Mercurial > repos > devteam > bwa_wrappers
comparison bwa_wrapper.xml @ 1:150b3fe44caa draft
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> |