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comparison bcftools_reheader.xml @ 15:9d96f73b875f draft

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author wrtz
date Thu, 14 Jan 2016 17:51:12 -0500
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14:818ab4af6410 15:9d96f73b875f
1 <tool id="bcftools_reheader" name="BCFtools reheader" version="1.0.0">
2 <description>Modify header of VCF/BCF files, change sample names</description>
3 <command>
4 #if str( $input_file_index ) != "None":
5 ln -s -f $input input_file.${input.ext} &amp;&amp;
6 ln -s -f $input_file_index input_file.${input.ext}.tbi &amp;&amp;
7 #end if
8
9 bcftools reheader
10 --output "${output_file}"
11 #if str( $header ) != "None":
12 --header "${header}"
13 #end if
14 #if str( $samples ) != "None":
15 --samples "${samples}"
16 #end if
17 #if str( $input_file_index ) != "None":
18 input_file.${input.ext}
19 #else
20 $input
21 #end if
22 </command>
23 <inputs>
24 <param name="input" type="data" format="vcf,bcf,bgzip" label="VCF or BCF input file" help="Input file can optionally be compressed and indexed using Bgzip and Tabix Galaxy tools. In this case, select bgzipped file here and index below."/>
25 <param name="input_file_index" type="data" optional="true" label="Input file index" help="Tabix-generated index for input file. Run Tabix Galaxy tool on bgzipped input file to create index."/>
26 <param name="header" type="data" optional="True" label="New VCF header" help="-h"/>
27 <param name="samples" type="data" optional="True" label="New sample names" help="-s. Either new sample names, each on a separate line, in the same order as samples appear in the VCF file, or &quot;old_name new_name\n&quot; pairs separated by whitespaces, each on a separate line." />
28 </inputs>
29 <outputs>
30 <data name="output_file" format_source="input" label="${tool.name} on ${on_string}" />
31 </outputs>
32 <help>
33 **About this tool**
34
35 **BCFtools reheader**: Modify header of VCF/BCF files, change sample names.
36
37 Please see https://samtools.github.io/bcftools/bcftools.html for more info on options.
38 </help>
39 </tool>