diff blast_parser.xml @ 0:cc71440b759f draft default tip

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/blast_parser.xml	Tue Sep 22 01:58:00 2015 -0400
@@ -0,0 +1,59 @@
+<?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>