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comparison macros.xml @ 0:0d71d9467847 draft

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author devteam
date Wed, 22 Apr 2015 10:29:35 -0400
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1 <macros>
2 <xml name="requirements">
3 <requirements>
4 <requirement type="package" version="1.2">samtools</requirement>
5 <yield/>
6 </requirements>
7 </xml>
8 <xml name="citations">
9 <citations>
10 <citation type="bibtex">
11 @misc{SAM_def,
12 title={Definition of SAM/BAM format},
13 url = {https://samtools.github.io/hts-specs/SAMv1.pdf},}
14 </citation>
15 <citation type="doi">10.1093/bioinformatics/btp352</citation>
16 <citation type="doi">10.1093/bioinformatics/btr076</citation>
17 <citation type="doi">10.1093/bioinformatics/btr509</citation>
18 <citation type="bibtex">
19 @misc{Danecek_et_al,
20 Author={Danecek, P., Schiffels, S., Durbin, R.},
21 title={Multiallelic calling model in bcftools (-m)},
22 url = {http://samtools.github.io/bcftools/call-m.pdf},}
23 </citation>
24 <citation type="bibtex">
25 @misc{Durbin_VCQC,
26 Author={Durbin, R.},
27 title={Segregation based metric for variant call QC},
28 url = {http://samtools.github.io/bcftools/rd-SegBias.pdf},}
29 </citation>
30 <citation type="bibtex">
31 @misc{Li_SamMath,
32 Author={Li, H.},
33 title={Mathematical Notes on SAMtools Algorithms},
34 url = {http://www.broadinstitute.org/gatk/media/docs/Samtools.pdf},}
35 </citation>
36 <citation type="bibtex">
37 @misc{SamTools_github,
38 title={SAMTools GitHub page},
39 url = {https://github.com/samtools/samtools},}
40 </citation>
41 </citations>
42 </xml>
43 <xml name="version_command">
44 <version_command>samtools --version | head -n 1 | awk '{ print $2 }'</version_command>
45 </xml>
46 <xml name="stdio">
47 <stdio>
48 <exit_code range="1:" level="fatal" description="Error" />
49 </stdio>
50 </xml>
51 <token name="@no-chrom-options@">
52 -----
53
54 .. class:: warningmark
55
56 **No options available? How to re-detect metadata**
57
58 If you see a &quot;No options available&quot; within the &quot;**Select references (chromosomes and contigs) you would like to restrict bam to**&quot; drop down, you need to re-detect metadata for the dataset you are trying to process. To do this follow these steps:
59
60 1. Click on the **pencil** icon adjacent to the dataset in the history
61 2. A new menu will appear in the center pane of the interface
62 3. Click **Datatype** tab
63 4. Set **New Type** to **BAM**
64 5. Click **Save**
65
66 The medatada will be re-detected and you will be able to see the list of reference sequences in the &quot;**Select references (chromosomes and contigs) you would like to restrict bam to**&quot; drop-down.
67
68 </token>
69
70 </macros>