| Previous changeset 14:ac8250086ac3 (2022-03-16) Next changeset 16:2c68b0c38785 (2023-01-22) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/tb-profiler commit 9dd4c8aca212218a9e8f8a49013c255696191b0f |
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modified:
tb_profiler_profile.xml |
| b |
| diff -r ac8250086ac3 -r 45083d070fb8 tb_profiler_profile.xml --- a/tb_profiler_profile.xml Wed Mar 16 09:15:44 2022 +0000 +++ b/tb_profiler_profile.xml Sat Dec 31 15:36:09 2022 +0000 |
| b |
| @@ -1,7 +1,7 @@ <tool id="tb_profiler_profile" name="TB-Profiler Profile" version="@TOOL_VERSION@+galaxy0" profile="20.09"> <description>Infer strain types and drug resistance markers from sequences</description> <macros> - <token name="@TOOL_VERSION@">4.1.1</token> + <token name="@TOOL_VERSION@">4.4.0</token> </macros> <requirements> <requirement type="package" version="@TOOL_VERSION@">tb-profiler</requirement> @@ -67,6 +67,7 @@ <param name="platform" type="select" label="Platform"> <option value="illumina" selected="true">Illumina</option> <option value="nanopore">Nanopore</option> + <option value="pacbio">PacBio</option> </param> <conditional name="fastq_or_bam"> <param name="input_select" type="select" label="Input File Type"> @@ -144,9 +145,9 @@ <output name="output_txt"> <assert_contents> <has_line line="Drug-resistance: RR-TB" /> - <has_line line="lineage2.2.2	1.000	East-Asian (Beijing)	Beijing-RD105/RD207	RD105;RD207" /> + <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	p.Asp435Val	1.000	rifampicin" /> + <has_line line="761110	Rv0667	rpoB	missense_variant	p.Asp435Val	1.000	rifampicin	type=who_confidence|drug=rifampicin|who_confidence=Assoc w R" /> </assert_contents> </output> </test> @@ -159,9 +160,9 @@ <output name="output_txt"> <assert_contents> <has_line line="Drug-resistance: RR-TB" /> - <has_line line="lineage2.2.2	1.000	East-Asian (Beijing)	Beijing-RD105/RD207	RD105;RD207" /> + <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	p.Asp435Val	1.000	rifampicin" /> + <has_line line="761110	Rv0667	rpoB	missense_variant	p.Asp435Val	1.000	rifampicin	type=who_confidence|drug=rifampicin|who_confidence=Assoc w R" /> </assert_contents> </output> </test> @@ -171,15 +172,14 @@ <param name="output_format" value="txt" /> <param name="platform" value="illumina" /> <param name="options" value="yes" /> - <param name="call_whole_genome" value="true" /> <param name="min_allele_freq" value="0.25" /> <param name="min_allele_freq_reporting" value="0.33" /> <output name="output_txt"> <assert_contents> <has_line line="Drug-resistance: RR-TB" /> - <has_line line="lineage2.2.2	1.000	East-Asian (Beijing)	Beijing-RD105/RD207	RD105;RD207" /> + <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	p.Asp435Val	1.000	rifampicin" /> + <has_line line="761110	Rv0667	rpoB	missense_variant	p.Asp435Val	1.000	rifampicin	type=who_confidence|drug=rifampicin|who_confidence=Assoc w R" /> </assert_contents> </output> </test> |