Mercurial > repos > iuc > lofreq_filter

annotate lofreq_filter.xml @ 4:950d1d49d678 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 841c48994eb214a2f8718b1d1aca22bc38598528"
author iuc
date Mon, 15 Jun 2020 13:12:17 -0400
parents fdba1586551d
children 7dfca164d2e3
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950d1d49d678 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 841c48994eb214a2f8718b1d1aca22bc38598528"
iuc
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1 <tool id="lofreq_filter" name="Lofreq filter" version="@TOOL_VERSION@+galaxy0">
0
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2 <description>called variants posteriorly</description>
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3 <macros>
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4 <import>macros.xml</import>
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5 <xml name="snvqual_filter_config">
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6 <conditional name="snvqual_filter">
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7 <param name="snvqual" type="select"
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8 label="Filter SNVs based on call quality?">
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9 <option value="no">No, don't apply call quality filter</option>
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10 <option value="min-phred">Yes, filter on explicit QUAL threshold</option>
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11 <option value="mtc">Yes, filter on multiple testing corrected p-value</option>
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12 </param>
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13 <when value="no">
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14 </when>
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15 <when value="min-phred">
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16 <param argument="-Q" name="snvqual_thresh" type="integer" min="0" value="0"
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17 label="Minimum QUAL value"
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18 help="Specify the minimum value of the QUAL field required to retain a variant" />
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19 </when>
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20 <when value="mtc">
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21 <param argument="-r" name="snvqual_alpha" type="float" min="0" max="1" value="1"
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22 label="Multiple-testing corrected p-value threshold" />
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23 <param argument="-q" name="snvqual_mtc" type="select"
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24 label="Multiple testing correction method">
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25 <option value="bonf">Bonferroni</option>
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26 <option value="holm">Holm-Sidak</option>
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27 <option value="fdr">False-discovery rate</option>
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28 </param>
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29 <param argument="-s" name="snvqual_ntests" type="integer" min="1" value="1"
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30 label="Estimate of number of tests performed"
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31 help="Ideally, this would be the number of SNVs considered during variant calling. The lofreq variant caller emits this number as part of its output. For other variant callers, all you will typically have is a lower bound estimate given by the number of SNV records in your VCF input." />
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32 </when>
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33 </conditional>
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34 </xml>
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35 <xml name="indelqual_filter_config">
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36 <conditional name="indelqual_filter">
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37 <param name="indelqual" type="select"
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38 label="Filter indels based on call quality?">
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39 <option value="no">No, don't apply call quality filter</option>
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40 <option value="min-phred">Yes, filter on explicit QUAL threshold</option>
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41 <option value="mtc">Yes, filter on multiple testing corrected p-value</option>
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42 </param>
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43 <when value="no">
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44 </when>
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45 <when value="min-phred">
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46 <param argument="-K" name="indelqual_thresh" type="integer" min="0" value="0"
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47 label="Minimum QUAL value"
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48 help="Specify the minimum value of the QUAL field required to retain a variant" />
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49 </when>
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50 <when value="mtc">
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51 <param argument="-l" name="indelqual_alpha" type="float" min="0" max="1" value="1"
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52 label="Multiple-testing corrected p-value threshold" />
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53 <param argument="-k" name="indelqual_mtc" type="select"
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54 label="Multiple testing correction method">
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55 <option value="bonf">Bonferroni</option>
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56 <option value="holm">Holm-Sidak</option>
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57 <option value="fdr">False-discovery rate</option>
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58 </param>
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59 <param argument="-m" name="indelqual_ntests" type="integer" min="1" value="1"
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60 label="Estimate of number of tests performed"
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61 help="Ideally, this would be the number of indels considered during variant calling. The lofreq variant caller emits this number as part of its output. For other variant callers, all you will typically have is a lower bound estimate given by the number of indel records in your VCF input." />
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62 </when>
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63 </conditional>
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64 </xml>
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65 </macros>
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66 <expand macro="requirements" />
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67 <command detect_errors="exit_code"><![CDATA[
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68 ## filter variants with lofreq
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69 lofreq filter -i $invcf --no-defaults --verbose
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70 $flag_or_drop
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71 ${filter_by_type.keep_only}
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72 #if str($filter_by_type.keep_only) in ['', '--only-snvs']:
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73 #if str($filter_by_type.qual.snvqual_filter.snvqual) == 'min-phred':
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74 -Q ${filter_by_type.qual.snvqual_filter.snvqual_thresh}
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75 #elif str($filter_by_type.qual.snvqual_filter.snvqual) == 'mtc':
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76 -q ${filter_by_type.qual.snvqual_filter.snvqual_mtc}
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77 -r ${filter_by_type.qual.snvqual_filter.snvqual_alpha}
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78 -s ${filter_by_type.qual.snvqual_filter.snvqual_ntests}
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79 #end if
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80 #end if
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81 #if str($filter_by_type.keep_only) in ['', '--only-indels']:
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82 #if str($filter_by_type.qual.indelqual_filter.indelqual) == 'min-phred':
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83 -K ${filter_by_type.qual.indelqual_filter.indelqual_thresh}
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84 #elif str($filter_by_type.qual.indelqual_filter.indelqual) == 'mtc':
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85 -k ${filter_by_type.qual.indelqual_filter.indelqual_mtc}
6f9ffff040ce "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff changeset
86 -l ${filter_by_type.qual.indelqual_filter.indelqual_alpha}
6f9ffff040ce "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff changeset
87 -m ${filter_by_type.qual.indelqual_filter.indelqual_ntests}
6f9ffff040ce "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff changeset
88 #end if
6f9ffff040ce "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff changeset
89 #end if
6f9ffff040ce "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff changeset
90 -v ${coverage.cov_min}
6f9ffff040ce "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff changeset
91 -V ${coverage.cov_max}
6f9ffff040ce "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff changeset
92 -a ${af.af_min}
6f9ffff040ce "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff changeset
93 -A ${af.af_max}
6f9ffff040ce "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff changeset
94 #if str($sb.sb_filter.strand_bias) == 'max-phred':
6f9ffff040ce "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff changeset
95 -B ${sb.sb_filter.sb_thresh}
6f9ffff040ce "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff changeset
96 #elif str($sb.sb_filter.strand_bias) == 'mtc':
6f9ffff040ce "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff changeset
97 -b ${sb.sb_filter.sb_mtc}
6f9ffff040ce "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff changeset
98 -c ${sb.sb_filter.sb_alpha}
6f9ffff040ce "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff changeset
99 #end if
6f9ffff040ce "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff changeset
100 #if str($sb.sb_filter.strand_bias) != 'no':
6f9ffff040ce "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff changeset
101 ${sb.sb_filter.sb_compound}
6f9ffff040ce "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff changeset
102 ${sb.sb_filter.sb_indels}
6f9ffff040ce "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff changeset
103 #end if
6f9ffff040ce "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff changeset
104 -o filtered.vcf
6f9ffff040ce "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff changeset
105 ]]></command>
6f9ffff040ce "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff changeset
106 <inputs>
6f9ffff040ce "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff changeset
107 <param argument="-i" name="invcf" type="data" format="vcf,vcf_bgzip"
6f9ffff040ce "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff changeset
108 label="List of variants to filter" />
6f9ffff040ce "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff changeset
109 <conditional name="filter_by_type">
6f9ffff040ce "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff changeset
110 <param name="keep_only" type="select"
6f9ffff040ce "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff changeset
111 label="Types of variants to keep">
6f9ffff040ce "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff changeset
112 <option value="">SNVs and Indels</option>
6f9ffff040ce "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff changeset
113 <option value="--only-snvs">SNVs only</option>
6f9ffff040ce "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff changeset
114 <option value="--only-indels">Indels only</option>
6f9ffff040ce "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff changeset
115 </param>
6f9ffff040ce "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff changeset
116 <when value="">
6f9ffff040ce "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff changeset
117 <section name="qual" title="Quality-based filter options" expanded="True">
6f9ffff040ce "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff changeset
118 <expand macro="snvqual_filter_config" />
6f9ffff040ce "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff changeset
119 <expand macro="indelqual_filter_config" />
6f9ffff040ce "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff changeset
120 </section>
6f9ffff040ce "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff changeset
121 </when>
6f9ffff040ce "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff changeset
122 <when value="--only-snvs">
6f9ffff040ce "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff changeset
123 <section name="qual" title="Quality-based filter options" expanded="True">
6f9ffff040ce "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff changeset
124 <expand macro="snvqual_filter_config" />
6f9ffff040ce "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff changeset
125 </section>
6f9ffff040ce "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff changeset
126 </when>
6f9ffff040ce "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff changeset
127 <when value="--only-indels">
6f9ffff040ce "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff changeset
128 <section name="qual" title="Quality-based filter options" expanded="True">
6f9ffff040ce "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff changeset
129 <expand macro="indelqual_filter_config" />
6f9ffff040ce "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff changeset
130 </section>
6f9ffff040ce "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff changeset
131 </when>
6f9ffff040ce "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff changeset
132 </conditional>
6f9ffff040ce "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff changeset
133 <section name="coverage" title="Coverage-based filter options" expanded="True"
6f9ffff040ce "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff changeset
134 help="You can specify a range of acceptable coverage values at variant sites by setting minimum and maximum coverage. Set either value to zero to make the range unbounded on the corresponding side, or disable filtering based on coverage by setting both values to zero.">
6f9ffff040ce "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff changeset
135 <param argument="-v" name="cov_min" type="integer" min="0" value="10"
6f9ffff040ce "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff changeset
136 label="Minimum coverage"
6f9ffff040ce "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff changeset
137 help="The minimum coverage at a site required to keep variants" />
6f9ffff040ce "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff changeset
138 <param argument="-V" name="cov_max" type="integer" min="0" value="0"
6f9ffff040ce "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff changeset
139 label="Maximum coverage"
6f9ffff040ce "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff changeset
140 help="The maximum coverage at a site allowed to keep variants" />
6f9ffff040ce "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff changeset
141 </section>
6f9ffff040ce "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff changeset
142 <section name="af" title="Allele frequency filter options" expanded="True"
6f9ffff040ce "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff changeset
143 help="You can specify a range of acceptable allele frequencies at variant sites by setting minimum and maximum AF values. Set either value to zero to make the range unbounded on the corresponding side, or disable filtering based on allele frequency by setting both values to zero.">
1
fdba1586551d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9e41ac63171c3e3a6fd2b4d018d0c60c9f1fbae1"
iuc
parents: 0
diff changeset
144 <param argument="-a" name="af_min" type="float" min="0" max="1" value="0"
0
6f9ffff040ce "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff changeset
145 label="Minimum allele frequency"
6f9ffff040ce "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff changeset
146 help="To keep a variant its allele needs to be observed at this frequency at least." />
1
fdba1586551d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9e41ac63171c3e3a6fd2b4d018d0c60c9f1fbae1"
iuc
parents: 0
diff changeset
147 <param argument="-A" name="af_max" type="float" min="0" max="1" value="0"
0
6f9ffff040ce "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff changeset
148 label="Maximum allele frequency"
6f9ffff040ce "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff changeset
149 help="To keep a variant its allele is allowed to be observed at this frequency at most." />
6f9ffff040ce "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff changeset
150 </section>
6f9ffff040ce "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff changeset
151 <section name="sb" title="Strand bias filter options" expanded="True">
6f9ffff040ce "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff changeset
152 <conditional name="sb_filter">
6f9ffff040ce "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff changeset
153 <param name="strand_bias" type="select"
6f9ffff040ce "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff changeset
154 label="Filter variants based on supporting strand bias?">
6f9ffff040ce "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff changeset
155 <option value="no">No, don't apply strand-bias filter</option>
6f9ffff040ce "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff changeset
156 <option value="max-phred">Yes, filter on explicit SB threshold</option>
6f9ffff040ce "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff changeset
157 <option value="mtc" selected="True">Yes, filter on multiple testing corrected strand-bias p-value (lofreq default)</option>
6f9ffff040ce "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff changeset
158 </param>
6f9ffff040ce "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff changeset
159 <when value="no">
6f9ffff040ce "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff changeset
160 </when>
6f9ffff040ce "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff changeset
161 <when value="max-phred">
6f9ffff040ce "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff changeset
162 <param argument="-B" name="sb_thresh" type="integer" min="0" value="0"
6f9ffff040ce "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff changeset
163 label="" />
6f9ffff040ce "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff changeset
164 </when>
6f9ffff040ce "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff changeset
165 <when value="mtc">
6f9ffff040ce "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff changeset
166 <param argument="-c" name="sb_alpha" type="float" min="0" max="1" value="0.001"
6f9ffff040ce "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff changeset
167 label="Multiple-testing corrected p-value threshold" />
6f9ffff040ce "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff changeset
168 <param argument="-b" name="sb_mtc" type="select"
6f9ffff040ce "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff changeset
169 label="Multiple testing correction method">
6f9ffff040ce "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff changeset
170 <option value="bonf">Bonferroni</option>
6f9ffff040ce "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff changeset
171 <option value="holm">Holm-Sidak</option>
6f9ffff040ce "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff changeset
172 <option value="fdr" selected="True">False-discovery rate</option>
6f9ffff040ce "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff changeset
173 </param>
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174 <param name="sb_compound" type="boolean" checked="True" truevalue="" falsevalue="--sb-no-compound"
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175 label="Use compound strand-bias filter?"
6f9ffff040ce "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
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176 help="With compound filtering a variant is filtered only if it fails the strand-bias filter configured above AND has 85% of its supporting reads mapped to one reference genome strand. This guards against filtering based on statistically significant, but minor strand bias effects at high-coverage sites." />
6f9ffff040ce "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
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177 <param argument="--sb-incl-indels" name="sb_indels" type="boolean" checked="False" truevalue="--sb-incl-indels" falsevalue=""
6f9ffff040ce "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
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178 label="Apply to indels?"
6f9ffff040ce "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
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179 help="By default, indels are not filtered based on strand bias." />
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180 </when>
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181 </conditional>
6f9ffff040ce "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
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182 </section>
6f9ffff040ce "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
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183 <param argument="--print-all" name="flag_or_drop" type="select" display="radio"
6f9ffff040ce "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
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184 label="Action to be taken for variants that do not pass the filters defined above">
6f9ffff040ce "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
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185 <option value="">Drop variants not passing one or more filters</option>
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186 <option value="--print-all">Keep variants, but indicate failed filters in output FILTER column</option>
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187 </param>
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188 </inputs>
6f9ffff040ce "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
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189 <outputs>
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190 <data name="outvcf" format="vcf" from_work_dir="filtered.vcf"/>
6f9ffff040ce "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
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191 </outputs>
6f9ffff040ce "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
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192 <tests>
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193 <test>
6f9ffff040ce "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
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194 <!-- Mimick lofreq call default filtering -->
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195 <param name="invcf" ftype="vcf" value="call-out2.vcf" />
6f9ffff040ce "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
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196 <conditional name="filter_by_type">
6f9ffff040ce "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
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197 <section name="qual">
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198 <conditional name="snvqual_filter">
6f9ffff040ce "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
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199 <param name="snvqual" value="min-phred" />
6f9ffff040ce "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
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200 <param name="snvqual_thresh" value="38" />
6f9ffff040ce "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
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201 </conditional>
6f9ffff040ce "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
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202 <conditional name="indelqual_filter">
6f9ffff040ce "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
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203 <param name="indelqual" value="min-phred" />
6f9ffff040ce "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
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204 <param name="indelqual_thresh" value="20" />
6f9ffff040ce "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
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205 </conditional>
6f9ffff040ce "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
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206 </section>
6f9ffff040ce "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
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207 </conditional>
6f9ffff040ce "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
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208 <!-- lofreq call writes duplicate ##FILTER declarations, while
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iuc
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209 lofreq filter behaves correctly. => two additional diff lines -->
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210 <output name="outvcf" file="call-out1.vcf" lines_diff="6" />
6f9ffff040ce "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
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211 </test>
6f9ffff040ce "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
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212 <test>
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213 <!-- Express lofreq call default filtering as a
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214 multiple testing correction filter -->
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215 <param name="invcf" ftype="vcf" value="call-out2.vcf" />
6f9ffff040ce "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
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216 <conditional name="filter_by_type">
6f9ffff040ce "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
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217 <param name="keep_only" value="--only-snvs" />
6f9ffff040ce "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
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218 <section name="qual">
6f9ffff040ce "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
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219 <conditional name="snvqual_filter">
6f9ffff040ce "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
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220 <param name="snvqual" value="mtc" />
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221 <param name="snvqual_alpha" value="0.01" />
6f9ffff040ce "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
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222 <param name="snvqual_mtc" value="bonf" />
6f9ffff040ce "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
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223 <param name="snvqual_ntests" value="66" />
6f9ffff040ce "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
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224 </conditional>
6f9ffff040ce "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
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225 </section>
6f9ffff040ce "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
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226 </conditional>
6f9ffff040ce "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
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227 <!-- expect additional diff lines because of different
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228 ##FILTER declarations -->
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229 <output name="outvcf" file="call-out1.vcf" lines_diff="9" />
6f9ffff040ce "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
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230 </test>
6f9ffff040ce "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
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231 <test>
6f9ffff040ce "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
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232 <!-- Test print-all option -->
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233 <param name="invcf" ftype="vcf" value="call-out2.vcf" />
6f9ffff040ce "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
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234 <conditional name="filter_by_type">
6f9ffff040ce "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
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235 <section name="qual">
6f9ffff040ce "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
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236 <conditional name="snvqual_filter">
6f9ffff040ce "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
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237 <param name="snvqual" value="min-phred" />
6f9ffff040ce "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
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238 <param name="snvqual_thresh" value="38" />
6f9ffff040ce "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
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239 </conditional>
6f9ffff040ce "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
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240 <conditional name="indelqual_filter">
6f9ffff040ce "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
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241 <param name="indelqual" value="min-phred" />
6f9ffff040ce "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
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242 <param name="indelqual_thresh" value="20" />
6f9ffff040ce "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
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243 </conditional>
6f9ffff040ce "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
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244 </section>
6f9ffff040ce "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
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245 </conditional>
6f9ffff040ce "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
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246 <param name="flag_or_drop" value="--print-all" />
6f9ffff040ce "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
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247 <!-- All variants should be retained with print-all,
6f9ffff040ce "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
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248 but variants failing filters should be flagged with the names
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249 of those filters -->
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250 <output name="outvcf">
6f9ffff040ce "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
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251 <assert_contents>
6f9ffff040ce "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
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252 <has_line_matching expression="pBR322&#009;1134&#009;.&#009;C&#009;T&#009;49314&#009;PASS&#009;.+" />
6f9ffff040ce "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
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253 <has_line_matching expression="pBR322&#009;1193&#009;.&#009;G&#009;A&#009;0&#009;min_snvqual_38&#009;.+" />
6f9ffff040ce "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
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254 </assert_contents>
6f9ffff040ce "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
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255 </output>
6f9ffff040ce "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
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256 </test>
6f9ffff040ce "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
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257 </tests>
6f9ffff040ce "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
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258 <help><![CDATA[
6f9ffff040ce "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
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259 **What it does**
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260
6f9ffff040ce "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
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261 **Lofreq filter** tries to eliminate false-positive calls from a list of
6f9ffff040ce "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
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262 variants in VCF format.
6f9ffff040ce "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
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263
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264 To this end, it applies a variety of user-configurable filters to the input
6f9ffff040ce "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
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265 variants, which all operate on variant attributes expected to be embedded in
6f9ffff040ce "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
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266 the VCF input.
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267
6f9ffff040ce "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
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268 Specifically, certain filters expect:
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269
6f9ffff040ce "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
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270 - the `QUAL` field of the variant records to be set
6f9ffff040ce "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
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271 - any of the following subfields of a variant's `INFO` field:
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272
6f9ffff040ce "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
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273 * `DP` (required for coverage-based filtering)
6f9ffff040ce "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
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274 * `AF` (required for filtering based on variant allele frequency)
6f9ffff040ce "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
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275 * `SB` (required for filtering on strand bias)
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276 * `DP4` (required for the compound strand bias filter)
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277
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278 ------
6f9ffff040ce "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
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279
6f9ffff040ce "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
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280 **Note**:
6f9ffff040ce "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
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281
6f9ffff040ce "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
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282 .. class:: Warning mark
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283
6f9ffff040ce "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
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284 This tool is optimized for posterior filtering of variants called with
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285 `Lofreq call`, which outputs all variant attributes required by the various
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286 configurable filters.
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287
6f9ffff040ce "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
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288 If you are using `Lofreq filter` to filter VCF variant lists produced with
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289 other tools, be prepared for surprises.
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290
6f9ffff040ce "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
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291 In general, if any piece of variant information required for applying a
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292 given filter is missing from the input data, the tool will try to disable
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293 that filter. Watch out for corresponding warnings in the tool's standard
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294 output.
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295
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296 In addition, any p-value based filtering on variant qualities may behave
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297 incorrectly since different variant callers might use different QUAL scales.
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298 ]]></help>
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299 <expand macro="citations" />
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300 </tool>