Mercurial > repos > yhoogstrate > varscan_mpileup2snp_from_bam
changeset 0:212cc602c073
Uploaded
| author | yhoogstrate |
|---|---|
| date | Tue, 17 Dec 2013 04:41:07 -0500 |
| parents | |
| children | d0cd5668ec6b |
| files | varscan2_from_bam.xml |
| diffstat | 1 files changed, 41 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/varscan2_from_bam.xml Tue Dec 17 04:41:07 2013 -0500 @@ -0,0 +1,41 @@ +<?xml version="1.0" encoding="UTF-8"?> +<tool id="varscan2_from_bam" name="VarScan2 from BAM"> + <description>VarScan2 reading a *.bam file to avoid massive I/O resourcing.</description> + <requirements> + <requirement type="package" version="1.0.19">samtools-mpileup-parallel</requirement> + <requirement type="package" version="2.3.6">VarScan</requirement> + </requirements> + <command interpreter="bash"> + <!-- + VarScan2 url: + http://downloads.sourceforge.net/project/varscan/VarScan.v2.3.6.jar?r=http%3A%2F%2Fsourceforge.net%2Fprojects%2Fvarscan%2Ffiles%2F&ts=1377264954&use_mirror=freefr + + The following script is written in the "Cheetah" language: + http://www.cheetahtemplate.org/docs/users_guide_html_multipage/contents.html + --> + samtools mpileup -t $threads -f $reference_genome + #for $sample in $samples + ${sample.mapped_reads} + #end for + | java -jar VarScan.v2.2.jar pileup2snp > $output_table + </command> + + <input type="text" name="threads" value="8" min="1" /> + + <inputs> + <repeat name="samples" title="Samples" min="1"> + <param format="bam,sam" name="mapped_reads" type="data" label="Alignment file" help="Mapped reads in BAM or SAM format."/> + </repeat> + + <param format="fa,fasta" name="reference_genome" type="data" label="Gene Model Annotations" help="Reference genome (genome.fa) that corresponds to the *.bam file." /> + </inputs> + + <outputs> + <data format="tabular" name="output_table" label="${tool.name}" /> + </outputs> + + <help> + VarScan2.3.6 is NOT compatible with the latest versions (0.1.16 and 0.1.19) of samtools. + It is compatible with 0.1.6, until this is fixed please stay stick to 0.1.6. + </help> +</tool>