Mercurial > repos > iuc > tbprofiler
changeset 18:4839e590cb26 draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/tb-profiler commit 74ef4277d954bbbb0acd47ae6ef2d323485d5bf1
| author | iuc |
|---|---|
| date | Thu, 30 May 2024 11:31:53 +0000 |
| parents | d03af1c7002c |
| children | |
| files | tb_profiler_profile.xml test-data/rpoB_and_crispr.fastq.gz |
| diffstat | 2 files changed, 92 insertions(+), 19 deletions(-) [+] |
line wrap: on
line diff
--- a/tb_profiler_profile.xml Mon Mar 11 21:48:49 2024 +0000 +++ b/tb_profiler_profile.xml Thu May 30 11:31:53 2024 +0000 @@ -1,7 +1,7 @@ -<tool id="tb_profiler_profile" name="TB-Profiler Profile" version="@TOOL_VERSION@+galaxy0" profile="20.09"> +<tool id="tb_profiler_profile" name="TB-Profiler Profile" version="@TOOL_VERSION@+galaxy0" profile="23.2" license="AGPL-3.0-or-later"> <description>Infer strain types and drug resistance markers from sequences</description> <macros> - <token name="@TOOL_VERSION@">4.4.1</token> + <token name="@TOOL_VERSION@">6.2.1</token> </macros> <xrefs> <xref type="bio.tools">tb-profiler</xref> @@ -31,6 +31,7 @@ tb-profiler profile --platform '${platform.value}' + ${spoligotype} #if str($fastq_or_bam.input_select.value) in ("paired_fastq", "paired_collection_fastq", "single_fastq") -1 fastq_r1.'$r1_ext' #end if @@ -44,9 +45,17 @@ #if $advanced.options == 'yes' --mapper '${advanced.mapper}' --caller '${advanced.caller}' - --min_depth '${advanced.min_depth}' - --af '${advanced.min_allele_freq}' - --reporting_af '${advanced.min_allele_freq_reporting}' + --depth '${advanced.vf.min_depth_hard},${advanced.vf.min_depth_soft}' + --af '${advanced.vf.min_af_hard},${advanced.vf.min_af_soft}' + --strand '${advanced.vf.min_read_hard},${advanced.vf.min_read_soft}' + --sv-depth '${advanced.vf.min_sv_depth_hard},${advanced.vf.min_sv_depth_soft}' + --sv-af '${advanced.vf.min_sv_af_hard},${advanced.vf.min_sv_af_soft}' + --sv-len '${advanced.vf.max_sv_len_hard},${advanced.vf.max_sv_len_soft}' + ${advanced.suspect} + ${advanced.no_trim} + ${advanced.no_coverage_qc} + ${advanced.no_samclip} + ${advanced.no_delly} #end if #if $output_format == "pdf" @@ -58,7 +67,7 @@ #if str($fastq_or_bam.input_select) != "bam" && mv bam/tbprofiler.bam '${output_bam}' #end if - && bcftools view -Ov -o'${output_vcf}' vcf/tbprofiler.targets.csq.vcf.gz + && bcftools view -Ov -o'${output_vcf}' vcf/tbprofiler.targets.vcf.gz #if $output_format == "pdf" && mv results/tbprofiler.results.pdf '${output_pdf}' #else if $output_format == "txt" @@ -93,6 +102,8 @@ <param name="bam_input" type="data" format="bam" label="Bam" help="Warning!!!: The BAM files must have been created using the ensembl version of the genome."/> </when> </conditional> + <param argument="--spoligotype" type="boolean" label="Perform in-silico spoligotyping" checked="false" truevalue="--spoligotype" falsevalue="" + help="Uses spacers of CRISPR region to call a spoligotype."/> <param name="output_format" label="Output format" type="select"> <option value="txt" selected="true">Text</option> <option value="pdf">PDF</option> @@ -118,9 +129,38 @@ <option value="pilon">pilon</option> <option value="lofreq">lofreq</option> </param> - <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)"/> - <param name="min_allele_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_allele_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)"/> + <section name="vf" title="Variant Filters"> + <param name="min_depth_hard" argument="--depth" label="Min Depth (hard cutoff)" type="integer" value="0" min="0" + help="Minimum depth required to call variant. Bases with depth below this cutoff will be marked as missing (default: 0)"/> + <param name="min_depth_soft" argument="--depth" label="Min Depth (soft cutoff)" type="integer" value="10" min="0" + help="Minimum depth required to call variant. Variants at positions lower than this depth and above the hard cutoff will be marked as QC fail (default: 10)"/> + <param name="min_af_hard" argument="--af" type="float" value="0" label="Minimum allele frequency to call variants (hard cutoff)" min="0.0" max="1.0" + help="Minimum allele frequency to call variants (default: 0)" /> + <param name="min_af_soft" argument="--af" type="float" value="0.1" label="Minimum allele frequency to call variants (soft cutoff)" min="0.0" max="1.0" + help="Variants with an allele frequency lower than this (and higher than the hard cutoff) will be marked as QC fail (default 0.1)" /> + <param name="min_read_hard" argument="--strand" type="integer" value="0" label="Mininum read number per strand (hard cutoff)" min="0" + help="Minimum read number per strand to call variants (default: 0)" /> + <param name="min_read_soft" argument="--strand" type="integer" value="3" label="Mininum read number per strand (soft cutoff)" min="0" + help="Minimum read number per strand to report variants (default: 3). Variants with number of reads on each strand below this (and above the hard cutoff) will be marked as QC fail" /> + <param name="min_sv_depth_hard" argument="--sv-depth" type="integer" value="0" label="Min Depth for SV (hard cutoff)" min="0" + help="Minimum depth required to call structural variants (default: 0)" /> + <param name="min_sv_depth_soft" argument="--sv-depth" type="integer" value="10" label="Min Depth for SV (soft cutoff)" min="0" + help="Minimum depth required to call structural variants. Variants at positions lower than this depth and above the hard cutoff will be marked as QC fail" /> + <param name="min_sv_af_hard" argument="--sv-af" type="float" value="0.5" label="Min SV allele frequency (hard cutoff)" min="0.0" max="1.0" + help="Minimum allele frequency to call structural variants (default: 0.5)" /> + <param name="min_sv_af_soft" argument="--sv-af" type="float" value="0.9" label="Min SV allele frequency (soft cutoff)" min="0.0" max="1.0" + help="Variants with an allele frequency lower than this (and higher than the hard cutoff) will be marked as QC fail (default 0.9)" /> + <param name="max_sv_len_hard" argument="--sv-len" type="integer" value="100000" label="Max SV length (hard cutoff)" min="0" + help="Maximum length (length) of structural variants to call (default: 100000)" /> + <param name="max_sv_len_soft" argument="--sv-len" type="integer" value="50000" label="Max SV length (soft cutoff)" min="0" + help="Structural variants with length higher than this (and lower than the hard cutoff) will be marked as QC fail (default: 50000)" /> + </section> + <param argument="--suspect" label="Use ML predictions of resistance from the SUSPECT tool suite" type="boolean" checked="False" truevalue="--suspect" falsevalue="" + help="The SUSPECT tools offer ML-based predictions of RIF, PZA and BDQ resistance. Note that this uses a web service thus requires an Internet connection."/> + <param argument="--no_trim" label="Do not trim reads using trimmomatic" checked="false" type="boolean" truevalue="--no_trim" falsevalue="" /> + <param argument="--no_coverage_qc" label="Don't collect flagstats" type="boolean" truevalue="--no_coverage_qc" falsevalue="" /> + <param argument="--no_samclip" label="Don't removed clipped reads from variant calling" type="boolean" truevalue="--no_samclip" falsevalue="" /> + <param argument="--no_delly" label="Don't run delly for SV calling" type="boolean" truevalue="--no_delly" falsevalue="" /> </when> </conditional> </inputs> @@ -136,7 +176,6 @@ <data format="txt" name="output_txt" label="${tool.name} report on ${on_string}"> <filter>output_format == 'txt'</filter> </data> - </outputs> <tests> <test expect_num_outputs="4"> @@ -148,9 +187,9 @@ <output name="output_txt"> <assert_contents> <has_line line="Drug-resistance: RR-TB" /> - <has_line line="lineage2.2.2	1.000	Beijing-RD105/RD207	RD105;RD207" /> + <has_line line="lineage2.2.2	1.000	East-Asian (Beijing)	RD105;RD207" /> <has_line line="Rifampicin	R	rpoB p.Asp435Val (1.00)" /> - <has_line line="761110	Rv0667	rpoB	missense_variant	p.Asp435Val	1.000	rifampicin	type=who_confidence|drug=rifampicin|who_confidence=Assoc w R" /> + <has_line line="761110	Rv0667	rpoB	missense_variant	p.Asp435Val	1.000	rifampicin	Assoc w R" /> </assert_contents> </output> </test> @@ -163,9 +202,9 @@ <output name="output_txt"> <assert_contents> <has_line line="Drug-resistance: RR-TB" /> - <has_line line="lineage2.2.2	1.000	Beijing-RD105/RD207	RD105;RD207" /> + <has_line line="lineage2.2.2	1.000	East-Asian (Beijing)	RD105;RD207" /> <has_line line="Rifampicin	R	rpoB p.Asp435Val (1.00)" /> - <has_line line="761110	Rv0667	rpoB	missense_variant	p.Asp435Val	1.000	rifampicin	type=who_confidence|drug=rifampicin|who_confidence=Assoc w R" /> + <has_line line="761110	Rv0667	rpoB	missense_variant	p.Asp435Val	1.000	rifampicin	Assoc w R" /> </assert_contents> </output> </test> @@ -174,15 +213,38 @@ <param name="fastq" ftype="fastq.gz" value="rif_resistant.fastq.gz" /> <param name="output_format" value="txt" /> <param name="platform" value="illumina" /> - <param name="options" value="yes" /> - <param name="min_allele_freq" value="0.25" /> - <param name="min_allele_freq_reporting" value="0.33" /> + <conditional name="advanced"> + <param name="options" value="yes" /> + <section name="vf"> + <param name="min_depth_hard" value="40" /> + <param name="min_depth_soft" value="50" /> + </section> + </conditional> <output name="output_txt"> <assert_contents> + <has_line line="lineage2.2.2	1.000	East-Asian (Beijing)	RD105;RD207" /> + <has_line line="761110	Rv0667	rpoB	missense_variant	p.Asp435Val	1.000	rifampicin	Assoc w R" /> + </assert_contents> + </output> + <output name="results_json"> + <assert_contents> + <has_text text='"filter": "soft_fail",' /> + </assert_contents> + </output> + </test> + <test expect_num_outputs="4"> + <param name="input_select" value="single_fastq"/> + <param name="fastq" ftype="fastq.gz" value="rpoB_and_crispr.fastq.gz" /> + <param name="output_format" value="txt" /> + <param name="platform" value="illumina" /> + <param name="spoligotype" value="true" /> + <param name="options" value="no" /> + <output name="output_txt"> + <assert_contents> + <has_line line="Octal: 000000000000771" /> <has_line line="Drug-resistance: RR-TB" /> - <has_line line="lineage2.2.2	1.000	Beijing-RD105/RD207	RD105;RD207" /> <has_line line="Rifampicin	R	rpoB p.Asp435Val (1.00)" /> - <has_line line="761110	Rv0667	rpoB	missense_variant	p.Asp435Val	1.000	rifampicin	type=who_confidence|drug=rifampicin|who_confidence=Assoc w R" /> + <has_line line="761110	Rv0667	rpoB	missense_variant	p.Asp435Val	1.000	rifampicin	Assoc w R" /> </assert_contents> </output> </test> @@ -198,6 +260,17 @@ Produces a JSON output file by default. +In the Advanced options, you can select the mapper and variant caller to use, as well as set a number of filtering parameters. +Each of these typically has a "hard" and a "soft" cutoff. If a variant value is below the "hard" cutoff it is discarded, if +it is between the "hard" and "soft" values it is removed from the final predictions but added to the "qc_fail_variants" section +of the output. + +One of the advanced options is to use the SUSPECT tool suite to predict resistance to `rifampicin (RIF)`_, `pyrazinamide (PZA)`_ +and `bedaquiline (BDQ)`_. + +.. _rifampicin (RIF): https://www.nature.com/articles/s41598-020-74648-y +.. _pyrazinamide (PZA): https://www.nature.com/articles/s41598-020-58635-x +.. _bedaquiline (BDQ): https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0217169 ]]> </help> <citations> <citation type="doi">10.1186/s13073-019-0650-x</citation>