Mercurial > repos > iuc > tbprofiler
comparison tb_profiler_profile.xml @ 18:abb937e275a6 draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/tb-profiler commit fe5de3e1e0dc056c102ed13c9553ef2e0d6fcab6
| author | iuc |
|---|---|
| date | Sat, 16 Nov 2024 20:26:49 +0000 |
| parents | c961f3f5417f |
| children |
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| 17:c961f3f5417f | 18:abb937e275a6 |
|---|---|
| 1 <tool id="tb_profiler_profile" name="TB-Profiler Profile" version="@TOOL_VERSION@+galaxy1" profile="20.09" license="AGPL-3.0-or-later"> | 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> | 2 <description>Infer strain types and drug resistance markers from sequences</description> |
| 3 <macros> | 3 <macros> |
| 4 <token name="@TOOL_VERSION@">6.2.1</token> | 4 <token name="@TOOL_VERSION@">6.4.0</token> |
| 5 </macros> | 5 </macros> |
| 6 <xrefs> | 6 <xrefs> |
| 7 <xref type="bio.tools">tb-profiler</xref> | 7 <xref type="bio.tools">tb-profiler</xref> |
| 8 </xrefs> | 8 </xrefs> |
| 9 <requirements> | 9 <requirements> |
| 10 <requirement type="package" version="1.2.6">delly</requirement> | |
| 10 <requirement type="package" version="@TOOL_VERSION@">tb-profiler</requirement> | 11 <requirement type="package" version="@TOOL_VERSION@">tb-profiler</requirement> |
| 11 </requirements> | 12 </requirements> |
| 12 <command detect_errors="exit_code"><![CDATA[ | 13 <command detect_errors="exit_code"><![CDATA[ |
| 13 #if str($fastq_or_bam.input_select.value) in ("paired_fastq", "paired_collection_fastq", "single_fastq") | 14 #if str($fastq_or_bam.input_select.value) in ("paired_fastq", "paired_collection_fastq", "single_fastq") |
| 14 #if str($fastq_or_bam.input_select.value) == "paired_fastq" | 15 #if str($fastq_or_bam.input_select.value) == "paired_fastq" |
| 65 #end if | 66 #end if |
| 66 && mv results/tbprofiler.results.json $results_json | 67 && mv results/tbprofiler.results.json $results_json |
| 67 #if str($fastq_or_bam.input_select) != "bam" | 68 #if str($fastq_or_bam.input_select) != "bam" |
| 68 && mv bam/tbprofiler.bam '${output_bam}' | 69 && mv bam/tbprofiler.bam '${output_bam}' |
| 69 #end if | 70 #end if |
| 70 && bcftools view -Ov -o'${output_vcf}' vcf/tbprofiler.targets.vcf.gz | 71 && bcftools view -Ov -o '${output_vcf}' vcf/tbprofiler.targets.vcf.gz |
| 71 #if $output_format == "pdf" | 72 #if $output_format == "pdf" |
| 72 && mv results/tbprofiler.results.pdf '${output_pdf}' | 73 && mv results/tbprofiler.results.pdf '${output_pdf}' |
| 73 #else if $output_format == "txt" | 74 #else if $output_format == "txt" |
| 74 && mv results/tbprofiler.results.txt '${output_txt}' | 75 && mv results/tbprofiler.results.txt '${output_txt}' |
| 75 #end if | 76 #end if |
| 187 <output name="output_txt"> | 188 <output name="output_txt"> |
| 188 <assert_contents> | 189 <assert_contents> |
| 189 <has_line line="Drug-resistance: RR-TB" /> | 190 <has_line line="Drug-resistance: RR-TB" /> |
| 190 <has_line line="lineage2.2.2	1.000	East-Asian (Beijing)	RD105;RD207" /> | 191 <has_line line="lineage2.2.2	1.000	East-Asian (Beijing)	RD105;RD207" /> |
| 191 <has_line line="Rifampicin	R	rpoB p.Asp435Val (1.00)" /> | 192 <has_line line="Rifampicin	R	rpoB p.Asp435Val (1.00)" /> |
| 192 <has_line line="761110	Rv0667	rpoB	missense_variant	p.Asp435Val	1.000	rifampicin	Assoc w R" /> | 193 <has_line line="761110	Rv0667	rpoB	missense_variant	p.Asp435Val	43	1.000	rifampicin	Assoc w R" /> |
| 193 </assert_contents> | 194 </assert_contents> |
| 194 </output> | 195 </output> |
| 195 </test> | 196 </test> |
| 196 <test expect_num_outputs="3"> | 197 <test expect_num_outputs="3"> |
| 197 <param name="input_select" value="bam"/> | 198 <param name="input_select" value="bam"/> |
| 202 <output name="output_txt"> | 203 <output name="output_txt"> |
| 203 <assert_contents> | 204 <assert_contents> |
| 204 <has_line line="Drug-resistance: RR-TB" /> | 205 <has_line line="Drug-resistance: RR-TB" /> |
| 205 <has_line line="lineage2.2.2	1.000	East-Asian (Beijing)	RD105;RD207" /> | 206 <has_line line="lineage2.2.2	1.000	East-Asian (Beijing)	RD105;RD207" /> |
| 206 <has_line line="Rifampicin	R	rpoB p.Asp435Val (1.00)" /> | 207 <has_line line="Rifampicin	R	rpoB p.Asp435Val (1.00)" /> |
| 207 <has_line line="761110	Rv0667	rpoB	missense_variant	p.Asp435Val	1.000	rifampicin	Assoc w R" /> | 208 <has_line line="761110	Rv0667	rpoB	missense_variant	p.Asp435Val	43	1.000	rifampicin	Assoc w R" /> |
| 208 </assert_contents> | 209 </assert_contents> |
| 209 </output> | 210 </output> |
| 210 </test> | 211 </test> |
| 211 <test expect_num_outputs="4"> | 212 <test expect_num_outputs="4"> |
| 212 <param name="input_select" value="single_fastq"/> | 213 <param name="input_select" value="single_fastq"/> |
| 221 </section> | 222 </section> |
| 222 </conditional> | 223 </conditional> |
| 223 <output name="output_txt"> | 224 <output name="output_txt"> |
| 224 <assert_contents> | 225 <assert_contents> |
| 225 <has_line line="lineage2.2.2	1.000	East-Asian (Beijing)	RD105;RD207" /> | 226 <has_line line="lineage2.2.2	1.000	East-Asian (Beijing)	RD105;RD207" /> |
| 226 <has_line line="761110	Rv0667	rpoB	missense_variant	p.Asp435Val	1.000	rifampicin	Assoc w R" /> | 227 <has_line line="761110	Rv0667	rpoB	missense_variant	p.Asp435Val	43	1.000	rifampicin	Assoc w R" /> |
| 227 </assert_contents> | 228 </assert_contents> |
| 228 </output> | 229 </output> |
| 229 <output name="results_json"> | 230 <output name="results_json"> |
| 230 <assert_contents> | 231 <assert_contents> |
| 231 <has_text text='"filter": "soft_fail",' /> | 232 <has_text text='"filter": "soft_fail",' /> |
| 242 <output name="output_txt"> | 243 <output name="output_txt"> |
| 243 <assert_contents> | 244 <assert_contents> |
| 244 <has_line line="Octal: 000000000000771" /> | 245 <has_line line="Octal: 000000000000771" /> |
| 245 <has_line line="Drug-resistance: RR-TB" /> | 246 <has_line line="Drug-resistance: RR-TB" /> |
| 246 <has_line line="Rifampicin	R	rpoB p.Asp435Val (1.00)" /> | 247 <has_line line="Rifampicin	R	rpoB p.Asp435Val (1.00)" /> |
| 247 <has_line line="761110	Rv0667	rpoB	missense_variant	p.Asp435Val	1.000	rifampicin	Assoc w R" /> | 248 <has_line line="761110	Rv0667	rpoB	missense_variant	p.Asp435Val	35	1.000	rifampicin	Assoc w R" /> |
| 248 </assert_contents> | 249 </assert_contents> |
| 249 </output> | 250 </output> |
| 250 </test> | 251 </test> |
| 251 </tests> | 252 </tests> |
| 252 <help><![CDATA[ | 253 <help><![CDATA[ |