Mercurial > repos > iuc > tbprofiler
changeset 3:875b179915ba draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/tb-profiler commit 5679ad1f1d5cac6c6168ad91dd4ca3616d22ca35"
| author | iuc |
|---|---|
| date | Fri, 16 Aug 2019 16:26:11 -0400 |
| parents | b28542b6e5c3 |
| children | 289254ce4663 |
| files | macros.xml tb_profiler_profile.xml test-data/example.vcf test-data/example.vcf.gz test-data/rif_resistant.bam |
| diffstat | 5 files changed, 30 insertions(+), 2 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros.xml Fri Aug 16 16:26:11 2019 -0400 @@ -0,0 +1,3 @@ +<macros> + <token name="@TOOL_VERSION@">2.6</token> +</macros>
--- a/tb_profiler_profile.xml Tue Jul 16 08:28:56 2019 -0400 +++ b/tb_profiler_profile.xml Fri Aug 16 16:26:11 2019 -0400 @@ -1,7 +1,10 @@ -<tool id="tb_profiler_profile" name="TB-Profiler Profile" version="2.4"> +<tool id="tb_profiler_profile" name="TB-Profiler Profile" version="@TOOL_VERSION@+galaxy0"> <description>Infer strain types and drug resistance markers from sequences</description> + <macros> + <import>macros.xml</import> + </macros> <requirements> - <requirement type="package" version="2.4">tb-profiler</requirement> + <requirement type="package" version="@TOOL_VERSION@">tb-profiler</requirement> </requirements> <command detect_errors="exit_code"><![CDATA[ #if str($fastq_or_bam.input_select.value) in ("paired_fastq", "paired_collection_fastq", "single_fastq") @@ -42,6 +45,8 @@ --min_gene_frac '${advanced.min_gene_frac}' --mapper '${advanced.mapper}' --min_depth '${advanced.min_depth}' + --af '${min_allel_freq}' + --reporting_af '${min_allel_freq_reporting}' #end if #if $output_format == "pdf" @@ -113,6 +118,8 @@ <option value="bowtie2">bowtie2</option> </param> <param name="min_gene_frac" label="Minimum Gene Fraction" type="float" value="0.9" help="Used to infer a deletion if the fraction of a gene covered falls below this value. Also used to see if sample is high quality to continue by checking the fraction for rpoB (where deletion should not occur). (default: 0.9)" /> + <param name="min_allel_freq" argument="--af" type="float" value="0.1" label="Minimum allele frequency to call variants" help=" Minimum allele frequency to call variants (default: 0.1)" /> + <param name="min_allel_freq_reporting" argument="--reporting_af" value="0.1" label="Reporting Minimum allele frequency to call variants" type="float" help=" Minimum allele frequency to call variants (default: 0.1)"/> </when> </conditional> </inputs>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/example.vcf Fri Aug 16 16:26:11 2019 -0400 @@ -0,0 +1,18 @@ +##fileformat=VCFv4.0 +##INFO=<ID=NS,Number=1,Type=Integer,Description="Number of Samples With Data"> +##INFO=<ID=AC,Number=.,Type=Integer,Description="Allele Count"> +##INFO=<ID=AN,Number=1,Type=Integer,Description="Number of Alleles With Data"> +##INFO=<ID=AF,Number=.,Type=Float,Description="Allele Frequency"> +##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype"> +#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT X1 X2 X3 X4 X5 X6 +1 10 1:10 A T 100 PASS NS=5;AC=0;AN=10;AF=0.000000 GT 0/0 ./. 0/0 0/0 0/0 0/0 +1 20 1:20 G C 100 PASS NS=0;AC=0;AN=0 GT ./. ./. ./. ./. ./. ./. +1 30 1:30 C A 100 PASS NS=6;AC=0;AN=12;AF=0.000000 GT 0/0 0/0 0/0 0/0 0/0 0/0 +1 40 1:40 A C 100 PASS NS=6;AC=0;AN=12;AF=0.000000 GT 0/0 0/0 0/0 0/0 0/0 0/0 +1 10000 1:10000 G C 100 PASS NS=6;AC=0;AN=12;AF=0.000000 GT 0/0 0/0 0/0 0/0 0/0 0/0 +1 20000 1:20000 T A 100 PASS NS=6;AC=12;AN=12;AF=1.000000 GT 1/1 1/1 1/1 1/1 1/1 1/1 +4 5000 4:5000 A T 100 PASS NS=6;AC=12;AN=12;AF=1.000000 GT 1/1 1/1 1/1 1/1 1/1 1/1 +4 6000 4:6000 C T 100 PASS NS=6;AC=11;AN=12;AF=0.916667 GT 1/1 1/1 1/1 1/1 0/1 1/1 +X 800 X:800 A C 100 PASS NS=6;AC=12;AN=12;AF=1.000000 GT 1/1 1/1 1/1 1/1 1/1 1/1 +X 900 X:900 A T 100 PASS NS=6;AC=12;AN=12;AF=1.000000 GT 1/1 1/1 1/1 1/1 1/1 1/1 +X 1000 X:1000 T G 100 PASS NS=5;AC=10;AN=10;AF=1.000000 GT 1/1 1/1 1/1 1/1 1/1 ./.