Mercurial > repos > jjohnson > pileup_to_vcf
view pileup_to_vcf.xml @ 1:bb0ac51f1b02
Handle delection char: *
author | Jim Johnson <jj@umn.edu> |
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date | Mon, 18 Feb 2013 19:11:47 -0600 |
parents | 3890f8ba0e4d |
children | d6de2d1f4af9 |
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<tool id="pileup_to_vcf" name="Pileup to VCF" version="2.0"> <description>Converts a pileup to VCF with filtering</description> <command interpreter="python">pileup_to_vcf.py -i $input_file -o $output_file #if $min_cvrg.__str__ != '': --min_coverage $min_cvrg #end if #if $min_base_qual.__str__ != '': --min_base_qual $min_base_qual #end if #if $min_var_pct.__str__ != '': --min_allele_freq $min_var_pct #end if #if $depth_as.__str__ != 'None': --report_depth $depth_as #end if $allow_multiples $snps_only #if $cols.select_order == 'yes' : #if $chrom_col.__str__ != '': --chrom_col $chrom_col #end if #if $pos_col.__str__ != '': --pos_col $pos_col #end if #if $ref_col.__str__ != '': --ref_col $ref_col #end if #if $cvrg_col.__str__ != '': --coverage_col $cvrg_col #end if #if $base_call_col.__str__ != '': --base_call_col $base_call_col #end if #if $base_qual_col.__str__ != '': --base_qual_col $base_qual_col #end if #end if </command> <inputs> <param name="input_file" type="data" format="pileup,tabular" label="Source File" optional="false"/> <conditional name="cols"> <param name="select_order" type="select" label="Set column positions for non-standard pileup"> <option value="no" selected="true">Use the default pileup columns</option> <option value="yes">Select the column position that represents each pileup column</option> </param> <when value="no"/> <when value="yes"> <param name="chrom_col" type="data_column" data_ref="input_file" label="Chromosome Column"/> <param name="pos_col" type="data_column" data_ref="input_file" label="Position Column"/> <param name="ref_col" type="data_column" data_ref="input_file" label="Reference Base Column"/> <param name="cvrg_col" type="data_column" data_ref="input_file" label="Depth Column"/> <param name="base_call_col" type="data_column" data_ref="input_file" label="Base Call Column"/> <param name="base_qual_col" type="data_column" data_ref="input_file" label="Base Quality Column"/> </when> </conditional> <param name="min_base_qual" type="integer" label="Minimum Base Quality" optional="true" value="20" help="Don't consider a read if the base call quality is below this threshold"/> <param name="min_cvrg" type="integer" label="Minimum Coverage Depth" optional="true" value="5" help="Any position below the threshold will be omitted from the resulting VCF"/> <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."/> <param name="allow_multiples" type="boolean" truevalue="-m" falsevalue="" chacked="true" label="Allow Multiple Alleles for a Position?" help="Multiple alleles may be output in the VCF if the allowable frequency is below 0.5, otherwise only one will be reported"/> <param name="snps_only" type="boolean" truevalue="-s" falsevalue="" chacked="false" label="Only report SNPs, not indels" /> <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"> <option value="ref" selected="true">Reads at this position</option> <option value="qual">Reads at this position taht pass the base call quality threshold</option> <option value="all"></option> </param> </inputs> <outputs> <data format="vcf" metadata_source="input_file" name="output_file" /> </outputs> <stdio> <exit_code range="1:" level="fatal" description="Bad input dataset" /> </stdio> <tests> <test> <param name="input_file" ftype="pileup" value="test.pileup" /> <param name="select_order" value="no"/> <param name="min_base_qual" value="0"/> <param name="min_cvrg" value="0"/> <param name="min_var_pct" value=".1"/> <param name="allow_multiples" value="True"/> <param name="snps_only" value="False"/> <param name="depth_as" value="ref"/> <output name="output_file"> <assert_contents> <has_text_matching expression="seq2\t156\t.\tA\tG,AAG\t.\tPASS\t.*" /> <has_text_matching expression="chr1\t158571283\t.\tA\tC,T\t.\tPASS\t.*" /> </assert_contents> </output> </test> <test> <param name="input_file" ftype="pileup" value="test.pileup" /> <param name="select_order" value="no"/> <param name="min_base_qual" value="20"/> <param name="min_cvrg" value="5"/> <param name="min_var_pct" value=".1"/> <param name="allow_multiples" value="True"/> <param name="snps_only" value="False"/> <param name="depth_as" value="ref"/> <output name="output_file"> <assert_contents> <has_text_matching expression="seq2\t156\t.\tA\tG,AAG\t.\tPASS\t.*" /> <has_text_matching expression="chr1\t158571283\t.\tA\tC\t.\tPASS\t.*" /> </assert_contents> </output> </test> </tests> <help> Pileup to VCF converts the output of a pileup tool to a VCF representing any alleles that surpass a user specified frequency, optionally presenting multiple alleles for a given position if the allele frequency is set below 0.5. This tool assumes that any filtering for base call quality and mapping quality has been done in previous processing. </help> </tool>