Mercurial > repos > devteam > samtools_flagstat

annotate macros.xml @ 6:28eb6a47be96 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_flagstat commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
author iuc
date Tue, 09 May 2017 11:16:36 -0400
parents 7b6dcfbdc6a9
children 5d3100bf5357
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
4
10b658bef71a planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents:
diff changeset
1 <macros>
10b658bef71a planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents:
diff changeset
2 <xml name="requirements">
10b658bef71a planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents:
diff changeset
3 <requirements>
6
28eb6a47be96 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_flagstat commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
iuc
parents: 5
diff changeset
4 <requirement type="package" version="1.3.1">samtools</requirement>
4
10b658bef71a planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents:
diff changeset
5 <yield/>
10b658bef71a planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents:
diff changeset
6 </requirements>
10b658bef71a planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents:
diff changeset
7 </xml>
6
28eb6a47be96 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_flagstat commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
iuc
parents: 5
diff changeset
8 <token name="@TOOL_VERSION@">1.3.1</token>
4
10b658bef71a planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents:
diff changeset
9 <xml name="citations">
10b658bef71a planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents:
diff changeset
10 <citations>
10b658bef71a planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents:
diff changeset
11 <citation type="bibtex">
10b658bef71a planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents:
diff changeset
12 @misc{SAM_def,
10b658bef71a planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents:
diff changeset
13 title={Definition of SAM/BAM format},
6
28eb6a47be96 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_flagstat commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
iuc
parents: 5
diff changeset
14 url = {https://samtools.github.io/hts-specs/},}
4
10b658bef71a planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents:
diff changeset
15 </citation>
10b658bef71a planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents:
diff changeset
16 <citation type="doi">10.1093/bioinformatics/btp352</citation>
10b658bef71a planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents:
diff changeset
17 <citation type="doi">10.1093/bioinformatics/btr076</citation>
10b658bef71a planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents:
diff changeset
18 <citation type="doi">10.1093/bioinformatics/btr509</citation>
10b658bef71a planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents:
diff changeset
19 <citation type="bibtex">
10b658bef71a planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents:
diff changeset
20 @misc{Danecek_et_al,
10b658bef71a planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents:
diff changeset
21 Author={Danecek, P., Schiffels, S., Durbin, R.},
10b658bef71a planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents:
diff changeset
22 title={Multiallelic calling model in bcftools (-m)},
10b658bef71a planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents:
diff changeset
23 url = {http://samtools.github.io/bcftools/call-m.pdf},}
10b658bef71a planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents:
diff changeset
24 </citation>
10b658bef71a planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents:
diff changeset
25 <citation type="bibtex">
10b658bef71a planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents:
diff changeset
26 @misc{Durbin_VCQC,
10b658bef71a planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents:
diff changeset
27 Author={Durbin, R.},
10b658bef71a planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents:
diff changeset
28 title={Segregation based metric for variant call QC},
10b658bef71a planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents:
diff changeset
29 url = {http://samtools.github.io/bcftools/rd-SegBias.pdf},}
10b658bef71a planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents:
diff changeset
30 </citation>
10b658bef71a planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents:
diff changeset
31 <citation type="bibtex">
10b658bef71a planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents:
diff changeset
32 @misc{Li_SamMath,
10b658bef71a planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents:
diff changeset
33 Author={Li, H.},
10b658bef71a planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents:
diff changeset
34 title={Mathematical Notes on SAMtools Algorithms},
10b658bef71a planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents:
diff changeset
35 url = {http://www.broadinstitute.org/gatk/media/docs/Samtools.pdf},}
10b658bef71a planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents:
diff changeset
36 </citation>
10b658bef71a planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents:
diff changeset
37 <citation type="bibtex">
10b658bef71a planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents:
diff changeset
38 @misc{SamTools_github,
10b658bef71a planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents:
diff changeset
39 title={SAMTools GitHub page},
10b658bef71a planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents:
diff changeset
40 url = {https://github.com/samtools/samtools},}
10b658bef71a planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents:
diff changeset
41 </citation>
10b658bef71a planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents:
diff changeset
42 </citations>
10b658bef71a planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents:
diff changeset
43 </xml>
10b658bef71a planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents:
diff changeset
44 <xml name="version_command">
6
28eb6a47be96 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_flagstat commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
iuc
parents: 5
diff changeset
45 <version_command><![CDATA[samtools 2>&1 | grep Version]]></version_command>
4
10b658bef71a planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents:
diff changeset
46 </xml>
10b658bef71a planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents:
diff changeset
47 <xml name="stdio">
10b658bef71a planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents:
diff changeset
48 <stdio>
10b658bef71a planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents:
diff changeset
49 <exit_code range="1:" level="fatal" description="Error" />
10b658bef71a planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents:
diff changeset
50 </stdio>
10b658bef71a planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents:
diff changeset
51 </xml>
10b658bef71a planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents:
diff changeset
52 <token name="@no-chrom-options@">
10b658bef71a planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents:
diff changeset
53 -----
10b658bef71a planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents:
diff changeset
54
10b658bef71a planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents:
diff changeset
55 .. class:: warningmark
10b658bef71a planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents:
diff changeset
56
10b658bef71a planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents:
diff changeset
57 **No options available? How to re-detect metadata**
10b658bef71a planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents:
diff changeset
58
10b658bef71a planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents:
diff changeset
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:
10b658bef71a planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents:
diff changeset
60
10b658bef71a planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents:
diff changeset
61 1. Click on the **pencil** icon adjacent to the dataset in the history
10b658bef71a planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents:
diff changeset
62 2. A new menu will appear in the center pane of the interface
10b658bef71a planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents:
diff changeset
63 3. Click **Datatype** tab
10b658bef71a planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents:
diff changeset
64 4. Set **New Type** to **BAM**
10b658bef71a planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents:
diff changeset
65 5. Click **Save**
10b658bef71a planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents:
diff changeset
66
10b658bef71a planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents:
diff changeset
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.
10b658bef71a planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents:
diff changeset
68 </token>
10b658bef71a planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents:
diff changeset
69 </macros>