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 |
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| 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> |