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