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comparison delly.xml @ 29:0d00263ce9ed draft

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author malbuquerque
date Tue, 20 Jan 2015 19:05:56 -0500
parents 226f241f0c92
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28:442f1fdf6dfc 29:0d00263ce9ed
1 <tool id="delly" name="DELLY" version="0.6.1">
2
3 <description>structural variant discovery by integrated paired-end and split-read analysis</description>
4
5 <requirements>
6 <requirement type="package" version="0.6.1">delly</requirement>
7 <requirement type="set_environment">DELLY_DIR</requirement>
8 </requirements>
9
10
11 <command>
12
13 <!-- BAM and BAI linking, (1) link BAM to new BAM file & (2) link BAM metadata to new BAI file -->
14 #for $i, $s in enumerate( $repeatBam )
15 ln -s $s.sortedBam ./input$(i).bam;
16 ln -s $s.sortedBam.metadata.bam_index ./input$(i).bam.bai;
17 #end for
18
19 <!-- Sets args to a list of types selected -->
20 #if not isinstance( $type.value, list ):
21 #set $args = [ $type.value ]
22 #else:
23 #set $args = $type.value
24 #end if
25
26 <!-- Run Delly Jobs for each type selected -->
27 #for $option in $args
28 <!-- NEED TO FIX -->
29 <!-- Delly should be automatically installed into the galaxy instance and should not be running off
30 the computers specific tool set -->
31 \$DELLY_DIR/src/delly -t $option -o ./output.$(option).vcf -q $mapQual -s $madCutoff
32 #if $option == "DEL"
33 -m $minFlank
34 #end if
35 -u $genoQual -v $vcfgeno -g $genome
36
37 <!-- add each input bam to command -->
38 #for $i, $s in enumerate( $repeatBam )
39 ./input$(i).bam
40 #end for
41 ;
42 #end for
43
44 <!-- Combine VCF Files and Sort Lexographically -->
45 #set $option = $args[0]
46 grep ^\# output.$(option).vcf > $outfile;
47 grep ^\# -v output.$(option).vcf > variants.txt;
48
49 <!-- If we called more than a single variant type, concatenate all the other types variant output -->
50 #if isinstance( $type.value, list ):
51 #for $option in $args[1:]
52 grep ^\# -v output.$(option).vcf >> variants.txt;
53 #end for
54 #end if
55
56 <!-- Sort all variant output, assuming that it will sort lexographically by chromosome, then position, ID -->
57 <!-- In future, maybe develop a script to sort by bam header -->
58 sort -k1,1d -k2,2n -k3,3d variants.txt > sortedVariants.txt;
59
60 <!-- Filter Variants that have Passed Quality Checks -->
61 #if $filterCalls
62 awk '{if ($7 == "PASS") print $0;}' sortedVariants.txt >> $outfile;
63 #else
64 cat sortedVariants.txt >> $outfile;
65 #end if
66
67 </command>
68
69 <inputs>
70
71 <!-- General Options -->
72 <param name="type" type="select" multiple="true" display="checkboxes" label="Variant Types">
73 <option value="DEL" selected="true">Deletions</option>
74 <option value="DUP" selected="true">Tandem Duplications</option>
75 <option value="INV" selected="true">Inversions</option>
76 <option value="TRA" selected="true">Translocations</option>
77 </param>
78 <repeat name="repeatBam" title="Bam Alignment" min="1" default="1" >
79 <param format="bam" name="sortedBam" type="data" label="File" />
80 </repeat>
81 <param name="excludeFile" type="data" optional="true" label="Chromosomes to Exclude"/>
82 <param name="filterCalls" type="boolean" value="false" label="Filter Poor Variant Calls"/>
83
84 <!-- Paired End Options -->
85 <param name="mapQual" type="integer" value="0" min="0" max="255" label="PE - Minimum Mapping Quality" />
86 <param name="madCutoff" type="integer" value="9" min="0" max="255" label="PE - Insert Size Cutoff" />
87
88 <!-- SR Options -->
89 <param format="fasta" name="genome" type="data" optional="true" label="SR - Genome Fasta File" />
90 <param name="minFlank" type="integer" value="13" label="SR - Minimum Flanking Sequence" />
91
92 <!-- Genotyping Options -->
93 <param format="vcf" name="vcfgeno" type="data" optional="true" label="GT - Input VCF" />
94 <param name="genoQual" type="integer" value="20" min="0" max="255" label="GT - Minimum Mapping Quality" />
95
96 </inputs>
97
98 <outputs>
99 <data format="vcf" name="outfile" />
100 </outputs>
101
102 <help>
103
104 </help>
105
106 </tool>