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comparison bwa_wrapper.xml @ 1:150b3fe44caa draft

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Updated command line format per dev team standards.
author devteam <devteam@galaxyproject.org>
date Tue, 02 Apr 2013 12:23:14 -0400
parents ffa8aaa14f7c
children b4427dbb6ced
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0:ffa8aaa14f7c 1:150b3fe44caa
11 #if $input1.ext == "fastqillumina": 11 #if $input1.ext == "fastqillumina":
12 --illumina1.3 12 --illumina1.3
13 #end if 13 #end if
14 14
15 ## reference source 15 ## reference source
16 --fileSource=$genomeSource.refGenomeSource 16 --fileSource="${genomeSource.refGenomeSource}"
17 #if $genomeSource.refGenomeSource == "history": 17 #if $genomeSource.refGenomeSource == "history":
18 ##build index on the fly 18 ##build index on the fly
19 --ref="${genomeSource.ownFile}" 19 --ref="${genomeSource.ownFile}"
20 --dbkey=$dbkey 20 --dbkey="${dbkey}"
21 #else: 21 #else:
22 ##use precomputed indexes 22 ##use precomputed indexes
23 --ref="${genomeSource.indices.fields.path}" 23 --ref="${genomeSource.indices.fields.path}"
24 --do_not_build_index 24 --do_not_build_index
25 #end if 25 #end if
26 26
27 ## input file(s) 27 ## input file(s)
28 --input1=$paired.input1 28 --input1="${paired.input1}"
29 #if $paired.sPaired == "paired": 29 #if $paired.sPaired == "paired":
30 --input2=$paired.input2 30 --input2="${paired.input2}"
31 #end if 31 #end if
32 32
33 ## output file 33 ## output file
34 --output=$output 34 --output="${output}"
35 35
36 ## run parameters 36 ## run parameters
37 --genAlignType=$paired.sPaired 37 --genAlignType="${paired.sPaired}"
38 --params=$params.source_select 38 --params="${params.source_select}"
39 #if $params.source_select != "pre_set": 39 #if $params.source_select != "pre_set":
40 --maxEditDist=$params.maxEditDist 40 --maxEditDist="${params.maxEditDist}"
41 --fracMissingAligns=$params.fracMissingAligns 41 --fracMissingAligns="${params.fracMissingAligns}"
42 --maxGapOpens=$params.maxGapOpens 42 --maxGapOpens="${params.maxGapOpens}"
43 --maxGapExtens=$params.maxGapExtens 43 --maxGapExtens="${params.maxGapExtens}"
44 --disallowLongDel=$params.disallowLongDel 44 --disallowLongDel="${params.disallowLongDel}"
45 --disallowIndel=$params.disallowIndel 45 --disallowIndel="${params.disallowIndel}"
46 --seed=$params.seed 46 --seed="${params.seed}"
47 --maxEditDistSeed=$params.maxEditDistSeed 47 --maxEditDistSeed="${params.maxEditDistSeed}"
48 --mismatchPenalty=$params.mismatchPenalty 48 --mismatchPenalty="${params.mismatchPenalty}"
49 --gapOpenPenalty=$params.gapOpenPenalty 49 --gapOpenPenalty="${params.gapOpenPenalty}"
50 --gapExtensPenalty=$params.gapExtensPenalty 50 --gapExtensPenalty="${params.gapExtensPenalty}"
51 --suboptAlign="${params.suboptAlign}" 51 --suboptAlign="${params.suboptAlign}"
52 --noIterSearch=$params.noIterSearch 52 --noIterSearch="${params.noIterSearch}"
53 --outputTopN=$params.outputTopN 53 --outputTopN="${params.outputTopN}"
54 --outputTopNDisc=$params.outputTopNDisc 54 --outputTopNDisc="${params.outputTopNDisc}"
55 --maxInsertSize=$params.maxInsertSize 55 --maxInsertSize="${params.maxInsertSize}"
56 --maxOccurPairing=$params.maxOccurPairing 56 --maxOccurPairing="${params.maxOccurPairing}"
57 #if $params.readGroup.specReadGroup == "yes" 57 #if $params.readGroup.specReadGroup == "yes"
58 --rgid="$params.readGroup.rgid" 58 --rgid="${params.readGroup.rgid}"
59 --rgcn="$params.readGroup.rgcn" 59 --rgcn="${params.readGroup.rgcn}"
60 --rgds="$params.readGroup.rgds" 60 --rgds="${params.readGroup.rgds}"
61 --rgdt="$params.readGroup.rgdt" 61 --rgdt="${params.readGroup.rgdt}"
62 --rgfo="$params.readGroup.rgfo" 62 --rgfo="${params.readGroup.rgfo}"
63 --rgks="$params.readGroup.rgks" 63 --rgks="${params.readGroup.rgks}"
64 --rglb="$params.readGroup.rglb" 64 --rglb="${params.readGroup.rglb}"
65 --rgpg="$params.readGroup.rgpg" 65 --rgpg="${params.readGroup.rgpg}"
66 --rgpi="$params.readGroup.rgpi" 66 --rgpi="${params.readGroup.rgpi}"
67 --rgpl="$params.readGroup.rgpl" 67 --rgpl="${params.readGroup.rgpl}"
68 --rgpu="$params.readGroup.rgpu" 68 --rgpu="${params.readGroup.rgpu}"
69 --rgsm="$params.readGroup.rgsm" 69 --rgsm="${params.readGroup.rgsm}"
70 #end if 70 #end if
71 #end if 71 #end if
72 72
73 ## suppress output SAM header 73 ## suppress output SAM header
74 --suppressHeader=$suppressHeader 74 --suppressHeader="${suppressHeader}"
75 </command> 75 </command>
76 <inputs> 76 <inputs>
77 <conditional name="genomeSource"> 77 <conditional name="genomeSource">
78 <param name="refGenomeSource" type="select" label="Will you select a reference genome from your history or use a built-in index?"> 78 <param name="refGenomeSource" type="select" label="Will you select a reference genome from your history or use a built-in index?">
79 <option value="indexed">Use a built-in index</option> 79 <option value="indexed">Use a built-in index</option>