Mercurial > repos > jjohnson > pileup_to_vcf
comparison pileup_to_vcf.xml @ 2:d6de2d1f4af9
Fix read depth reporting
author | Jim Johnson <jj@umn.edu> |
---|---|
date | Sun, 03 Mar 2013 20:38:43 -0600 |
parents | 3890f8ba0e4d |
children | fafa105e5f58 |
comparison
equal
deleted
inserted
replaced
1:bb0ac51f1b02 | 2:d6de2d1f4af9 |
---|---|
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."/> | 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."/> |
59 <param name="allow_multiples" type="boolean" truevalue="-m" falsevalue="" chacked="true" label="Allow Multiple Alleles for a Position?" | 59 <param name="allow_multiples" type="boolean" truevalue="-m" falsevalue="" chacked="true" label="Allow Multiple Alleles for a Position?" |
60 help="Multiple alleles may be output in the VCF if the allowable frequency is below 0.5, otherwise only one will be reported"/> | 60 help="Multiple alleles may be output in the VCF if the allowable frequency is below 0.5, otherwise only one will be reported"/> |
61 <param name="snps_only" type="boolean" truevalue="-s" falsevalue="" chacked="false" label="Only report SNPs, not indels" /> | 61 <param name="snps_only" type="boolean" truevalue="-s" falsevalue="" chacked="false" label="Only report SNPs, not indels" /> |
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"> | 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"> |
63 <option value="ref" selected="true">Reads at this position</option> | 63 <option value="source">Read coverage reported in pileup</option> |
64 <option value="ref" selected="true">Reads at this position that have a base call</option> | |
64 <option value="qual">Reads at this position taht pass the base call quality threshold</option> | 65 <option value="qual">Reads at this position taht pass the base call quality threshold</option> |
65 <option value="all"></option> | 66 <option value="all">All reads and indels</option> |
66 </param> | 67 </param> |
67 </inputs> | 68 </inputs> |
68 <outputs> | 69 <outputs> |
69 <data format="vcf" metadata_source="input_file" name="output_file" /> | 70 <data format="vcf" metadata_source="input_file" name="output_file" /> |
70 </outputs> | 71 </outputs> |