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1 <tool id="vcfgeno2haplo" name="VCFgenotype-to-haplotype:" version="0.0.1">
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2 <requirements>
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3 <requirement type="package" version="586c5ae5d57a38dae6b32ea831fb1f7cfa14c9bd">vcflib</requirement>
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4 </requirements>
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5 <description>Convert genotype-based phased alleles into haplotype alleles</description>
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6 <command>
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7 #set $reference_fasta_filename = "localref.fa"
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8 #if str( $reference_source.reference_source_selector ) == "history":
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9 ln -s "${reference_source.ref_file}" "${reference_fasta_filename}" &&
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10 #else:
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11 #set $reference_fasta_filename = str( $reference_source.ref_file.fields.path )
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12 #end if
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13 vcfgeno2haplo ${output_option} -w ${window_size} -r "${reference_fasta_filename}" "${input_vcf}" > "${out_file1}"</command>
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14 <inputs>
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15 <conditional name="reference_source">
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16 <param name="reference_source_selector" type="select" label="Choose the source for the reference genome">
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17 <option value="cached">Locally cached</option>
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18 <option value="history">History</option>
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19 </param>
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20 <when value="cached">
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21 <param name="ref_file" type="select" label="Select reference genome">
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22 <options from_data_table="fasta_indexes">
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23 <!--<filter type="data_meta" key="dbkey" ref="input_bam" column="value"/>-->
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24 </options>
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25 <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file"/>
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26 </param>
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27 <param name="input_vcf" type="data" format="vcf" label="Select VCF dataset">
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28 <!-- Validators are commented to allow users apply too to any build. May need to be revised in the future
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29 <validator type="unspecified_build" />
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30 <validator type="dataset_metadata_in_data_table" table_name="fasta_indexes" metadata_name="dbkey" metadata_column="1" message="Sequences are not currently available for the specified build." />
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31 -->
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32 </param>
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33 </when>
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34 <when value="history"> <!-- FIX ME!!!! -->
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35 <param name="ref_file" type="data" format="fasta" label="Using reference file" />
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36 <param name="input_vcf" type="data" format="vcf" label="Select VCF dataset" />
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37 </when>
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38 </conditional>
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39 <param name="window_size" type="text" size="4" value="30" label="compare records up to this many bp away (window size)" help="--window-size option (default = 30)" />
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40 <param name="output_option" type="boolean" truevalue="-o" falsevalue="" label="What to report?" help="--only-variants option" />
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41 <!-- <option value=" ">Output entire haplotype</option>
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42 <option value="-o">Don't output the entire haplotype, just concatenate REF/ALT strings (delimited by ":")</option>
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43 </param> -->
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44 </inputs>
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45 <outputs>
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46 <data format="vcf" name="out_file1" />
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47 </outputs>
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48 <stdio>
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49 <exit_code range="1:" level="fatal" />
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50 </stdio>
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51 <tests>
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52 <test>
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53 <param name="reference_source_selector" value="history" />
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54 <param name="output_option" value="true" />
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55 <param name="window_size" value="5000" />
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56 <param name="input_vcf" value="vcflib-phix.vcf"/>
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57 <param name="ref_file" value="vcflib-test-genome-phix.fa" />
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58 <output name="out_file1" file="vcfgeno2haplo-test1.vcf"/>
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59 </test>
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60 </tests>
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61 <help>
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62
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63 Convert genotype-based phased alleles within a window size specified by -w option into haplotype alleles. Will break haplotype construction when encountering non-phased genotypes on input.
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64
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65 The options are::
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66
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67 -r, --reference FILE FASTA reference file, required with -i and -u
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68 -w, --window-size N Merge variants at most this many bp apart (default 30)
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69 -o, --only-variants Don't output the entire haplotype, just concatenate
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70 REF/ALT strings (delimited by ":")
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71
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72 ----
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73
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74 Vcfgeno2haplo is a part of VCFlib toolkit developed by Erik Garrison (https://github.com/ekg/vcflib).
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75
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76 </help>
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77 </tool>
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