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1 <tool id="delly" name="DELLY" version="0.6.1">
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2
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3 <description>structural variant discovery by integrated paired-end and split-read analysis</description>
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4
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5 <requirements>
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6 <requirement type="package" version="0.6.1">delly</requirement>
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7 <requirement type="set_environment">DELLY_DIR</requirement>
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8 </requirements>
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9
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10
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11 <command>
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12
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13 <!-- BAM and BAI linking, (1) link BAM to new BAM file & (2) link BAM metadata to new BAI file -->
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14 #for $i, $s in enumerate( $repeatBam )
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15 ln -s $s.sortedBam ./input$(i).bam;
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16 ln -s $s.sortedBam.metadata.bam_index ./input$(i).bam.bai;
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17 #end for
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18
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19 <!-- Sets args to a list of types selected -->
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20 #if not isinstance( $type.value, list ):
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21 #set $args = [ $type.value ]
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22 #else:
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23 #set $args = $type.value
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24 #end if
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25
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26 <!-- Run Delly Jobs for each type selected -->
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27 #for $option in $args
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28 <!-- NEED TO FIX -->
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29 <!-- Delly should be automatically installed into the galaxy instance and should not be running off
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30 the computers specific tool set -->
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31 \$DELLY_DIR/src/delly -t $option -o ./output.$(option).vcf -q $mapQual -s $madCutoff
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32 #if $option == "DEL"
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33 -m $minFlank
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34 #end if
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35 -u $genoQual -v $vcfgeno -g $genome
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36
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37 <!-- add each input bam to command -->
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38 #for $i, $s in enumerate( $repeatBam )
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39 ./input$(i).bam
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40 #end for
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41 ;
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42 #end for
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43
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44 <!-- Combine VCF Files and Sort Lexographically -->
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45 #set $option = $args[0]
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46 grep ^\# output.$(option).vcf > $outfile;
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47 grep ^\# -v output.$(option).vcf > variants.txt;
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48
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49 <!-- If we called more than a single variant type, concatenate all the other types variant output -->
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50 #if isinstance( $type.value, list ):
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51 #for $option in $args[1:]
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52 grep ^\# -v output.$(option).vcf >> variants.txt;
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53 #end for
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54 #end if
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55
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56 <!-- Sort all variant output, assuming that it will sort lexographically by chromosome, then position, ID -->
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57 <!-- In future, maybe develop a script to sort by bam header -->
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58 sort -k1,1d -k2,2n -k3,3d variants.txt > sortedVariants.txt;
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59
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60 <!-- Filter Variants that have Passed Quality Checks -->
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61 #if $filterCalls
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62 awk '{if ($7 == "PASS") print $0;}' sortedVariants.txt >> $outfile;
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63 #else
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64 cat sortedVariants.txt >> $outfile;
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65 #end if
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66
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67 </command>
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68
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69 <inputs>
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70
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71 <!-- General Options -->
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72 <param name="type" type="select" multiple="true" display="checkboxes" label="Variant Types">
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73 <option value="DEL" selected="true">Deletions</option>
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74 <option value="DUP" selected="true">Tandem Duplications</option>
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75 <option value="INV" selected="true">Inversions</option>
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76 <option value="TRA" selected="true">Translocations</option>
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77 </param>
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78 <repeat name="repeatBam" title="Bam Alignment" min="1" default="1" >
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79 <param format="bam" name="sortedBam" type="data" label="File" />
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80 </repeat>
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81 <param name="excludeFile" type="data" optional="true" label="Chromosomes to Exclude"/>
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82 <param name="filterCalls" type="boolean" value="false" label="Filter Poor Variant Calls"/>
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83
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84 <!-- Paired End Options -->
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85 <param name="mapQual" type="integer" value="0" min="0" max="255" label="PE - Minimum Mapping Quality" />
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86 <param name="madCutoff" type="integer" value="9" min="0" max="255" label="PE - Insert Size Cutoff" />
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87
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88 <!-- SR Options -->
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89 <param format="fasta" name="genome" type="data" optional="true" label="SR - Genome Fasta File" />
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90 <param name="minFlank" type="integer" value="13" label="SR - Minimum Flanking Sequence" />
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91
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92 <!-- Genotyping Options -->
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93 <param format="vcf" name="vcfgeno" type="data" optional="true" label="GT - Input VCF" />
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94 <param name="genoQual" type="integer" value="20" min="0" max="255" label="GT - Minimum Mapping Quality" />
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95
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96 </inputs>
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97
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98 <outputs>
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99 <data format="vcf" name="outfile" />
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100 </outputs>
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101
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102 <help>
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103
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104 </help>
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105
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106 </tool>
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