|
0
|
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>
|
|
1
|
6 <requirement type="package" version="1.0" >openssl</requirement>
|
|
0
|
7 </requirements>
|
|
|
8 <command>
|
|
|
9 perl $__tool_directory__/fpfilter.pl
|
|
|
10 --vcf-file ${vcf}
|
|
|
11 --bam-file ${bam}
|
|
|
12 --bam-index ${bam.metadata.bam_index}
|
|
|
13 --sample ${sample}
|
|
1
|
14
|
|
|
15
|
|
|
16 #if $reference_source.reference_source_selector == "history"
|
|
|
17 --reference $reference_source.reference
|
|
|
18 #end if
|
|
|
19 #if $reference_source.reference_source_selector == "cached"
|
|
|
20 --reference $reference_source.ref_file.fields.path
|
|
|
21 #end if
|
|
|
22
|
|
0
|
23 --output ${output}
|
|
|
24 --min-read-pos ${min_read_pos}
|
|
|
25 --min-var-freq ${min_var_freq}
|
|
|
26 --min-var-count ${min_var_count}
|
|
|
27 --min-strandedness ${min_strandness}
|
|
|
28 --max-mm-qualsum-diff ${max_mm_qualsum_diff}
|
|
|
29 --max-var-mm-qualsum ${max_var_mm_qualsum}
|
|
|
30 --max-mapqual-diff ${max_mapqual_diff}
|
|
|
31 --max-readlen-diff ${max_readlen_diff}
|
|
|
32 --min-var-dist-3 ${min_var_dist_3}
|
|
|
33 </command>
|
|
|
34
|
|
|
35 <inputs>
|
|
|
36 <param name="vcf" format="vcf" type="data" label="VCF File" help="The input VCF file. Must have a GT field." />
|
|
|
37 <param name="bam" format="bam" type="data" label="bam file" help="The BAM file of the sample you are filtering on. Typically the tumor." />
|
|
|
38 <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." />
|
|
1
|
39 <conditional name="reference_source">
|
|
|
40 <param name="reference_source_selector" type="select" label="Will you select a reference genome from your history or use a built-in index?">
|
|
|
41 <option value="cached">Use a built-in genome</option>
|
|
|
42 <option value="history">Use a genome from history as reference</option>
|
|
|
43 </param>
|
|
|
44 <when value="cached">
|
|
|
45 <param name="ref_file" type="select" label="Using reference genome" help="Select genome from the list">
|
|
|
46 <options from_data_table="fpf_index">
|
|
|
47 <filter type="sort_by" column="2" />
|
|
|
48 <validator type="no_options" message="No indexes are available" />
|
|
|
49 </options>
|
|
|
50 <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file"/>
|
|
|
51 </param>
|
|
|
52 </when>
|
|
|
53 <when value="history">
|
|
|
54 <param name="reference" type="data" format="fasta" label="Use the following dataset as the reference sequence" help="You can upload a FASTA sequence to the history and use it as reference" />
|
|
|
55 </when>
|
|
|
56 </conditional>
|
|
0
|
57 <param name="min_read_pos" type="float" value="0.10" label="Min Read Pos" help="Minimum average relative distance from start/end of read." />
|
|
|
58 <param name="min_var_freq" type="float" value="0.05" label="Min Var Freq" help="Minimum variant allele frequency." />
|
|
|
59 <param name="min_var_count" type="integer" value="4" label="Min Var Count" help="Minimum number of variant-supporting reads." />
|
|
|
60
|
|
|
61 <param name="min_strandness" type="float" value="0.01" label="Min Strandness" help="Minimum representation of variant allele on each strand." />
|
|
|
62 <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)." />
|
|
|
63
|
|
|
64 <param name="max_var_mm_qualsum" type="integer" value="100" label="Max var mm qualsum" help="Maximum mismatch quality sum of reference-supporting reads." />
|
|
|
65 <param name="max_mapqual_diff" type="integer" value="30" label="Max mapqual diff" help="Maximum difference of mapping quality between variant and reference reads." />
|
|
|
66
|
|
|
67 <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)" />
|
|
|
68 <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" />
|
|
|
69
|
|
|
70 </inputs>
|
|
|
71
|
|
|
72 <outputs>
|
|
|
73 <data format="vcf" name="output" label="FP Filtered VCF" />
|
|
|
74 </outputs>
|
|
|
75 <stdio>
|
|
|
76 <exit_code range="1:" level="fatal" />
|
|
|
77 </stdio>
|
|
|
78 <help>
|
|
|
79 --vcf-file the input VCF file. Must have a GT field.
|
|
|
80 --bam-file the BAM file of the sample you are filtering on. Typically the tumor.
|
|
|
81 --sample the sample name of the sample you want to filter on in the VCF file.
|
|
|
82 --reference-sequence a fasta containing the reference sequence the BAM file was aligned to.
|
|
|
83 --output the filename of the output VCF file
|
|
|
84 --min-read-pos minimum average relative distance from start/end of read
|
|
|
85 --min-var-freq minimum variant allele frequency
|
|
|
86 --min-var-count minimum number of variant-supporting reads
|
|
|
87 --min-strandedness minimum representation of variant allele on each strand
|
|
|
88 --max-mm-qualsum-diff maximum difference of mismatch quality sum between variant and reference reads (paralog filter)
|
|
|
89 --max_var_mm_qualsum maximum mismatch quality sum of reference-supporting reads
|
|
|
90 --max-mapqual-diff maximum difference of mapping quality between variant and reference reads
|
|
|
91 --max-readlen-diff maximum difference of average supporting read length between variant and reference reads (paralog filter)
|
|
|
92 --min-var-dist-3 minimum average distance to effective 3prime end of read (real end or Q2) for variant-supporting reads
|
|
|
93
|
|
|
94 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
|
|
|
95 </help>
|
|
|
96
|
|
|
97 <tests>
|
|
|
98 <test>
|
|
|
99 </test>
|
|
|
100 </tests>
|
|
|
101
|
|
|
102 </tool>
|
