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comparison macros.xml @ 0:770db64c4cfc draft

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author greg
date Thu, 01 Nov 2018 10:23:32 -0400
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-1:000000000000 0:770db64c4cfc
1 <macros>
2 <token name="@VERSION@">1.4.0</token>
3 <xml name="requirements">
4 <requirements>
5 <requirement type="package" version="1.9">bcftools</requirement>
6 <requirement type="package" version="1.9">htslib</requirement>
7 <yield />
8 </requirements>
9 </xml>
10 <xml name="citations">
11 <citations>
12 <citation type="doi">10.1093/bioinformatics/btp352</citation>
13 <yield />
14 </citations>
15 </xml>
16 <token name="@THREADS@">
17 --threads \${GALAXY_SLOTS:-4}
18 </token>
19 <token name="@PREPARE_ENV@">
20 <![CDATA[
21 export BCFTOOLS_PLUGINS=`which bcftools | sed 's,bin/bcftools,libexec/bcftools,'`;
22 ]]>
23 </token>
24 <xml name="macro_input">
25 <param name="input_file" type="data" format="vcf,vcf_bgzip,bcf,bcf_bgzip" label="VCF/BCF Data" />
26 </xml>
27 <token name="@PREPARE_INPUT_FILE@">
28 <![CDATA[
29 ## May need to symlink input if there is an associated
30 #set $input_vcf = 'input.vcf.gz'
31 #if $input_file.is_of_type('vcf')
32 bgzip -c '$input_file' > $input_vcf &&
33 bcftools index $input_vcf &&
34 #elif $input_file.is_of_type('vcf_bgzip')
35 ln -s '$input_file' $input_vcf &&
36 #elif $input_file.is_of_type('bcf')
37 #set $input_vcf = 'input.bcf'
38 ln -s '$input_file' $input_vcf &&
39 #if $input_file.metadata.bcf_index:
40 ln -s '${input_file.metadata.bcf_index}' ${input_vcf}.csi &&
41 #else
42 bcftools index $input_vcf &&
43 #end if
44 #elif $input_file.is_of_type('bcf_bgzip')
45 ln -s '$input_file' $input_vcf &&
46 #end if
47 ]]>
48 </token>
49 <token name="@INPUT_FILE@">
50 $input_vcf
51 </token>
52 <xml name="macro_select_output_type">
53 <param name="output_type" type="select">
54 <option value="b">compressed BCF</option>
55 <option value="u">uncompressed BCF</option>
56 <option value="z">compressed VCF</option>
57 <option value="v">uncompressed VCF</option>
58 </param>
59 </xml>
60 <token name="@OUTPUT_TYPE@">
61 #if str($output_type) != "__none__":
62 --output-type '${output_type}'
63 #end if
64 </token>
65
66 <xml name="macro_vcf_output">
67 <data name="output_file" format="vcf">
68 <change_format>
69 <when input="output_type" value="b" format="bcf" />
70 <when input="output_type" value="u" format="bcf" />
71 <when input="output_type" value="z" format="vcf_bgzip" />
72 <when input="output_type" value="v" format="vcf" />
73 </change_format>
74 </data>
75 </xml>
76
77 <token name="@OUTPUT_HELP@">
78 <![CDATA[
79 Output Type
80 -----------
81
82 Output compressed BCF (b), or uncompressed VCF (v).
83 Use the BCF option when piping between bcftools subcommands to speed up
84 performance by removing unecessary compression/decompression
85 and VCF<->BCF conversion.
86
87 This Galaxy tool recommends using the compressed BCF format
88 as piping is not implemented, and uncompressed data would
89 use unnecessary amounts of space.
90 ]]></token>
91 </macros>
92