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comparison macros.xml @ 0:0637018367e0 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/cram_to_bam commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
author iuc
date Tue, 09 May 2017 11:18:56 -0400
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children d459230531aa
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-1:000000000000 0:0637018367e0
1 <macros>
2 <xml name="requirements">
3 <requirements>
4 <requirement type="package" version="1.3.1">samtools</requirement>
5 <yield/>
6 </requirements>
7 </xml>
8 <token name="@TOOL_VERSION@">1.3.1</token>
9 <xml name="citations">
10 <citations>
11 <citation type="bibtex">
12 @misc{SAM_def,
13 title={Definition of SAM/BAM format},
14 url = {https://samtools.github.io/hts-specs/},}
15 </citation>
16 <citation type="doi">10.1093/bioinformatics/btp352</citation>
17 <citation type="doi">10.1093/bioinformatics/btr076</citation>
18 <citation type="doi">10.1093/bioinformatics/btr509</citation>
19 <citation type="bibtex">
20 @misc{Danecek_et_al,
21 Author={Danecek, P., Schiffels, S., Durbin, R.},
22 title={Multiallelic calling model in bcftools (-m)},
23 url = {http://samtools.github.io/bcftools/call-m.pdf},}
24 </citation>
25 <citation type="bibtex">
26 @misc{Durbin_VCQC,
27 Author={Durbin, R.},
28 title={Segregation based metric for variant call QC},
29 url = {http://samtools.github.io/bcftools/rd-SegBias.pdf},}
30 </citation>
31 <citation type="bibtex">
32 @misc{Li_SamMath,
33 Author={Li, H.},
34 title={Mathematical Notes on SAMtools Algorithms},
35 url = {http://www.broadinstitute.org/gatk/media/docs/Samtools.pdf},}
36 </citation>
37 <citation type="bibtex">
38 @misc{SamTools_github,
39 title={SAMTools GitHub page},
40 url = {https://github.com/samtools/samtools},}
41 </citation>
42 </citations>
43 </xml>
44 <xml name="version_command">
45 <version_command><![CDATA[samtools 2>&1 | grep Version]]></version_command>
46 </xml>
47 <xml name="stdio">
48 <stdio>
49 <exit_code range="1:" level="fatal" description="Error" />
50 </stdio>
51 </xml>
52 <token name="@no-chrom-options@">
53 -----
54
55 .. class:: warningmark
56
57 **No options available? How to re-detect metadata**
58
59 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:
60
61 1. Click on the **pencil** icon adjacent to the dataset in the history
62 2. A new menu will appear in the center pane of the interface
63 3. Click **Datatype** tab
64 4. Set **New Type** to **BAM**
65 5. Click **Save**
66
67 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.
68 </token>
69 </macros>