Mercurial > repos > brenninc > samtools_flag_filter_1_2
comparison samtools_macros.xml @ 0:97bb72be07f9 draft default tip
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author | brenninc |
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date | Tue, 10 May 2016 03:59:17 -0400 |
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-1:000000000000 | 0:97bb72be07f9 |
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1 <?xml version="1.0"?> | |
2 <!-- Copied from https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/samtools/samtools_slice_bam --> | |
3 <macros> | |
4 <xml name="requirements"> | |
5 <requirements> | |
6 <requirement type="package" version="1.2">samtools</requirement> | |
7 <yield/> | |
8 </requirements> | |
9 </xml> | |
10 <xml name="citations"> | |
11 <citations> | |
12 <citation type="bibtex"> | |
13 @misc{SAM_def, | |
14 title={Definition of SAM/BAM format}, | |
15 url = {https://samtools.github.io/hts-specs/SAMv1.pdf},} | |
16 </citation> | |
17 <citation type="doi">10.1093/bioinformatics/btp352</citation> | |
18 <citation type="doi">10.1093/bioinformatics/btr076</citation> | |
19 <citation type="doi">10.1093/bioinformatics/btr509</citation> | |
20 <citation type="bibtex"> | |
21 @misc{Danecek_et_al, | |
22 Author={Danecek, P., Schiffels, S., Durbin, R.}, | |
23 title={Multiallelic calling model in bcftools (-m)}, | |
24 url = {http://samtools.github.io/bcftools/call-m.pdf},} | |
25 </citation> | |
26 <citation type="bibtex"> | |
27 @misc{Durbin_VCQC, | |
28 Author={Durbin, R.}, | |
29 title={Segregation based metric for variant call QC}, | |
30 url = {http://samtools.github.io/bcftools/rd-SegBias.pdf},} | |
31 </citation> | |
32 <citation type="bibtex"> | |
33 @misc{Li_SamMath, | |
34 Author={Li, H.}, | |
35 title={Mathematical Notes on SAMtools Algorithms}, | |
36 url = {http://www.broadinstitute.org/gatk/media/docs/Samtools.pdf},} | |
37 </citation> | |
38 <citation type="bibtex"> | |
39 @misc{SamTools_github, | |
40 title={SAMTools GitHub page}, | |
41 url = {https://github.com/samtools/samtools},} | |
42 </citation> | |
43 </citations> | |
44 </xml> | |
45 <xml name="version_command"> | |
46 <version_command>samtools --version | head -n 1 | awk '{ print $2 }'</version_command> | |
47 </xml> | |
48 <xml name="stdio"> | |
49 <stdio> | |
50 <exit_code range="1:" level="fatal" description="Error" /> | |
51 </stdio> | |
52 </xml> | |
53 <token name="@no-chrom-options@"> | |
54 ----- | |
55 | |
56 .. class:: warningmark | |
57 | |
58 **No options available? How to re-detect metadata** | |
59 | |
60 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: | |
61 | |
62 1. Click on the **pencil** icon adjacent to the dataset in the history | |
63 2. A new menu will appear in the center pane of the interface | |
64 3. Click **Datatype** tab | |
65 4. Set **New Type** to **BAM** | |
66 5. Click **Save** | |
67 | |
68 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. | |
69 | |
70 </token> | |
71 | |
72 </macros> |