Mercurial > repos > jjohnson > pileup_to_vcf

comparison pileup_to_vcf.xml @ 9:c0a6e8f595ec default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Add option to set VCF ID field value, this can be used to ID germline variants for SnpSift
author Jim Johnson <jj@umn.edu>
date Thu, 11 Apr 2013 10:28:10 -0500
parents 8688e29ba96f
children
comparison
equal deleted inserted replaced
8:07cd87e94fbe 9:c0a6e8f595ec
1 <tool id="pileup_to_vcf" name="Pileup to VCF" version="2.1"> 1 <tool id="pileup_to_vcf" name="Pileup to VCF" version="2.2">
2 <description>Converts a pileup to VCF with filtering</description> 2 <description>Converts a pileup to VCF with filtering</description>
3 <command interpreter="python">pileup_to_vcf.py -i $input_file -o $output_file 3 <command interpreter="python">pileup_to_vcf.py -i $input_file -o $output_file
4 #if $min_cvrg.__str__ != '': 4 #if $min_cvrg.__str__ != '':
5 --min_coverage $min_cvrg 5 --min_coverage $min_cvrg
6 #end if 6 #end if
13 #if $depth_as.__str__ != 'None': 13 #if $depth_as.__str__ != 'None':
14 --report_depth $depth_as 14 --report_depth $depth_as
15 #end if 15 #end if
16 $allow_multiples 16 $allow_multiples
17 $snps_only 17 $snps_only
18 #if $vcf_id.__str__ != '':
19 --id $vcf_id
20 #end if
18 #if $cols.select_order == 'yes' : 21 #if $cols.select_order == 'yes' :
19 #if $chrom_col.__str__ != '': 22 #if $chrom_col.__str__ != '':
20 --chrom_col $chrom_col 23 --chrom_col $chrom_col
21 #end if 24 #end if
22 #if $pos_col.__str__ != '': 25 #if $pos_col.__str__ != '':
63 <option value="source">Read coverage reported in pileup</option> 66 <option value="source">Read coverage reported in pileup</option>
64 <option value="ref" selected="true">Reads at this position that have a base call</option> 67 <option value="ref" selected="true">Reads at this position that have a base call</option>
65 <option value="qual">Reads at this position taht pass the base call quality threshold</option> 68 <option value="qual">Reads at this position taht pass the base call quality threshold</option>
66 <option value="all">All reads and indels</option> 69 <option value="all">All reads and indels</option>
67 </param> 70 </param>
71 <param name="vcf_id" type="text" optional="true" value="" label="The VCF ID" help="The VCF output will use this as the ID field value">
72 <validator type="regex" message="whitespace characters not allowed">^\S*$</validator>
73 </param>
68 </inputs> 74 </inputs>
69 <outputs> 75 <outputs>
70 <data format="vcf" metadata_source="input_file" name="output_file" /> 76 <data format="vcf" metadata_source="input_file" name="output_file" />
71 </outputs> 77 </outputs>
72 <stdio> 78 <stdio>