Mercurial > repos > iuc > tbprofiler
changeset 4:c2656b729ee9 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/tb-profiler commit a51548708ea975c0a7b135a2cbaa5d094f3c5602"
| author | iuc |
|---|---|
| date | Tue, 15 Oct 2019 14:35:47 -0400 |
| parents | 19793eecc9f0 |
| children | 4272bd430a01 |
| files | macros.xml tb_profiler_profile.xml |
| diffstat | 2 files changed, 6 insertions(+), 3 deletions(-) [+] |
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--- a/macros.xml Fri Aug 16 16:26:31 2019 -0400 +++ b/macros.xml Tue Oct 15 14:35:47 2019 -0400 @@ -1,3 +1,3 @@ <macros> - <token name="@TOOL_VERSION@">2.6</token> + <token name="@TOOL_VERSION@">2.6.1</token> </macros>
--- a/tb_profiler_profile.xml Fri Aug 16 16:26:31 2019 -0400 +++ b/tb_profiler_profile.xml Tue Oct 15 14:35:47 2019 -0400 @@ -41,6 +41,7 @@ --threads "\${GALAXY_SLOTS:-1}" #if $advanced.options == 'yes' + '${advanced.call_whole_genome}' --call_method '${advanced.call_method}' --min_gene_frac '${advanced.min_gene_frac}' --mapper '${advanced.mapper}' @@ -58,7 +59,7 @@ #if str($fastq_or_bam.input_select) != "bam" && mv bam/tbprofiler.bam '${output_bam}' #end if - && bcftools view -Ov -o'${output_vcf}' vcf/tbprofiler.targets.csq.bcf + && bcftools view -Ov -o'${output_vcf}' vcf/tbprofiler.targets.csq.vcf.gz #if $output_format == "pdf" && mv results/tbprofiler.results.pdf '${output_pdf}' #else if $output_format == "txt" @@ -109,6 +110,8 @@ <option value="high">High</option> <option value="optimise">Optimise</option> </param> + <param label="Call variants on the whole genome" type="boolean" argument="--call_whole_genome" + truevalue="--call_whole_genome" falsevalue="" help="Call variants on whole genome (Useful if you need to use whole genome variants later)" /> <param label="Minimum coverage fraction to infer deletion" type="float" help="Used to infer a deletion if the fraction of a gene covered falls below this value." argument="--min_gene_frac" value="0.9" /> <param name="min_depth" label="Min Depth" type="integer" value="10" help="Minimum depth required to call variant. Bases with depth below this cutoff will be marked as missing (default: 10)"/> @@ -173,7 +176,7 @@ Summary ======= -The pipeline aligns reads to the H37Rv reference using bowtie2, BWA or minimap2 and then calls variants using SAMtools. These variants are then compared to a drug-resistance database. We also predict the number of reads supporting drug resistance variants as an insight into hetero-resistance (not applicable for minION data). +The pipeline aligns reads to the H37Rv reference using bowtie2, BWA or minimap2 and then calls variants using GATK. These variants are then compared to a drug-resistance database. We also predict the number of reads supporting drug resistance variants as an insight into hetero-resistance (not applicable for minION data). Produces a JSON output file by default.