Output File</description>

<command>
   /bin/awk 
   'BEGIN {FS="\t"} {if($11 &lt;= $evalue &amp;&amp;  $13 &gt;= $qcovs) print $0 }'  
   $blastoutfile  
   &gt; $parsed_blastfile_above_cutoff;

   /bin/awk 
   '{FS="\t"} {if($11 &gt; $evalue ||  $13 &lt; $qcovs) print $0 }'  
   $blastoutfile 
   &gt; $parsed_blastfile_below_cutoff;

   /bin/sed -e '/^&gt;/s/$/@@@@/' -e 's/^&gt;/#/' $trinityassembledfile 
      |  tr -d '\n' 
      |  tr "#" '\n' 
      |  sed -e 's/^/&gt;/' -e 's/@@@@/\n/' 
      |  sed -e  "1d"  
      &gt; $oneline_file;

   /bin/awk 
   'BEGIN {FS="|"} {print "grep -w -A 1 \""$1"\" $oneline_file &gt;&gt; $blastfile_below_cutoff"}' 
   $parsed_blastfile_below_cutoff  
   &gt; pick_below_sh;

   /bin/sh pick_below_sh;

   /bin/awk 
   'BEGIN {FS="|"} {print "grep -w -A 1 \""$1"\" $oneline_file &gt;&gt; $blastfile_above_cutoff"}' 
   $parsed_blastfile_above_cutoff  
   &gt; pick_above_sh;
   
   /bin/sh pick_above_sh;
   
</command>

<inputs>
	<param name="blastoutfile" type="data" format="tabular" label="blast output file"/>
	<param name="trinityassembledfile" type="data" format="fasta" label="Trinity Assembled [fasta file]" /> 
	<param name="evalue" type="float"  value='1e-05'  label="EVALUE" help="default (evalue &lt; = 1e-05)"/>
	<param name="qcovs" type="integer"  value='95'  label="Query Coverage" help="default (qcovs &gt;  = 95)"/>
</inputs>
 
<outputs>
	<data name="parsed_blastfile_above_cutoff" format="tabular" label="parsed_blastfile (Above Cutoff Value)" />
	<data name="parsed_blastfile_below_cutoff" format="tabular" label="parsed_blastfile (Below cutoff Value)" />
	<data name="oneline_file" format="fasta" label="parsed_trinity_assembled_file (oneline_file)" />
	<data name="blastfile_below_cutoff" format="fasta" label="blast fasta file (Below cutoff Value)" />
	<data name="blastfile_above_cutoff" format="fasta" label="blast fasta file (Above cutoff Value)" />
</outputs>

<tests/>
<help>blast output parser tool</help>


</tool>