Mercurial > repos > iuc > tbprofiler
changeset 2:49b819f88c2b draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/tb-profiler commit da74c7f8419319266b84dcac128ad84d8fc2216d
| author | iuc |
|---|---|
| date | Tue, 16 Jul 2019 08:29:18 -0400 |
| parents | 5182e1a99313 |
| children | 19793eecc9f0 |
| files | tb_profiler_profile.xml |
| diffstat | 1 files changed, 13 insertions(+), 15 deletions(-) [+] |
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--- a/tb_profiler_profile.xml Thu Apr 04 13:52:45 2019 -0400 +++ b/tb_profiler_profile.xml Tue Jul 16 08:29:18 2019 -0400 @@ -1,7 +1,7 @@ -<tool id="tb_profiler_profile" name="TB-Profiler Profile" version="2.1.0"> - <description>Infer strain types and drug resistance markers from sequences</description> +<tool id="tb_profiler_profile" name="TB-Profiler Profile" version="2.4"> + <description>Infer strain types and drug resistance markers from sequences</description> <requirements> - <requirement type="package" version="2.1.0">tb-profiler</requirement> + <requirement type="package" version="2.4">tb-profiler</requirement> </requirements> <command detect_errors="exit_code"><![CDATA[ #if str($fastq_or_bam.input_select.value) in ("paired_fastq", "paired_collection_fastq", "single_fastq") @@ -60,7 +60,7 @@ && mv results/tbprofiler.results.txt '${output_txt}' #end if - ]]></command> + ]]> </command> <inputs> <param name="platform" type="select" label="Platform"> <option value="Illumina" selected="true">Illumina</option> @@ -82,7 +82,7 @@ </when> <when value="single_fastq"> <param label="Reads" name="fastq" type="data" format="fastq,fastq.gz,fastqsanger,fastqsanger.gz" /> - </when> + </when> <when value="bam"> <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."/> </when> @@ -104,9 +104,7 @@ <option value="high">High</option> <option value="optimise">Optimise</option> </param> - <param label="Minimum coverage fraction to infer deletion" type="float" - help="Used to infer a deletion if the fraction of a gene covered falls below this value." - argument="--min_gene_frac" value="0.9" /> + <param label="Minimum coverage fraction to infer deletion" type="float" help="Used to infer a deletion if the fraction of a gene covered falls below this value." argument="--min_gene_frac" value="0.9" /> <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="mapper" label="Mapper" type="select" help="Mapping tools to use (default: bwa)"> @@ -142,9 +140,9 @@ <output name="output_txt"> <assert_contents> <has_line line="Drug-resistance: Drug-resistant" /> - <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	c.3225T>C	1.000" /> + <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" /> </assert_contents> </output> </test> @@ -157,9 +155,9 @@ <output name="output_txt"> <assert_contents> <has_line line="Drug-resistance: Drug-resistant" /> - <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	c.3225T>C	1.000" /> + <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" /> </assert_contents> </output> </test> @@ -172,7 +170,7 @@ Produces a JSON output file by default. - ]]></help> + ]]> </help> <citations> <citation type="bibtex"> @UNPUBLISHED{Phelan2016,