Mercurial > repos > iuc > tbprofiler
changeset 14:ac8250086ac3 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/tb-profiler commit 7598f8402d6adaab0e7c9a3cd426914f700be336"
| author | iuc |
|---|---|
| date | Wed, 16 Mar 2022 09:15:44 +0000 |
| parents | 809dfc93d593 |
| children | 45083d070fb8 |
| files | tb_profiler_profile.xml |
| diffstat | 1 files changed, 17 insertions(+), 10 deletions(-) [+] |
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--- a/tb_profiler_profile.xml Mon Sep 06 17:20:56 2021 +0000 +++ b/tb_profiler_profile.xml Wed Mar 16 09:15:44 2022 +0000 @@ -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@">3.0.8</token> + <token name="@TOOL_VERSION@">4.1.1</token> </macros> <requirements> <requirement type="package" version="@TOOL_VERSION@">tb-profiler</requirement> @@ -27,9 +27,7 @@ #end if tb-profiler profile - --platform '${platform.value}' - #if str($fastq_or_bam.input_select.value) in ("paired_fastq", "paired_collection_fastq", "single_fastq") -1 fastq_r1.'$r1_ext' #end if @@ -42,6 +40,7 @@ --threads "\${GALAXY_SLOTS:-1}" #if $advanced.options == 'yes' --mapper '${advanced.mapper}' + --caller '${advanced.caller}' --min_depth '${advanced.min_depth}' --af '${advanced.min_allele_freq}' --reporting_af '${advanced.min_allele_freq_reporting}' @@ -102,10 +101,18 @@ <when value="no"> </when> <when value="yes"> - <param name="mapper" label="Mapper" type="select" help="Mapping tools to use (default: bwa)"> + <param argument="mapper" label="Mapper" type="select" help="Mapping tools to use (default: bwa)"> <option value="bwa" selected="true">bwa</option> <option value="minimap2">minimap2</option> <option value="bowtie2">bowtie2</option> + <option value="bwa-mem2">bwa-mem2</option> + </param> + <param argument="caller" label="Variant caller" help="Variant calling tool to use" type="select"> + <option value="freebayes" selected="true">freebayes</option> + <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)"/> <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)" /> @@ -136,10 +143,10 @@ <param name="options" value="no" /> <output name="output_txt"> <assert_contents> - <has_line line="Drug-resistance: Pre-MDR" /> + <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="Rifampicin	R	rpoB p.Asp435Val (1.00)" /> - <has_line line="763031	Rv0667	rpoB	c.3225T>C	1.000" /> + <has_line line="761110	Rv0667	rpoB	p.Asp435Val	1.000	rifampicin" /> </assert_contents> </output> </test> @@ -151,10 +158,10 @@ <param name="options" value="no" /> <output name="output_txt"> <assert_contents> - <has_line line="Drug-resistance: Pre-MDR" /> + <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="Rifampicin	R	rpoB p.Asp435Val (1.00)" /> - <has_line line="763031	Rv0667	rpoB	c.3225T>C	1.000" /> + <has_line line="761110	Rv0667	rpoB	p.Asp435Val	1.000	rifampicin" /> </assert_contents> </output> </test> @@ -169,10 +176,10 @@ <param name="min_allele_freq_reporting" value="0.33" /> <output name="output_txt"> <assert_contents> - <has_line line="Drug-resistance: Pre-MDR" /> + <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="Rifampicin	R	rpoB p.Asp435Val (1.00)" /> - <has_line line="763031	Rv0667	rpoB	c.3225T>C	1.000" /> + <has_line line="761110	Rv0667	rpoB	p.Asp435Val	1.000	rifampicin" /> </assert_contents> </output> </test>