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1 <tool id="filter_vcf" name="Filter VCF" version="1.0">
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2 <description>filters a VCF file</description>
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3 <requirements>
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4 <requirement type="package" version="2.7.10">python</requirement>
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5 <requirement type="package" version="0.6.8dev">pyvcf</requirement>
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6 <requirement type="package" version="3.11">pyyaml</requirement>
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3
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7 <requirement type="package" version="2.0.2">bintrees</requirement>
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8 <requirement type="package" version="1.66">biopython</requirement>
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9 <requirement type="package" version="1.4">matplotlib</requirement>
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9
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10 <requirement type="package" version="0.23.1">cython</requirement>
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3
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11 <requirement type="package" version="1.0">phephenix</requirement>
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0
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12 </requirements>
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13 <stdio>
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14 <!-- Assume anything other than zero is an error -->
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15 <exit_code range="1:" />
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16 <exit_code range=":-1" />
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17 </stdio>
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18 <command interpreter="bash">
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19 filter_vcf.sh
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20 $output
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21 $input
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17
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22 #if str($onlygood) == "false":
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23 onlygood
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24 #else
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25 NOTTHERE
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26 #end if
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27 #for $sf in $snp_filter:
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28 #for $name, $param in $sf.snp_filter_type.iteritems():
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29 #if $name not in [ "__current_case__", "snp_filter_type_selector" ]:
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30 ${name}:"${param}"
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31 #end if
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32 #end for
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33 #end for
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34 </command>
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35
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36 <inputs>
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37 <param name="input" type="data" format="vcf" label="VCF File to filter" />
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38
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39 <repeat name="snp_filter" title="SNP Filter" help="">
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40 <conditional name="snp_filter_type">
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41 <param name="snp_filter_type_selector" type="select" label="SNP Filter Type">
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42 <option value="gq_score_option">GQ score</option>
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43 <option value="dp4_ratio_option">DP4 ratio</option>
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44 <option value="ad_ratio_option">AD ratio</option>
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45 <option value="mq_score_option">MQ score</option>
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46 <option value="min_depth_option">Minimum depth</option>
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47 <option value="uncall_gt_option">Uncall GT</option>
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48 <option value="mq0_ratio_option">MQ0 ratio</option>
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49 <option value="qual_score_option">Quality score</option>
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50 <option value="mq0f_ratio_option">MQ0F ratio</option>
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51 </param>
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52 <when value="gq_score_option">
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53 <param name="gq_score" type="integer" value="0" label="Minimum GC score" help="Type integer"/>
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54 </when>
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55 <when value="dp4_ratio_option">
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56 <param name="dp4_ratio" type="float" value="0.9" label="Minimum DP4 ratio" help="Type float"/>
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57 </when>
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58 <when value="ad_ratio_option">
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59 <param name="ad_ratio" type="float" value="0.9" label="Minimum AD ratio" help="Type float"/>
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60 </when>
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61 <when value="mq_score_option">
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62 <param name="mq_score" type="integer" value="30" label="Minimum MQ score" help="Type integer"/>
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63 </when>
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64 <when value="min_depth_option">
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65 <param name="min_depth" type="integer" value="5" label="Minimum depth" help="Type integer"/>
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66 </when>
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67 <when value="uncall_gt_option">
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68 <param name="uncall_gt" type="text" value="" hidden="True"/>
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69 </when>
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70 <when value="mq0_ratio_option">
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71 <param name="mq0_ratio" type="float" value="0.05" label="Minimim MQ0 ratio" help="Type float"/>
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72 </when>
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73 <when value="qual_score_option">
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74 <param name="qual_score" type="integer" value="30" label="Minimim quality score" help="Type integer"/>
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75 </when>
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76 <when value="mq0f_ratio_option">
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77 <param name="mq0f_ratio" type="float" value="0.05" label="Minimum MQ0F ratio" help="Type float"/>
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78 </when>
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79 </conditional>
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80 </repeat>
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81 <param name="onlygood" type="select" label="Write only good variants to output" help="Write only variants that PASS all filters. ">
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82 <option value="true" selected="true">Write all</option>
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83 <option value="false">Write only good</option>
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84 </param>
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0
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85 </inputs>
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86
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87 <outputs>
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88 <data format="vcf" name="output" label="${tool.name} on ${on_string}: filtered VCF" />
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89 </outputs>
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90 <tests>
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91 <test>
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92 <param name="input" value="test_input.vcf" ftype="vcf" />
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93 <param name="min_depth" value="100" />
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94 <output name="output" file="test_output.vcf" ftype="vcf" />
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95 </test>
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96 </tests>
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97 <help>
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98
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99 usage: filter_vcf.py [-h] \-\-vcf VCF \-\-filters FILTERS \-\-output OUTPUT
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100
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101 optional arguments:
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102
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103 -h, \-\-help show this help message and exit
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104
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105 \-\-vcf VCF, -v VCF VCF file to (re)filter.
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106
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107 \-\-filters FILTERS, -f FILTERS Filter(s) to apply as key:threshold pairs, separated by comma.
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108
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109 \-\-output OUTPUT, -o OUTPUT Location for filtered VCF to be written.
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110
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111 </help>
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112 </tool>
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