Mercurial > repos > yusuf > miseq_bam_variants
comparison MiSeqBAMtoVariants.xml @ 0:1a23ea467feb default tip
intial commit
| author | Yusuf Ali <ali@yusuf.email> |
|---|---|
| date | Thu, 26 Mar 2015 09:36:17 -0600 |
| parents | |
| children |
comparison
equal
deleted
inserted
replaced
| -1:000000000000 | 0:1a23ea467feb |
|---|---|
| 1 <?xml version="1.0"?> | |
| 2 | |
| 3 <tool id="call_miseq_vars" name="Call miSeq variants"> | |
| 4 <description>using a BAM file</description> | |
| 5 <version_string>echo 1.0.0</version_string> | |
| 6 <command interpreter="perl">call_miseq_variants $__tool_data_path__ geno . $inputBAM ${targetBED}.bed ${ref_genome}.bed ${ref_genome}.fa 12</command> | |
| 7 <inputs> | |
| 8 <param format="bam" name="inputBAM" type="data" label="Source BAM (mapped and realigned reads) file"/> | |
| 9 <param name="ref_genome" type="genomebuild" label="Reference genome" help="against which the reads were aligned"/> | |
| 10 <param name="targetBED" type="select" display="radio" dynamic_options="kit_fileOptions()" label="The enrichment (capture) kit used for the sequencing experiment"/> | |
| 11 </inputs> | |
| 12 <outputs> | |
| 13 <data format="achri_snp_table" label="Confident genotypes" name="confident_genotypes" from_work_dir="geno.combined.collapsed.confident.hgvs.txt"/> | |
| 14 <data format="achri_snp_table" label="Marginal genotypes" name="marginal_genotypes" from_work_dir="geno.combined.collapsed.marginal.hgvs.txt"/> | |
| 15 <data format="text" label="Genotyping log" name="genotyping log" from_work_dir="geno.call_variants.log.txt"/> | |
| 16 </outputs> | |
| 17 | |
| 18 <!-- the following code populates the selection from the public dbSNP datasets available in the local Galaxy installation --> | |
| 19 <code file="capture_kits.py"/> | |
| 20 <tests/> | |
| 21 | |
| 22 <help> | |
| 23 This tool runs a BAM file against multiple genotypers (FreeBayes 0.8.7, GATKHaplotypeCaller 3.1) and generates a consensus (confident) table of variant calls, | |
| 24 including caveats about haplotype phase inconsistencies and other potential false positive indicators. | |
| 25 </help> | |
| 26 | |
| 27 </tool> |