Mercurial > repos > jbrayet > samtools_sort_docker
changeset 4:6024acc63f80 draft
Deleted selected files
| author | jbrayet |
|---|---|
| date | Wed, 18 Nov 2015 06:57:38 -0500 |
| parents | 6829a4f31c3f |
| children | e95f34f52fc8 |
| files | macros.xml |
| diffstat | 1 files changed, 0 insertions(+), 71 deletions(-) [+] |
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--- a/macros.xml Wed Nov 18 05:55:12 2015 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,71 +0,0 @@ -<macros> - <xml name="requirements"> - <requirements> - <requirement type="package" version="0.1">docker_samtools</requirement> - <container type="docker">samtools:1.0</container> - <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>