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1 <?xml version="1.0"?>
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2 <tool id="blast_parser_using_awk" name="BLAST OUTPUT PARSER" version="0.0.1">
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3
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4 <description>parses Blast Output File</description>
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5
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6 <command>
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7 /bin/awk
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8 'BEGIN {FS="\t"} {if($11 <= $evalue && $13 >= $qcovs) print $0 }'
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9 $blastoutfile
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10 > $parsed_blastfile_above_cutoff;
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11
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12 /bin/awk
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13 '{FS="\t"} {if($11 > $evalue || $13 < $qcovs) print $0 }'
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14 $blastoutfile
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15 > $parsed_blastfile_below_cutoff;
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16
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17 /bin/sed -e '/^>/s/$/@@@@/' -e 's/^>/#/' $trinityassembledfile
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18 | tr -d '\n'
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19 | tr "#" '\n'
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20 | sed -e 's/^/>/' -e 's/@@@@/\n/'
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21 | sed -e "1d"
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22 > $oneline_file;
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23
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24 /bin/awk
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25 'BEGIN {FS="|"} {print "grep -w -A 1 \""$1"\" $oneline_file >> $blastfile_below_cutoff"}'
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26 $parsed_blastfile_below_cutoff
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27 > pick_below_sh;
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28
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29 /bin/sh pick_below_sh;
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30
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31 /bin/awk
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32 'BEGIN {FS="|"} {print "grep -w -A 1 \""$1"\" $oneline_file >> $blastfile_above_cutoff"}'
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33 $parsed_blastfile_above_cutoff
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34 > pick_above_sh;
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35
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36 /bin/sh pick_above_sh;
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37
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38 </command>
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39
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40 <inputs>
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41 <param name="blastoutfile" type="data" format="tabular" label="blast output file"/>
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42 <param name="trinityassembledfile" type="data" format="fasta" label="Trinity Assembled [fasta file]" />
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43 <param name="evalue" type="float" value='1e-05' label="EVALUE" help="default (evalue < = 1e-05)"/>
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44 <param name="qcovs" type="integer" value='95' label="Query Coverage" help="default (qcovs > = 95)"/>
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45 </inputs>
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46
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47 <outputs>
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48 <data name="parsed_blastfile_above_cutoff" format="tabular" label="parsed_blastfile (Above Cutoff Value)" />
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49 <data name="parsed_blastfile_below_cutoff" format="tabular" label="parsed_blastfile (Below cutoff Value)" />
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50 <data name="oneline_file" format="fasta" label="parsed_trinity_assembled_file (oneline_file)" />
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51 <data name="blastfile_below_cutoff" format="fasta" label="blast fasta file (Below cutoff Value)" />
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52 <data name="blastfile_above_cutoff" format="fasta" label="blast fasta file (Above cutoff Value)" />
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53 </outputs>
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54
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55 <tests/>
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56 <help>blast output parser tool</help>
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57
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58
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59 </tool>
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