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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/tb-profiler commit 7dba70c70c9fe33353a0fd21803b11cfddc42c32
author iuc
date Tue, 21 Oct 2025 10:24:35 +0000
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1 <tool id="tb_profiler_profile" name="TB-Profiler Profile" version="@TOOL_VERSION@+galaxy0" profile="20.09" license="AGPL-3.0-or-later">
2 <description>Infer strain types and drug resistance markers from sequences</description>
3
4 <macros>
5 <import>macros.xml</import>
6 </macros>
7
8 <xrefs>
9 <xref type="bio.tools">tb-profiler</xref>
10 </xrefs>
11
12 <requirements>
13 <requirement type="package" version="@TOOL_VERSION@">tb-profiler</requirement>
14 </requirements>
15
16 <expand macro="version_command"/>
17
18 <command detect_errors="exit_code"><![CDATA[
19 #if str($fastq_or_bam.input_select.value) in ("paired_fastq", "paired_collection_fastq", "single_fastq")
20 #if str($fastq_or_bam.input_select.value) == "paired_fastq"
21 #set r1_ext = $fastq_or_bam.read1.extension
22 #set r2_ext = $fastq_or_bam.read2.extension
23 ln -s '$fastq_or_bam.read1' fastq_r1.'$r1_ext' &&
24 ln -s '$fastq_or_bam.read2' fastq_r2.'$r2_ext' &&
25 #else if str($fastq_or_bam.input_select.value) == "single_fastq"
26 #set r1_ext = $fastq_or_bam.fastq.extension
27 ln -s '$fastq_or_bam.fastq' fastq_r1.'$r1_ext' &&
28 #else if str($fastq_or_bam.input_select.value) == "paired_collection_fastq"
29 #set r1_ext = $fastq_or_bam.fastq_collection.forward.extension
30 #set r2_ext = $fastq_or_bam.fastq_collection.reverse.extension
31 ln -s '$fastq_or_bam.fastq_collection.forward' fastq_r1.'$r1_ext' &&
32 ln -s '$fastq_or_bam.fastq_collection.reverse' fastq_r2.'$r2_ext' &&
33 #end if
34 #else if str($fastq_or_bam.input_select.value) == "bam"
35 ln -s '$fastq_or_bam.bam_input' input.bam &&
36 #end if
37
38 tb-profiler profile
39 --platform '${platform.value}'
40 ${spoligotype}
41 #if str($fastq_or_bam.input_select.value) in ("paired_fastq", "paired_collection_fastq", "single_fastq")
42 -1 fastq_r1.'$r1_ext'
43 #end if
44 #if str($fastq_or_bam.input_select.value) in ("paired_fastq", "paired_collection_fastq")
45 -2 fastq_r2.'$r1_ext'
46 #else if str($fastq_or_bam.input_select.value) == "bam"
47 --bam input.bam
48 #end if
49
50 --threads "\${GALAXY_SLOTS:-1}"
51 #if $advanced.options == 'yes'
52 --mapper '${advanced.mapper}'
53 --caller '${advanced.caller}'
54 --depth '${advanced.vf.min_depth_hard},${advanced.vf.min_depth_soft}'
55 --af '${advanced.vf.min_af_hard},${advanced.vf.min_af_soft}'
56 --strand '${advanced.vf.min_read_hard},${advanced.vf.min_read_soft}'
57 --sv-depth '${advanced.vf.min_sv_depth_hard},${advanced.vf.min_sv_depth_soft}'
58 --sv-af '${advanced.vf.min_sv_af_hard},${advanced.vf.min_sv_af_soft}'
59 --sv-len '${advanced.vf.max_sv_len_hard},${advanced.vf.max_sv_len_soft}'
60 ${advanced.suspect}
61 ${advanced.no_trim}
62 ${advanced.no_coverage_qc}
63 ${advanced.no_samclip}
64 ${advanced.no_delly}
65 #end if
66
67 #if $output_format == "pdf"
68 --pdf
69 #else if $output_format == "txt"
70 --txt
71 #end if
72 && mv results/tbprofiler.results.json $results_json
73 #if str($fastq_or_bam.input_select) != "bam"
74 && mv bam/tbprofiler.bam '${output_bam}'
75 #end if
76 && bcftools view -Ov -o '${output_vcf}' vcf/tbprofiler.targets.vcf.gz
77 #if $output_format == "pdf"
78 && mv results/tbprofiler.results.pdf '${output_pdf}'
79 #else if $output_format == "txt"
80 && mv results/tbprofiler.results.txt '${output_txt}'
81 #end if
82
83 ]]> </command>
84 <inputs>
85 <param name="platform" type="select" label="Platform">
86 <option value="illumina" selected="true">Illumina</option>
87 <option value="nanopore">Nanopore</option>
88 <option value="pacbio">PacBio</option>
89 </param>
90 <conditional name="fastq_or_bam">
91 <param name="input_select" type="select" label="Input File Type">
92 <option value="paired_fastq">Paired Fastq</option>
93 <option value="paired_collection_fastq">Paired Collection Fastq</option>
94 <option value="single_fastq">Single Fastq</option>
95 <option value="bam">BAM</option>
96 </param>
97 <when value="paired_fastq">
98 <param name="read1" type="data" format="fastq" label="Read1" help="First read file (default: None)"/>
99 <param name="read2" type="data" format="fastq" optional="true" label="Read2" help="Second read file (default: None)"/>
100 </when>
101 <when value="paired_collection_fastq">
102 <param label="Reads (collection)" name="fastq_collection" type="data_collection" collection_type="paired" format="fastq,fastq.gz,fastqsanger,fastqsanger.gz" />
103 </when>
104 <when value="single_fastq">
105 <param label="Reads" name="fastq" type="data" format="fastq,fastq.gz,fastqsanger,fastqsanger.gz" />
106 </when>
107 <when value="bam">
108 <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."/>
109 </when>
110 </conditional>
111 <param argument="--spoligotype" type="boolean" label="Perform in-silico spoligotyping" checked="false" truevalue="--spoligotype" falsevalue=""
112 help="Uses spacers of CRISPR region to call a spoligotype."/>
113 <param name="output_format" label="Output format" type="select">
114 <option value="txt" selected="true">Text</option>
115 <option value="pdf">PDF</option>
116 </param>
117 <conditional name="advanced">
118 <param label="Select advanced options" type="select" name="options">
119 <option value="yes">Yes</option>
120 <option value="no" selected="true">No</option>
121 </param>
122 <when value="no">
123 </when>
124 <when value="yes">
125 <param argument="mapper" label="Mapper" type="select" help="Mapping tools to use (default: bwa)">
126 <option value="bwa" selected="true">bwa</option>
127 <option value="minimap2">minimap2</option>
128 <option value="bowtie2">bowtie2</option>
129 <option value="bwa-mem2">bwa-mem2</option>
130 </param>
131 <param argument="caller" label="Variant caller" help="Variant calling tool to use" type="select">
132 <option value="freebayes" selected="true">freebayes</option>
133 <option value="bcftools">bcftools</option>
134 <option value="gatk">gatk</option>
135 <option value="pilon">pilon</option>
136 <option value="lofreq">lofreq</option>
137 </param>
138 <section name="vf" title="Variant Filters">
139 <param name="min_depth_hard" argument="--depth" label="Min Depth (hard cutoff)" type="integer" value="0" min="0"
140 help="Minimum depth required to call variant. Bases with depth below this cutoff will be marked as missing (default: 0)"/>
141 <param name="min_depth_soft" argument="--depth" label="Min Depth (soft cutoff)" type="integer" value="10" min="0"
142 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)"/>
143 <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"
144 help="Minimum allele frequency to call variants (default: 0)" />
145 <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"
146 help="Variants with an allele frequency lower than this (and higher than the hard cutoff) will be marked as QC fail (default 0.1)" />
147 <param name="min_read_hard" argument="--strand" type="integer" value="0" label="Mininum read number per strand (hard cutoff)" min="0"
148 help="Minimum read number per strand to call variants (default: 0)" />
149 <param name="min_read_soft" argument="--strand" type="integer" value="3" label="Mininum read number per strand (soft cutoff)" min="0"
150 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" />
151 <param name="min_sv_depth_hard" argument="--sv-depth" type="integer" value="0" label="Min Depth for SV (hard cutoff)" min="0"
152 help="Minimum depth required to call structural variants (default: 0)" />
153 <param name="min_sv_depth_soft" argument="--sv-depth" type="integer" value="10" label="Min Depth for SV (soft cutoff)" min="0"
154 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" />
155 <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"
156 help="Minimum allele frequency to call structural variants (default: 0.5)" />
157 <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"
158 help="Variants with an allele frequency lower than this (and higher than the hard cutoff) will be marked as QC fail (default 0.9)" />
159 <param name="max_sv_len_hard" argument="--sv-len" type="integer" value="100000" label="Max SV length (hard cutoff)" min="0"
160 help="Maximum length (length) of structural variants to call (default: 100000)" />
161 <param name="max_sv_len_soft" argument="--sv-len" type="integer" value="50000" label="Max SV length (soft cutoff)" min="0"
162 help="Structural variants with length higher than this (and lower than the hard cutoff) will be marked as QC fail (default: 50000)" />
163 </section>
164 <param argument="--suspect" label="Use ML predictions of resistance from the SUSPECT tool suite" type="boolean" checked="False" truevalue="--suspect" falsevalue=""
165 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."/>
166 <param argument="--no_trim" label="Do not trim reads using trimmomatic" checked="false" type="boolean" truevalue="--no_trim" falsevalue="" />
167 <param argument="--no_coverage_qc" label="Don't collect flagstats" type="boolean" truevalue="--no_coverage_qc" falsevalue="" />
168 <param argument="--no_samclip" label="Don't removed clipped reads from variant calling" type="boolean" truevalue="--no_samclip" falsevalue="" />
169 <param argument="--no_delly" label="Don't run delly for SV calling" type="boolean" truevalue="--no_delly" falsevalue="" />
170 </when>
171 </conditional>
172 </inputs>
173 <outputs>
174 <data name="results_json" format="json" from_work_dir="results/tbprofiler.results.json" label="${tool.name} on ${on_string}: Results.json"/>
175 <data format="vcf" name="output_vcf" label="${tool.name} VCF on ${on_string}" />
176 <data format="bam" name="output_bam" label="${tool.name} BAM on ${on_string}">
177 <filter>fastq_or_bam['input_select'] != 'bam'</filter>
178 </data>
179 <data format="pdf" name="output_pdf" label="${tool.name} PDF report on ${on_string}">
180 <filter>output_format == 'pdf'</filter>
181 </data>
182 <data format="txt" name="output_txt" label="${tool.name} report on ${on_string}">
183 <filter>output_format == 'txt'</filter>
184 </data>
185 </outputs>
186 <tests>
187 <test expect_num_outputs="4">
188 <conditional name="fastq_or_bam">
189 <param name="input_select" value="single_fastq"/>
190 <param name="fastq" ftype="fastq.gz" value="rif_resistant.fastq.gz" />
191 </conditional>
192 <param name="output_format" value="txt" />
193 <param name="platform" value="illumina" />
194 <conditional name="advanced">
195 <param name="options" value="no" />
196 </conditional>
197 <output name="output_txt">
198 <assert_contents>
199 <has_line line="Drug-resistance: RR-TB" />
200 <has_line line="lineage2.2.2&#009;100.000&#009;East-Asian (Beijing)&#009;RD105;RD207" />
201 <has_line line="Rifampicin&#009;R&#009;rpoB p.Asp435Val (1.00)" />
202 <has_line line="761110&#009;Rv0667&#009;rpoB&#009;missense_variant&#009;p.Asp435Val&#009;43&#009;1.000&#009;rifampicin&#009;Assoc w R" />
203 </assert_contents>
204 </output>
205 </test>
206 <test expect_num_outputs="3">
207 <conditional name="fastq_or_bam">
208 <param name="input_select" value="bam"/>
209 <param name="bam_input" ftype="bam" value="rif_resistant.bam" />
210 </conditional>
211 <param name="output_format" value="txt" />
212 <param name="platform" value="illumina" />
213 <conditional name="advanced">
214 <param name="options" value="no" />
215 </conditional>
216 <output name="output_txt">
217 <assert_contents>
218 <has_line line="Drug-resistance: RR-TB" />
219 <has_line line="lineage2.2.2&#009;100.000&#009;East-Asian (Beijing)&#009;RD105;RD207" />
220 <has_line line="Rifampicin&#009;R&#009;rpoB p.Asp435Val (1.00)" />
221 <has_line line="761110&#009;Rv0667&#009;rpoB&#009;missense_variant&#009;p.Asp435Val&#009;43&#009;1.000&#009;rifampicin&#009;Assoc w R" />
222 </assert_contents>
223 </output>
224 </test>
225 <test expect_num_outputs="4">
226 <conditional name="fastq_or_bam">
227 <param name="input_select" value="single_fastq"/>
228 <param name="fastq" ftype="fastq.gz" value="rif_resistant.fastq.gz" />
229 </conditional>
230 <param name="output_format" value="txt" />
231 <param name="platform" value="illumina" />
232 <conditional name="advanced">
233 <param name="options" value="yes" />
234 <section name="vf">
235 <param name="min_depth_hard" value="40" />
236 <param name="min_depth_soft" value="50" />
237 </section>
238 </conditional>
239 <output name="output_txt">
240 <assert_contents>
241 <has_line line="lineage2.2.2&#009;100.000&#009;East-Asian (Beijing)&#009;RD105;RD207" />
242 <has_line line="761110&#009;Rv0667&#009;rpoB&#009;missense_variant&#009;p.Asp435Val&#009;43&#009;1.000&#009;rifampicin&#009;Assoc w R" />
243 </assert_contents>
244 </output>
245 <output name="results_json">
246 <assert_contents>
247 <has_text text='"filter": "soft_fail",' />
248 </assert_contents>
249 </output>
250 </test>
251 <test expect_num_outputs="4">
252 <conditional name="fastq_or_bam">
253 <param name="input_select" value="single_fastq"/>
254 <param name="fastq" ftype="fastq.gz" value="rpoB_and_crispr.fastq.gz" />
255 </conditional>
256 <param name="output_format" value="txt" />
257 <param name="platform" value="illumina" />
258 <param name="spoligotype" value="true" />
259 <conditional name="advanced">
260 <param name="options" value="no" />
261 </conditional>
262 <output name="output_txt">
263 <assert_contents>
264 <has_line line="Octal: 000000000000771" />
265 <has_line line="Drug-resistance: RR-TB" />
266 <has_line line="Rifampicin&#009;R&#009;rpoB p.Asp435Val (1.00)" />
267 <has_line line="761110&#009;Rv0667&#009;rpoB&#009;missense_variant&#009;p.Asp435Val&#009;35&#009;1.000&#009;rifampicin&#009;Assoc w R" />
268 </assert_contents>
269 </output>
270 </test>
271 </tests>
272 <help><![CDATA[
273 Summary
274 =======
275
276 The pipeline aligns reads to the H37Rv reference using BWA, bowtie2 or minimap2 and then calls variants
277 (using bcftools, GATK4 or freebayes). These variants are then compared to a drug-resistance database.
278 TB-Profiler also predicts the number of reads supporting drug resistance variants as an insight into
279 hetero-resistance (not applicable for MinION data).
280
281 Produces a JSON output file by default.
282
283 In the Advanced options, you can select the mapper and variant caller to use, as well as set a number of filtering parameters.
284 Each of these typically has a "hard" and a "soft" cutoff. If a variant value is below the "hard" cutoff it is discarded, if
285 it is between the "hard" and "soft" values it is removed from the final predictions but added to the "qc_fail_variants" section
286 of the output.
287
288 One of the advanced options is to use the SUSPECT tool suite to predict resistance to `rifampicin (RIF)`_, `pyrazinamide (PZA)`_
289 and `bedaquiline (BDQ)`_.
290
291 .. _rifampicin (RIF): https://www.nature.com/articles/s41598-020-74648-y
292 .. _pyrazinamide (PZA): https://www.nature.com/articles/s41598-020-58635-x
293 .. _bedaquiline (BDQ): https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0217169
294 ]]> </help>
295 <citations>
296 <citation type="doi">10.1186/s13073-019-0650-x</citation>
297 </citations>
298 </tool>