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comparison fpfilter.xml @ 1:0f17ca98338e draft default tip

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author elixir-it
date Sat, 21 Sep 2019 13:20:34 -0400
parents 276875076be1
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0:276875076be1 1:0f17ca98338e
1 <tool id="fpfilter" name="fpfilter" version="0.0.1"> 1 <tool id="fpfilter" name="fpfilter" version="0.0.1">
2 <description></description> 2 <description></description>
3 <requirements> 3 <requirements>
4 <requirement type="package" version="0.8" >bam-readcount</requirement> 4 <requirement type="package" version="0.8" >bam-readcount</requirement>
5 <requirement type="package" >samtools</requirement> 5 <requirement type="package" >samtools</requirement>
6 <requirement type="package" version="1.0" >openssl</requirement>
6 </requirements> 7 </requirements>
7 <command> 8 <command>
8 perl $__tool_directory__/fpfilter.pl 9 perl $__tool_directory__/fpfilter.pl
9 --vcf-file ${vcf} 10 --vcf-file ${vcf}
10 --bam-file ${bam} 11 --bam-file ${bam}
11 --bam-index ${bam.metadata.bam_index} 12 --bam-index ${bam.metadata.bam_index}
12 --sample ${sample} 13 --sample ${sample}
13 --reference ${reference} 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
14 --output ${output} 23 --output ${output}
15 --min-read-pos ${min_read_pos} 24 --min-read-pos ${min_read_pos}
16 --min-var-freq ${min_var_freq} 25 --min-var-freq ${min_var_freq}
17 --min-var-count ${min_var_count} 26 --min-var-count ${min_var_count}
18 --min-strandedness ${min_strandness} 27 --min-strandedness ${min_strandness}
25 34
26 <inputs> 35 <inputs>
27 <param name="vcf" format="vcf" type="data" label="VCF File" help="The input VCF file. Must have a GT field." /> 36 <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." /> 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." />
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." /> 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." />
30 <param name="reference" format="fasta" type="data" label="Reference Genome" help="A fasta containing the reference sequence the BAM file was aligned to"/> 39 <conditional name="reference_source">
31 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>
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." /> 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." />
33 <param name="min_var_freq" type="float" value="0.05" label="Min Var Freq" help="Minimum variant allele frequency." /> 58 <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." /> 59 <param name="min_var_count" type="integer" value="4" label="Min Var Count" help="Minimum number of variant-supporting reads." />
35 60
36 <param name="min_strandness" type="float" value="0.01" label="Min Strandness" help="Minimum representation of variant allele on each strand." /> 61 <param name="min_strandness" type="float" value="0.01" label="Min Strandness" help="Minimum representation of variant allele on each strand." />