tbprofiler: tb_profiler_profile.xml comparison

comparison tb_profiler_profile.xml @ 18:4839e590cb26 draft

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	51dd22484644

comparison

equal deleted inserted replaced

-:d03af1c7002c
+:4839e590cb26
-<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>
 </xrefs>
 <requirements>
 ln -s '$fastq_or_bam.bam_input' input.bam &&
 #end if
 tb-profiler profile
 --platform '${platform.value}'
+${spoligotype}
 #if str($fastq_or_bam.input_select.value) in ("paired_fastq", "paired_collection_fastq", "single_fastq")
 -1 fastq_r1.'$r1_ext'
 #end if
 #if str($fastq_or_bam.input_select.value) in ("paired_fastq", "paired_collection_fastq")
 -2 fastq_r2.'$r1_ext'
 --threads "\${GALAXY_SLOTS:-1}"
 #if $advanced.options == 'yes'
 --mapper '${advanced.mapper}'
 --caller '${advanced.caller}'
---min_depth '${advanced.min_depth}'
+--depth '${advanced.vf.min_depth_hard},${advanced.vf.min_depth_soft}'
---af '${advanced.min_allele_freq}'
+--af '${advanced.vf.min_af_hard},${advanced.vf.min_af_soft}'
---reporting_af '${advanced.min_allele_freq_reporting}'
+--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"
 --pdf
 #else if $output_format == "txt"
 #end if
 && mv results/tbprofiler.results.json $results_json
 #if str($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 $output_format == "txt"
 && mv results/tbprofiler.results.txt '${output_txt}'
 #end if
 </when>
 <when value="bam">
 <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>
 </param>
 <conditional name="advanced">
 <option value="bcftools">bcftools</option>
 <option value="gatk">gatk</option>
 <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)"/>
+<section name="vf" title="Variant Filters">
-<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_depth_hard" argument="--depth" label="Min Depth (hard cutoff)" type="integer" value="0" min="0"
-<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)"/>
+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>
 <outputs>
 <data name="results_json" format="json" from_work_dir="results/tbprofiler.results.json" label="${tool.name} on ${on_string}: Results.json"/>
 <filter>output_format == 'pdf'</filter>
 </data>
 <data format="txt" name="output_txt" label="${tool.name} report on ${on_string}">
 <filter>output_format == 'txt'</filter>
 </data>
 </outputs>
 <tests>
 <test expect_num_outputs="4">
 <param name="input_select" value="single_fastq"/>
 <param name="fastq" ftype="fastq.gz" value="rif_resistant.fastq.gz" />
 <param name="platform" value="illumina" />
 <param name="options" value="no" />
 <output name="output_txt">
 <assert_contents>
 <has_line line="Drug-resistance: RR-TB" />
-<has_line line="lineage2.2.2&#009;1.000&#009;Beijing-RD105/RD207&#009;RD105;RD207" />
+<has_line line="lineage2.2.2&#009;1.000&#009;East-Asian (Beijing)&#009;RD105;RD207" />
 <has_line line="Rifampicin&#009;R&#009;rpoB p.Asp435Val (1.00)" />
-<has_line line="761110&#009;Rv0667&#009;rpoB&#009;missense_variant&#009;p.Asp435Val&#009;1.000&#009;rifampicin&#009;type=who_confidence|drug=rifampicin|who_confidence=Assoc w R" />
+<has_line line="761110&#009;Rv0667&#009;rpoB&#009;missense_variant&#009;p.Asp435Val&#009;1.000&#009;rifampicin&#009;Assoc w R" />
 </assert_contents>
 </output>
 </test>
 <test expect_num_outputs="3">
 <param name="input_select" value="bam"/>
 <param name="platform" value="illumina" />
 <param name="options" value="no" />
 <output name="output_txt">
 <assert_contents>
 <has_line line="Drug-resistance: RR-TB" />
-<has_line line="lineage2.2.2&#009;1.000&#009;Beijing-RD105/RD207&#009;RD105;RD207" />
+<has_line line="lineage2.2.2&#009;1.000&#009;East-Asian (Beijing)&#009;RD105;RD207" />
 <has_line line="Rifampicin&#009;R&#009;rpoB p.Asp435Val (1.00)" />
-<has_line line="761110&#009;Rv0667&#009;rpoB&#009;missense_variant&#009;p.Asp435Val&#009;1.000&#009;rifampicin&#009;type=who_confidence|drug=rifampicin|who_confidence=Assoc w R" />
+<has_line line="761110&#009;Rv0667&#009;rpoB&#009;missense_variant&#009;p.Asp435Val&#009;1.000&#009;rifampicin&#009;Assoc w R" />
 </assert_contents>
 </output>
 </test>
 <test expect_num_outputs="4">
 <param name="input_select" value="single_fastq"/>
 <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" />
+<conditional name="advanced">
-<param name="min_allele_freq" value="0.25" />
+<param name="options" value="yes" />
-<param name="min_allele_freq_reporting" value="0.33" />
+<section name="vf">
-<output name="output_txt">
+<param name="min_depth_hard" value="40" />
-<assert_contents>
+<param name="min_depth_soft" value="50" />
+</section>
+</conditional>
+<output name="output_txt">
+<assert_contents>
+<has_line line="lineage2.2.2&#009;1.000&#009;East-Asian (Beijing)&#009;RD105;RD207" />
+<has_line line="761110&#009;Rv0667&#009;rpoB&#009;missense_variant&#009;p.Asp435Val&#009;1.000&#009;rifampicin&#009;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&#009;1.000&#009;Beijing-RD105/RD207&#009;RD105;RD207" />
 <has_line line="Rifampicin&#009;R&#009;rpoB p.Asp435Val (1.00)" />
-<has_line line="761110&#009;Rv0667&#009;rpoB&#009;missense_variant&#009;p.Asp435Val&#009;1.000&#009;rifampicin&#009;type=who_confidence|drug=rifampicin|who_confidence=Assoc w R" />
+<has_line line="761110&#009;Rv0667&#009;rpoB&#009;missense_variant&#009;p.Asp435Val&#009;1.000&#009;rifampicin&#009;Assoc w R" />
 </assert_contents>
 </output>
 </test>
 </tests>
 <help><![CDATA[
 TB-Profiler also predicts 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.
+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>
 </citations>
 </tool>

Mercurial > repos > iuc > tbprofiler

comparison tb_profiler_profile.xml @ 18:4839e590cb26 draft