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1 <tool id="pileup_to_vcf" name="Pileup to VCF" version="2.0">
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2 <description>Converts a pileup to VCF with filtering</description>
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3 <command interpreter="python">pileup_to_vcf.py -i $input_file -o $output_file
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4 #if $min_cvrg.__str__ != '':
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5 --min_coverage $min_cvrg
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6 #end if
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7 #if $min_base_qual.__str__ != '':
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8 --min_base_qual $min_base_qual
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9 #end if
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10 #if $min_var_pct.__str__ != '':
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11 --min_allele_freq $min_var_pct
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12 #end if
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13 #if $depth_as.__str__ != 'None':
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14 --report_depth $depth_as
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15 #end if
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16 $allow_multiples
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17 $snps_only
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18 #if $cols.select_order == 'yes' :
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19 #if $chrom_col.__str__ != '':
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20 --chrom_col $chrom_col
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21 #end if
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22 #if $pos_col.__str__ != '':
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23 --pos_col $pos_col
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24 #end if
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25 #if $ref_col.__str__ != '':
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26 --ref_col $ref_col
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27 #end if
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28 #if $cvrg_col.__str__ != '':
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29 --coverage_col $cvrg_col
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30 #end if
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31 #if $base_call_col.__str__ != '':
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32 --base_call_col $base_call_col
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33 #end if
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34 #if $base_qual_col.__str__ != '':
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35 --base_qual_col $base_qual_col
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36 #end if
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37 #end if
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38 </command>
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39 <inputs>
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40 <param name="input_file" type="data" format="pileup,tabular" label="Source File" optional="false"/>
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41 <conditional name="cols">
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42 <param name="select_order" type="select" label="Set column positions for non-standard pileup">
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43 <option value="no" selected="true">Use the default pileup columns</option>
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44 <option value="yes">Select the column position that represents each pileup column</option>
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45 </param>
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46 <when value="no"/>
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47 <when value="yes">
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48 <param name="chrom_col" type="data_column" data_ref="input_file" label="Chromosome Column"/>
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49 <param name="pos_col" type="data_column" data_ref="input_file" label="Position Column"/>
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50 <param name="ref_col" type="data_column" data_ref="input_file" label="Reference Base Column"/>
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51 <param name="cvrg_col" type="data_column" data_ref="input_file" label="Depth Column"/>
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52 <param name="base_call_col" type="data_column" data_ref="input_file" label="Base Call Column"/>
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53 <param name="base_qual_col" type="data_column" data_ref="input_file" label="Base Quality Column"/>
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54 </when>
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55 </conditional>
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56 <param name="min_base_qual" type="integer" label="Minimum Base Quality" optional="true" value="20" help="Don't consider a read if the base call quality is below this threshold"/>
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57 <param name="min_cvrg" type="integer" label="Minimum Coverage Depth" optional="true" value="5" help="Any position below the threshold will be omitted from the resulting VCF"/>
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58 <param name="min_var_pct" type="float" label="Minimum Frequency of a Specific Allele" option="true" value="0.5" help="If an allele does not meet the minimum frequency it will be omitted from the resulting VCF."/>
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59 <param name="allow_multiples" type="boolean" truevalue="-m" falsevalue="" chacked="true" label="Allow Multiple Alleles for a Position?"
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60 help="Multiple alleles may be output in the VCF if the allowable frequency is below 0.5, otherwise only one will be reported"/>
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61 <param name="snps_only" type="boolean" truevalue="-s" falsevalue="" chacked="false" label="Only report SNPs, not indels" />
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62 <param name="depth_as" type="select" label="Report DP and SAF with read coverage of" help="The reported read voverage depth: DP, and the calculation of specific allele frequency (SAF) of variants">
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2
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63 <option value="source">Read coverage reported in pileup</option>
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64 <option value="ref" selected="true">Reads at this position that have a base call</option>
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0
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65 <option value="qual">Reads at this position taht pass the base call quality threshold</option>
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2
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66 <option value="all">All reads and indels</option>
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0
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67 </param>
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68 </inputs>
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69 <outputs>
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70 <data format="vcf" metadata_source="input_file" name="output_file" />
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71 </outputs>
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72 <stdio>
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73 <exit_code range="1:" level="fatal" description="Bad input dataset" />
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74 </stdio>
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75 <tests>
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76 <test>
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77 <param name="input_file" ftype="pileup" value="test.pileup" />
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78 <param name="select_order" value="no"/>
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79 <param name="min_base_qual" value="0"/>
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80 <param name="min_cvrg" value="0"/>
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81 <param name="min_var_pct" value=".1"/>
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82 <param name="allow_multiples" value="True"/>
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83 <param name="snps_only" value="False"/>
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84 <param name="depth_as" value="ref"/>
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85 <output name="output_file">
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86 <assert_contents>
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87 <has_text_matching expression="seq2\t156\t.\tA\tG,AAG\t.\tPASS\t.*" />
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88 <has_text_matching expression="chr1\t158571283\t.\tA\tC,T\t.\tPASS\t.*" />
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89 </assert_contents>
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90 </output>
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91 </test>
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92 <test>
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93 <param name="input_file" ftype="pileup" value="test.pileup" />
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94 <param name="select_order" value="no"/>
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95 <param name="min_base_qual" value="20"/>
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96 <param name="min_cvrg" value="5"/>
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97 <param name="min_var_pct" value=".1"/>
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98 <param name="allow_multiples" value="True"/>
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99 <param name="snps_only" value="False"/>
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100 <param name="depth_as" value="ref"/>
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101 <output name="output_file">
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102 <assert_contents>
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103 <has_text_matching expression="seq2\t156\t.\tA\tG,AAG\t.\tPASS\t.*" />
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104 <has_text_matching expression="chr1\t158571283\t.\tA\tC\t.\tPASS\t.*" />
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105 </assert_contents>
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106 </output>
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107 </test>
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108
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109 </tests>
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110 <help>
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111 Pileup to VCF converts the output of a pileup tool to a VCF representing any alleles that surpass a user specified frequency, optionally presenting multiple alleles for a given position if the allele frequency is set below 0.5. This tool assumes that any filtering for base call quality and mapping quality has been done in previous processing.
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112 </help>
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113 </tool>
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