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