srma_wrapper.py #if $refGenomeSource.refGenomeSource_type == "history": --ref=$refGenomeSource.ownFile #else: --refUID=$refGenomeSource.ref --refLocations=${GALAXY_DATA_INDEX_DIR}/srma_index.loc #end if --input=$input --inputIndex=${input.metadata.bam_index} --output=$output --params=$params.source_select --fileSource=$refGenomeSource.refGenomeSource_type --jarBin="${GALAXY_DATA_INDEX_DIR}/shared/jars" #if $params.source_select == "full": --offset=$params.offset --minMappingQuality=$params.minMappingQuality --minAlleleProbability=$params.minAlleleProbability --minAlleleCoverage=$params.minAlleleCoverage --range=$params.range --correctBases=$params.correctBases --useSequenceQualities=$params.useSequenceQualities --maxHeapSize=$params.maxHeapSize #end if --jarFile="srma.jar" Use a built-in reference Use one from the history Commonly Used Full Parameter List

**What it does** SRMA is a short read micro re-aligner for next-generation high throughput sequencing data. Sequence alignment algorithms examine each read independently. When indels occur towards the ends of reads, the alignment can lead to false SNPs as well as improperly placed indels. This tool aims to perform a re-alignment of each read to a graphical representation of all alignments within a local region to provide a better overall base-resolution consensus. Currently this tool works well with and has been tested on 30x diploid coverage genome sequencing data from Illumina and ABI SOLiD technology. This tool may not work well with 454 data, as indels are a significant error mode for 454 data. ------ Please cite the website "http://srma.sourceforge.net" as well as: Homer N, and Nelson SF. SRMA: short read micro re-aligner. 2010. ------ **Know what you are doing** .. class:: warningmark There is no such thing (yet) as an automated gearshift in short read mapping. It is all like stick-shift driving in San Francisco. In other words = running this tool with default parameters will probably not give you meaningful results. A way to deal with this is to **understand** the parameters by carefully reading the `documentation`__ and experimenting. Fortunately, Galaxy makes experimenting easy. .. __: http://srma.sourceforge.net/ ------ **Input formats** SRMA accepts a BAM input file. Note that this file should have been generated from a SAM file which contains the header. ------ **Outputs** The output is in BAM format, see http://samtools.sourceforge.net for more details. ------- **SRMA settings** All of the options have a default value. You can change any of them. Most of the options in SRMA have been implemented here. ------ **SRMA parameter list** This is an exhaustive list of SRMA options: For **SRMA**:: INPUT=File I=File The input SAM or BAM file. Required. OUTPUT=File O=File The output SAM or BAM file. Default value: null. REFERENCE=File R=File The reference FASTA file. Required. OFFSET=Integer The alignment offset. Default value: 20. This option can be set to 'null' to clear the default value. MIN_MAPQ=Integer The minimum mapping quality. Default value: 0. This option can be set to 'null' to clear the default value. MINIMUM_ALLELE_PROBABILITY=Double The minimum allele probability conditioned on coverage (for the binomial quantile). Default value: 0.1. This option can be set to 'null' to clear the default value. MINIMUM_ALLELE_COVERAGE=Integer The minimum haploid coverage for the consensus. Default value: 3. This option can be set to 'null' to clear the default value. RANGE=String A range to examine. Default value: null. CORRECT_BASES=Boolean Correct bases. Default value: false. This option can be set to 'null' to clear the default value. Possible values: {true, false} USE_SEQUENCE_QUALITIES=BooleanUse sequence qualities Default value: true. This option can be set to 'null' to clear the default value. Possible values: {true, false} MAX_HEAP_SIZE=Integer The maximum number of nodes on the heap before re-alignment is ignored Default value: 8192. This option can be set to 'null' to clear the default value.