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1 <tool id="factera" name="FACTERA" version="1.4.3">
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2
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3 <description>Fusion And Chromosomal Translocation Enumeration and Recovery Algorithm</description>
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4
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5 <requirements>
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6 <requirement type="package" version="0.1.19">samtools</requirement>
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7 <requirement type="package" version="2.2.26+">blast+</requirement>
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8 <requirement type="package" version="310">ucsc_user_apps</requirement>
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9 <requirement type="package" version="5.18.1">perl</requirement>
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10 <requirement type="package" version="1.4.3">factera</requirement>
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11 <requirement type="package" version="3.0608">perl_descriptive_statistics</requirement>
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12 <requirement type="set_environment">FACTERA_DIR</requirement>
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13 </requirements>
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14
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15 <command>
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16 <!-- Run commands using Galaxy perl -->
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17
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18 ln -s $sortedBam ./input.bam;
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19 ln -s $sortedBam.metadata.bam_index ./input.bam.bai;
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20
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21
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22 #if $cond.additionalOpt == "no"
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23 perl \$FACTERA_DIR/factera-v1.4.3.pl -F -o ./ input.bam $exonBed $genome2Bit;
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24 #else
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25 perl \$FACTERA_DIR/factera-v1.4.3.pl -F -r $cond.r -m $cond.m -x $cond.x -s $cond.s -f $cond.f -S $cond.S
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26 -k $cond.k -c $cond.c -b $cond.b -p $cond.p -a $cond.a -o ./ input.bam $exonBed $genome2Bit;
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27 #end if
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28
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29 <!-- Keep only the fusion file -->
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30 if [ -e *fusions.txt ]; then cat *fusions.txt > $outfile ; else echo "No Fusions" > $outfile ; fi
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31 </command>
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32
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33 <inputs>
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34 <param format="bam" name="sortedBam" type="data" label="Alignment in BAM format" />
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35 <param format="bed" name="exonBed" type="data" label="Genomic coordinates with gene/exon names in fourth column" />
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36 <param format="twobit" name="genome2Bit" type="data" label="Two bit reference sequence" />
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37 <conditional name="cond">
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38 <param type="select" name="additionalOpt" label="Additional Options">
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39 <option value="yes">Yes</option>
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40 <option value="no" selected="True">No</option>
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41 </param>
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42 <when value="yes">
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43 <!-- Names follow command line flags in factera.pl -->
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44 <param type="integer" name="r" label="Minimum number of breakpoint-scanning reads required for output" value="5"/>
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45 <param type="integer" name="m" label="Minimum number of discordant reads required for each candidate fusion" value="2"/>
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46 <param type="integer" name="x" label="Maximum number of breakpoints to examine for each pair of genomic regions" value="5"/>
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47 <param type="integer" name="s" label="Minimum number of reads with the same breakpoint" value="1"/>
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48 <param type="float" name="f" min="0" max="1" label="Minimum fraction of read bases required for alignment to fusion template" value=".9"/>
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49 <param type="float" name="S" min="0" max="1" label="Minimum similarity required for read to match fusion template" value=".95"/>
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50 <param type="integer" name="k" label="K-mer size (number of bases) for fragment comparison" value="10"/>
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51 <param type="integer" name="c" label="Minimum size of soft-clipped region to consider" value="16"/>
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52 <param type="integer" name="b" label="Number of bases flanking breakpoint for fusion template" value="500"/>
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53 <param type="integer" name="p" label="Number of threads for blastn search" value="4"/>
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54 <param type="integer" name="a" label="Number of bases flanking breakpoint to provide in output" value="50"/>
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55 </when>
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56 </conditional>
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57 </inputs>
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58
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59 <outputs>
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60 <data format="tabular" name="outfile" />
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61 </outputs>
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62
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63 <help>This tool does Factera</help>
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64
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65 </tool>
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