Mercurial > repos > devteam > bwa_wrappers
comparison bwa_color_wrapper.xml @ 1:150b3fe44caa draft
Updated command line format per dev team standards.
author | devteam <devteam@galaxyproject.org> |
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date | Tue, 02 Apr 2013 12:23:14 -0400 |
parents | ffa8aaa14f7c |
children | b4427dbb6ced |
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0:ffa8aaa14f7c | 1:150b3fe44caa |
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8 bwa_wrapper.py | 8 bwa_wrapper.py |
9 --threads="4" | 9 --threads="4" |
10 --color-space | 10 --color-space |
11 | 11 |
12 ## reference source | 12 ## reference source |
13 --fileSource=$genomeSource.refGenomeSource | 13 --fileSource="${genomeSource.refGenomeSource}" |
14 #if $genomeSource.refGenomeSource == "history": | 14 #if $genomeSource.refGenomeSource == "history": |
15 ##build index on the fly | 15 ##build index on the fly |
16 --ref="${genomeSource.ownFile}" | 16 --ref="${genomeSource.ownFile}" |
17 --dbkey=$dbkey | 17 --dbkey="${dbkey}" |
18 #else: | 18 #else: |
19 ##use precomputed indexes | 19 ##use precomputed indexes |
20 --ref="${genomeSource.indices.fields.path}" | 20 --ref="${genomeSource.indices.fields.path}" |
21 --do_not_build_index | 21 --do_not_build_index |
22 #end if | 22 #end if |
23 | 23 |
24 ## input file(s) | 24 ## input file(s) |
25 --input1=$paired.input1 | 25 --input1="${paired.input1}" |
26 #if $paired.sPaired == "paired": | 26 #if $paired.sPaired == "paired": |
27 --input2=$paired.input2 | 27 --input2="${paired.input2}" |
28 #end if | 28 #end if |
29 | 29 |
30 ## output file | 30 ## output file |
31 --output=$output | 31 --output="${output}" |
32 | 32 |
33 ## run parameters | 33 ## run parameters |
34 --genAlignType=$paired.sPaired | 34 --genAlignType="${paired.sPaired}" |
35 --params=$params.source_select | 35 --params="${params.source_select}" |
36 #if $params.source_select != "pre_set": | 36 #if $params.source_select != "pre_set": |
37 --maxEditDist=$params.maxEditDist | 37 --maxEditDist="${params.maxEditDist}" |
38 --fracMissingAligns=$params.fracMissingAligns | 38 --fracMissingAligns="${params.fracMissingAligns}" |
39 --maxGapOpens=$params.maxGapOpens | 39 --maxGapOpens="${params.maxGapOpens}" |
40 --maxGapExtens=$params.maxGapExtens | 40 --maxGapExtens="${params.maxGapExtens}" |
41 --disallowLongDel=$params.disallowLongDel | 41 --disallowLongDel="${params.disallowLongDel}" |
42 --disallowIndel=$params.disallowIndel | 42 --disallowIndel="${params.disallowIndel}" |
43 --seed=$params.seed | 43 --seed="${params.seed}" |
44 --maxEditDistSeed=$params.maxEditDistSeed | 44 --maxEditDistSeed="${params.maxEditDistSeed}" |
45 --mismatchPenalty=$params.mismatchPenalty | 45 --mismatchPenalty="${params.mismatchPenalty}" |
46 --gapOpenPenalty=$params.gapOpenPenalty | 46 --gapOpenPenalty="${params.gapOpenPenalty}" |
47 --gapExtensPenalty=$params.gapExtensPenalty | 47 --gapExtensPenalty="${params.gapExtensPenalty}" |
48 --suboptAlign="${params.suboptAlign}" | 48 --suboptAlign="${params.suboptAlign}" |
49 --noIterSearch=$params.noIterSearch | 49 --noIterSearch="${params.noIterSearch}" |
50 --outputTopN=$params.outputTopN | 50 --outputTopN="${params.outputTopN}" |
51 --outputTopNDisc=$params.outputTopNDisc | 51 --outputTopNDisc="${params.outputTopNDisc}" |
52 --maxInsertSize=$params.maxInsertSize | 52 --maxInsertSize="${params.maxInsertSize}" |
53 --maxOccurPairing=$params.maxOccurPairing | 53 --maxOccurPairing="${params.maxOccurPairing}" |
54 #if $params.readGroup.specReadGroup == "yes" | 54 #if $params.readGroup.specReadGroup == "yes" |
55 --rgid="$params.readGroup.rgid" | 55 --rgid="${params.readGroup.rgid}" |
56 --rgcn="$params.readGroup.rgcn" | 56 --rgcn="${params.readGroup.rgcn}" |
57 --rgds="$params.readGroup.rgds" | 57 --rgds="${params.readGroup.rgds}" |
58 --rgdt="$params.readGroup.rgdt" | 58 --rgdt="${params.readGroup.rgdt}" |
59 --rgfo="$params.readGroup.rgfo" | 59 --rgfo="${params.readGroup.rgfo}" |
60 --rgks="$params.readGroup.rgks" | 60 --rgks="${params.readGroup.rgks}" |
61 --rglb="$params.readGroup.rglb" | 61 --rglb="${params.readGroup.rglb}" |
62 --rgpg="$params.readGroup.rgpg" | 62 --rgpg="${params.readGroup.rgpg}" |
63 --rgpi="$params.readGroup.rgpi" | 63 --rgpi="${params.readGroup.rgpi}" |
64 --rgpl="$params.readGroup.rgpl" | 64 --rgpl="${params.readGroup.rgpl}" |
65 --rgpu="$params.readGroup.rgpu" | 65 --rgpu="${params.readGroup.rgpu}" |
66 --rgsm="$params.readGroup.rgsm" | 66 --rgsm="${params.readGroup.rgsm}" |
67 #end if | 67 #end if |
68 #end if | 68 #end if |
69 | 69 |
70 ## suppress output SAM header | 70 ## suppress output SAM header |
71 --suppressHeader=$suppressHeader | 71 --suppressHeader="${suppressHeader}" |
72 </command> | 72 </command> |
73 <requirements> | 73 <requirements> |
74 <requirement type="package">bwa</requirement> | 74 <requirement type="package">bwa</requirement> |
75 </requirements> | 75 </requirements> |
76 <inputs> | 76 <inputs> |