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Changeset 18:4839e590cb26 (2024-05-30)

Previous changeset 17:d03af1c7002c (2024-03-11) Next changeset 19:51dd22484644 (2024-06-20)

Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/tb-profiler commit 74ef4277d954bbbb0acd47ae6ef2d323485d5bf1

modified:
tb_profiler_profile.xml

added:
test-data/rpoB_and_crispr.fastq.gz

diff -r d03af1c7002c -r 4839e590cb26 tb_profiler_profile.xml
--- 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

b'@@ -1,7 +1,7 @@\n-<tool id="tb_profiler_profile" name="TB-Profiler Profile" version="@TOOL_VERSION@+galaxy0" profile="20.09">\n+<tool id="tb_profiler_profile" name="TB-Profiler Profile" version="@TOOL_VERSION@+galaxy0" profile="23.2" license="AGPL-3.0-or-later">\n <description>Infer strain types and drug resistance markers from sequences</description>\n <macros>\n- <token name="@TOOL_VERSION@">4.4.1</token>\n+ <token name="@TOOL_VERSION@">6.2.1</token>\n </macros>\n <xrefs>\n <xref type="bio.tools">tb-profiler</xref>\n@@ -31,6 +31,7 @@\n \n tb-profiler profile\n --platform \'${platform.value}\'\n+ ${spoligotype}\n #if str($fastq_or_bam.input_select.value) in ("paired_fastq", "paired_collection_fastq", "single_fastq")\n -1 fastq_r1.\'$r1_ext\'\n #end if\n@@ -44,9 +45,17 @@\n #if $advanced.options == \'yes\'\n --mapper \'${advanced.mapper}\'\n --caller \'${advanced.caller}\'\n- --min_depth \'${advanced.min_depth}\'\n- --af \'${advanced.min_allele_freq}\'\n- --reporting_af \'${advanced.min_allele_freq_reporting}\'\n+ --depth \'${advanced.vf.min_depth_hard},${advanced.vf.min_depth_soft}\'\n+ --af \'${advanced.vf.min_af_hard},${advanced.vf.min_af_soft}\'\n+ --strand \'${advanced.vf.min_read_hard},${advanced.vf.min_read_soft}\'\n+ --sv-depth \'${advanced.vf.min_sv_depth_hard},${advanced.vf.min_sv_depth_soft}\'\n+ --sv-af \'${advanced.vf.min_sv_af_hard},${advanced.vf.min_sv_af_soft}\'\n+ --sv-len \'${advanced.vf.max_sv_len_hard},${advanced.vf.max_sv_len_soft}\'\n+ ${advanced.suspect}\n+ ${advanced.no_trim}\n+ ${advanced.no_coverage_qc}\n+ ${advanced.no_samclip}\n+ ${advanced.no_delly}\n #end if\n \n #if $output_format == "pdf"\n@@ -58,7 +67,7 @@\n #if str($fastq_or_bam.input_select) != "bam"\n && mv bam/tbprofiler.bam \'${output_bam}\'\n #end if\n- && bcftools view -Ov -o\'${output_vcf}\' vcf/tbprofiler.targets.csq.vcf.gz\n+ && bcftools view -Ov -o\'${output_vcf}\' vcf/tbprofiler.targets.vcf.gz\n #if $output_format == "pdf"\n && mv results/tbprofiler.results.pdf \'${output_pdf}\'\n #else if $output_format == "txt"\n@@ -93,6 +102,8 @@\n <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."/>\n </when>\n </conditional>\n+ <param argument="--spoligotype" type="boolean" label="Perform in-silico spoligotyping" checked="false" truevalue="--spoligotype" falsevalue="" \n+ help="Uses spacers of CRISPR region to call a spoligotype."/>\n <param name="output_format" label="Output format" type="select">\n <option value="txt" selected="true">Text</option>\n <option value="pdf">PDF</option>\n@@ -118,9 +129,38 @@\n <option value="pilon">pilon</option>\n <option value="lofreq">lofreq</option>\n </param>\n- <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)"/>\n- <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)" />\n- <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)"/>\n+ <section name="vf" title="Variant Filters">\n+ <param name="min_depth_hard" argument="--depth" label="Min Depth (hard cutoff)" type="integer" value="0" min="0"\n+ '..b'09;R	rpoB p.Asp435Val (1.00)" />\n- <has_line line="761110	Rv0667	rpoB	missense_variant	p.Asp435Val	1.000	rifampicin	type=who_confidence|drug=rifampicin|who_confidence=Assoc w R" />\n+ <has_line line="761110	Rv0667	rpoB	missense_variant	p.Asp435Val	1.000	rifampicin	Assoc w R" />\n </assert_contents>\n </output>\n </test>\n@@ -174,15 +213,38 @@\n <param name="fastq" ftype="fastq.gz" value="rif_resistant.fastq.gz" />\n <param name="output_format" value="txt" />\n <param name="platform" value="illumina" />\n- <param name="options" value="yes" />\n- <param name="min_allele_freq" value="0.25" />\n- <param name="min_allele_freq_reporting" value="0.33" />\n+ <conditional name="advanced">\n+ <param name="options" value="yes" />\n+ <section name="vf">\n+ <param name="min_depth_hard" value="40" />\n+ <param name="min_depth_soft" value="50" />\n+ </section>\n+ </conditional>\n <output name="output_txt">\n <assert_contents>\n+ <has_line line="lineage2.2.2	1.000	East-Asian (Beijing)	RD105;RD207" />\n+ <has_line line="761110	Rv0667	rpoB	missense_variant	p.Asp435Val	1.000	rifampicin	Assoc w R" />\n+ </assert_contents>\n+ </output>\n+ <output name="results_json">\n+ <assert_contents>\n+ <has_text text=\'"filter": "soft_fail",\' />\n+ </assert_contents>\n+ </output>\n+ </test>\n+ <test expect_num_outputs="4">\n+ <param name="input_select" value="single_fastq"/>\n+ <param name="fastq" ftype="fastq.gz" value="rpoB_and_crispr.fastq.gz" />\n+ <param name="output_format" value="txt" />\n+ <param name="platform" value="illumina" />\n+ <param name="spoligotype" value="true" />\n+ <param name="options" value="no" />\n+ <output name="output_txt">\n+ <assert_contents>\n+ <has_line line="Octal: 000000000000771" />\n <has_line line="Drug-resistance: RR-TB" />\n- <has_line line="lineage2.2.2	1.000	Beijing-RD105/RD207	RD105;RD207" />\n <has_line line="Rifampicin	R	rpoB p.Asp435Val (1.00)" />\n- <has_line line="761110	Rv0667	rpoB	missense_variant	p.Asp435Val	1.000	rifampicin	type=who_confidence|drug=rifampicin|who_confidence=Assoc w R" />\n+ <has_line line="761110	Rv0667	rpoB	missense_variant	p.Asp435Val	1.000	rifampicin	Assoc w R" />\n </assert_contents>\n </output>\n </test>\n@@ -198,6 +260,17 @@\n \n Produces a JSON output file by default.\n \n+In the Advanced options, you can select the mapper and variant caller to use, as well as set a number of filtering parameters.\n+Each of these typically has a "hard" and a "soft" cutoff. If a variant value is below the "hard" cutoff it is discarded, if\n+it is between the "hard" and "soft" values it is removed from the final predictions but added to the "qc_fail_variants" section\n+of the output.\n+\n+One of the advanced options is to use the SUSPECT tool suite to predict resistance to `rifampicin (RIF)`_, `pyrazinamide (PZA)`_\n+and `bedaquiline (BDQ)`_.\n+\n+.. _rifampicin (RIF): https://www.nature.com/articles/s41598-020-74648-y\n+.. _pyrazinamide (PZA): https://www.nature.com/articles/s41598-020-58635-x\n+.. _bedaquiline (BDQ): https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0217169\n ]]> </help>\n <citations>\n <citation type="doi">10.1186/s13073-019-0650-x</citation>\n'

diff -r d03af1c7002c -r 4839e590cb26 test-data/rpoB_and_crispr.fastq.gz

Binary file test-data/rpoB_and_crispr.fastq.gz has changed