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1 <tool id="bcftools_reheader" name="BCFtools reheader" version="1.0.0">
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2 <description>Modify header of VCF/BCF files, change sample names</description>
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27
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3 <requirements>
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4 <requirement type="package" version="1.3">bcftools</requirement>
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5 </requirements>
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6 <command>
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7 #if str( $input_file_index ) != "None":
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8 ln -s -f $input input_file.${input.ext} &&
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9 ln -s -f $input_file_index input_file.${input.ext}.tbi &&
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10 #end if
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11
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12 bcftools reheader
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13 --output "${output_file}"
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14 #if str( $header ) != "None":
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15 --header "${header}"
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16 #end if
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17 #if str( $samples ) != "None":
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18 --samples "${samples}"
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19 #end if
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20 #if str( $input_file_index ) != "None":
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21 input_file.${input.ext}
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22 #else
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23 $input
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24 #end if
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25 </command>
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26 <inputs>
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27 <param name="input" type="data" format="vcf,bcf,bgzip" label="VCF or BCF input file" help="Input file can optionally be compressed and indexed using Bgzip and Tabix Galaxy tools. In this case, select bgzipped file here and index below."/>
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28 <param name="input_file_index" type="data" optional="true" label="Input file index" help="Tabix-generated index for input file. Run Tabix Galaxy tool on bgzipped input file to create index."/>
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29 <param name="header" type="data" optional="True" label="New VCF header" help="-h"/>
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30 <param name="samples" type="data" optional="True" label="New sample names" help="-s. Either new sample names, each on a separate line, in the same order as samples appear in the VCF file, or "old_name new_name\n" pairs separated by whitespaces, each on a separate line." />
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31 </inputs>
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32 <outputs>
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33 <data name="output_file" format_source="input" label="${tool.name} on ${on_string}" />
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34 </outputs>
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35 <help>
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36 **About this tool**
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37
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38 **BCFtools reheader**: Modify header of VCF/BCF files, change sample names.
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39
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40 Please see https://samtools.github.io/bcftools/bcftools.html for more info on options.
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41 </help>
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42 </tool>
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