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comparison fpfilter.xml @ 0:276875076be1 draft

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author elixir-it
date Tue, 03 Jul 2018 06:05:44 -0400
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1 <tool id="fpfilter" name="fpfilter" version="0.0.1">
2 <description></description>
3 <requirements>
4 <requirement type="package" version="0.8" >bam-readcount</requirement>
5 <requirement type="package" >samtools</requirement>
6 </requirements>
7 <command>
8 perl $__tool_directory__/fpfilter.pl
9 --vcf-file ${vcf}
10 --bam-file ${bam}
11 --bam-index ${bam.metadata.bam_index}
12 --sample ${sample}
13 --reference ${reference}
14 --output ${output}
15 --min-read-pos ${min_read_pos}
16 --min-var-freq ${min_var_freq}
17 --min-var-count ${min_var_count}
18 --min-strandedness ${min_strandness}
19 --max-mm-qualsum-diff ${max_mm_qualsum_diff}
20 --max-var-mm-qualsum ${max_var_mm_qualsum}
21 --max-mapqual-diff ${max_mapqual_diff}
22 --max-readlen-diff ${max_readlen_diff}
23 --min-var-dist-3 ${min_var_dist_3}
24 </command>
25
26 <inputs>
27 <param name="vcf" format="vcf" type="data" label="VCF File" help="The input VCF file. Must have a GT field." />
28 <param name="bam" format="bam" type="data" label="bam file" help="The BAM file of the sample you are filtering on. Typically the tumor." />
29 <param name="sample" type="text" label="Sample" value="sample" help="The sample name of the sample you want to filter on in the VCF file." />
30 <param name="reference" format="fasta" type="data" label="Reference Genome" help="A fasta containing the reference sequence the BAM file was aligned to"/>
31
32 <param name="min_read_pos" type="float" value="0.10" label="Min Read Pos" help="Minimum average relative distance from start/end of read." />
33 <param name="min_var_freq" type="float" value="0.05" label="Min Var Freq" help="Minimum variant allele frequency." />
34 <param name="min_var_count" type="integer" value="4" label="Min Var Count" help="Minimum number of variant-supporting reads." />
35
36 <param name="min_strandness" type="float" value="0.01" label="Min Strandness" help="Minimum representation of variant allele on each strand." />
37 <param name="max_mm_qualsum_diff" type="integer" value="50" label="Max mm qualsum diff" help="Maximum difference of mismatch quality sum between variant and reference reads (paralog filter)." />
38
39 <param name="max_var_mm_qualsum" type="integer" value="100" label="Max var mm qualsum" help="Maximum mismatch quality sum of reference-supporting reads." />
40 <param name="max_mapqual_diff" type="integer" value="30" label="Max mapqual diff" help="Maximum difference of mapping quality between variant and reference reads." />
41
42 <param name="max_readlen_diff" type="integer" value="25" label="Max readlen diff" help="Maximum difference of average supporting read length between variant and reference reads (paralog filter)" />
43 <param name="min_var_dist_3" type="float" value="0.20" label="Min var dist 3 " help="minimum average distance to effective 3prime end of read (real end or Q2) for variant-supporting reads" />
44
45 </inputs>
46
47 <outputs>
48 <data format="vcf" name="output" label="FP Filtered VCF" />
49 </outputs>
50 <stdio>
51 <exit_code range="1:" level="fatal" />
52 </stdio>
53 <help>
54 --vcf-file the input VCF file. Must have a GT field.
55 --bam-file the BAM file of the sample you are filtering on. Typically the tumor.
56 --sample the sample name of the sample you want to filter on in the VCF file.
57 --reference-sequence a fasta containing the reference sequence the BAM file was aligned to.
58 --output the filename of the output VCF file
59 --min-read-pos minimum average relative distance from start/end of read
60 --min-var-freq minimum variant allele frequency
61 --min-var-count minimum number of variant-supporting reads
62 --min-strandedness minimum representation of variant allele on each strand
63 --max-mm-qualsum-diff maximum difference of mismatch quality sum between variant and reference reads (paralog filter)
64 --max_var_mm_qualsum maximum mismatch quality sum of reference-supporting reads
65 --max-mapqual-diff maximum difference of mapping quality between variant and reference reads
66 --max-readlen-diff maximum difference of average supporting read length between variant and reference reads (paralog filter)
67 --min-var-dist-3 minimum average distance to effective 3prime end of read (real end or Q2) for variant-supporting reads
68
69 this wrapper has been developed from the existing script at https://github.com/ucscCancer/fpfilter-tool/blob/master/fpfilter.xml , only the requirement and part of the command line have been changed in order to make it suitable for CONDA
70 </help>
71
72 <tests>
73 <test>
74 </test>
75 </tests>
76
77 </tool>