Mercurial > repos > iuc > bcftools_plugin_vcf2sex

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 3edcac645f34d5a94884dedaf95c5774f4afc5c7
author iuc
date Sat, 11 Mar 2017 18:04:01 -0500
parents 5e036e905f69
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3:44628678a83e 4:cef5eb208e29
1 # bcftools (v1.3) 1 # bcftools (v1.3)
2 2
3 Copied from branch bcftools1.2: 3 Copied from branch bcftools1.2:
4 4
5 This aims to be a "faithful" rendering of the bcftool suite. I.e. options are 5 This aims to be a "faithful" rendering of the bcftool suite. I.e. options are
6 presented essentially as closely to the command line version as is useful. 6 presented essentially as closely to the command line version as is useful.
7 7
8 This may not appeal to all, if you'd like to see smaller and more dedicated 8 This may not appeal to all, if you'd like to see smaller and more dedicated
9 tools (e.g. "intersect", "union" and "complement" being separate tools instead 9 tools (e.g. "intersect", "union" and "complement" being separate tools instead
10 of all of them included in the "isec" tool,) please feel free to file an issue. 10 of all of them included in the "isec" tool,) please feel free to file an issue.
11 11
12 Updated for bcftools v1.3 12 Updated for bcftools v1.3
13 13
14 This was extended from the bcftools1.2 branch then greatly hand edited to 14 This was extended from the bcftools1.2 branch then greatly hand edited to
15 group params and manage param innteractions. 15 group params and manage param innteractions.
16 16
17 In the macros.xml there are macros and tokens to handle file input and output. 17 In the macros.xml there are macros and tokens to handle file input and output.
18 These use the datatypes currently available in galaxy: Vcf and Bcf 18 These use the datatypes currently available in galaxy: Vcf and Bcf
19 The macros take care of bgzip and indexing of inputs. 19 The macros take care of bgzip and indexing of inputs.
20 20
21 The convert command was split into 2 tools, "convert to vcf" and "convert from vcf" 21 The convert command was split into 2 tools, "convert to vcf" and "convert from vcf"
22 22
23 ## TODO: 23 ## TODO:
24 24
25 - stats needs a matplotlib tool dependency and pdflatex for generating a pdf of plots 25 - stats needs a matplotlib tool dependency and pdflatex for generating a pdf of plots
26 - cnv needs a matplotlib tool dependency for generating images, then a means to consolidate those. 26 - cnv needs a matplotlib tool dependency for generating images, then a means to consolidate those.
27 - cnv needs an input.vcf for testing, runs with bcftools cnv -s "HG00101" -o 'HG00101/' -p 5 mpileup.vcf 27 - cnv needs an input.vcf for testing, runs with bcftools cnv -s "HG00101" -o 'HG00101/' -p 5 mpileup.vcf
28 - roh needs a more useful input.vcf for testing 28 - roh needs a more useful input.vcf for testing
29 - plugin color chrs 29 - plugin color chrs
30 - plugin frameshifts 30 - plugin frameshifts
31 31
32 ## Status 32 ## Status
33 33
34 The wrappers were automatically generated in bulk. That doesn't get them 100% 34 The wrappers were automatically generated in bulk. That doesn't get them 100%
35 of the way there (e.g. meaningful test cases), so the rest of the process is a 35 of the way there (e.g. meaningful test cases), so the rest of the process is a