Mercurial > repos > brenninc > samtools_flag_filter_1_2
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author | brenninc |
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date | Tue, 10 May 2016 03:59:17 -0400 |
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<?xml version="1.0"?> <!-- Copied from https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/samtools/samtools_slice_bam --> <macros> <xml name="requirements"> <requirements> <requirement type="package" version="1.2">samtools</requirement> <yield/> </requirements> </xml> <xml name="citations"> <citations> <citation type="bibtex"> @misc{SAM_def, title={Definition of SAM/BAM format}, url = {https://samtools.github.io/hts-specs/SAMv1.pdf},} </citation> <citation type="doi">10.1093/bioinformatics/btp352</citation> <citation type="doi">10.1093/bioinformatics/btr076</citation> <citation type="doi">10.1093/bioinformatics/btr509</citation> <citation type="bibtex"> @misc{Danecek_et_al, Author={Danecek, P., Schiffels, S., Durbin, R.}, title={Multiallelic calling model in bcftools (-m)}, url = {http://samtools.github.io/bcftools/call-m.pdf},} </citation> <citation type="bibtex"> @misc{Durbin_VCQC, Author={Durbin, R.}, title={Segregation based metric for variant call QC}, url = {http://samtools.github.io/bcftools/rd-SegBias.pdf},} </citation> <citation type="bibtex"> @misc{Li_SamMath, Author={Li, H.}, title={Mathematical Notes on SAMtools Algorithms}, url = {http://www.broadinstitute.org/gatk/media/docs/Samtools.pdf},} </citation> <citation type="bibtex"> @misc{SamTools_github, title={SAMTools GitHub page}, url = {https://github.com/samtools/samtools},} </citation> </citations> </xml> <xml name="version_command"> <version_command>samtools --version | head -n 1 | awk '{ print $2 }'</version_command> </xml> <xml name="stdio"> <stdio> <exit_code range="1:" level="fatal" description="Error" /> </stdio> </xml> <token name="@no-chrom-options@"> ----- .. class:: warningmark **No options available? How to re-detect metadata** If you see a "No options available" within the "**Select references (chromosomes and contigs) you would like to restrict bam to**" drop down, you need to re-detect metadata for the dataset you are trying to process. To do this follow these steps: 1. Click on the **pencil** icon adjacent to the dataset in the history 2. A new menu will appear in the center pane of the interface 3. Click **Datatype** tab 4. Set **New Type** to **BAM** 5. Click **Save** The medatada will be re-detected and you will be able to see the list of reference sequences in the "**Select references (chromosomes and contigs) you would like to restrict bam to**" drop-down. </token> </macros>