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1 <tool id="delly" name="delly" version="">
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2 <description>structural variant prediction method</description>
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3 <parallelism method="basic"></parallelism>
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4
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5 <command interpreter="python">
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6 delly.py
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7 -b $bam
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8 -t
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9 #if $checkDel:
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10 DEL
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11 #end if
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12 #if $checkDup:
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13 DUP
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14 #end if
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15 #if $checkInv:
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16 INV
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17 #end if
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18 #if $checkTra:
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19 TRA
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20 #end if
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21 -q $map_qual
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22 -s $mad_cutoff
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23 -g $genome
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24 -m $min_flank
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25 -e $epsilon
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26 -o $output
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27 </command>
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28
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29 <inputs>
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30 <param format="bam" name="bam" type="data" label="bam file" help="" />
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31 <param name="checkDel" type="boolean" label="Check Deletion?" checked="true"/>
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32 <param name="checkDup" type="boolean" label="Check Duplication?" checked="true"/>
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33 <param name="checkInv" type="boolean" label="Check Inversion?" checked="true"/>
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34 <param name="checkTra" type="boolean" label="Check Translation?" checked="true"/>
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35 <param name="map_qual" type="integer" label="min. paired-end mapping quality" value="0" />
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36 <param name="mad_cutoff" type="integer" label="insert size cutoff, median+s*MAD (deletions only)" value="5" />
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37 <param name="min_flank" type="integer" label="minimum flanking sequence size" value="13" />
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38 <param name="epsilon" type="float" label="allowed epsilon deviation of PE vs. SR deletion" value="0.1" />
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39 <param name="genome" type="text" label="genome" value="null" />
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40 </inputs>
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41
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42 <outputs>
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43 <data format="vcf" name="output" label="VCF output of delly" />
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44 </outputs>
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45
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46 <help>
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47 DELLY is an integrated structural variant prediction method that can detect deletions, tandem duplications, inversions and translocations at single-nucleotide resolution in short-read massively parallel sequencing data.
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48 It uses paired-ends and split-reads to sensitively and accurately delineate genomic rearrangements throughout the genome.
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49
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50 DELLY (Version: 0.5.5)
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51 Contact: Tobias Rausch (rausch@embl.de)
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52
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53 Generic options:
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54 -? [ --help ] show help message
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55 -t [ --type ] arg (=DEL) SV analysis type (DEL, DUP, INV, TRA)
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56 -o [ --outfile ] arg (="sv.vcf") SV output file
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57 -x [ --exclude ] arg (="") file with chr to exclude
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58
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59 PE options:
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60 -q [ --map-qual ] arg (=0) min. paired-end mapping quality
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61 -s [ --mad-cutoff ] arg (=5) insert size cutoff, median+s*MAD (deletions only)
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62
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63 SR options:
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64 -g [ --genome ] arg genome fasta file
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65 -m [ --min-flank ] arg (=13) minimum flanking sequence size
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66
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67 Genotyping options:
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68 -v [ --vcfgeno ] arg (="site.vcf") input vcf file for genotyping only
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69 -u [ --geno-qual ] arg (=20) min. mapping quality for genotyping
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70 </help>
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71
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72 <tests>
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73 <test>
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74 </test>
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75 </tests>
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76
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77 </tool> |
