| Previous changeset 6:f7f32674f751 (2020-01-22) Next changeset 8:037a11682176 (2021-01-06) |
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Commit message:
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/tb-profiler commit 53f6ccebd38e89bb2e67b2eec3aee30b4e141b5b" |
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modified:
tb_profiler_profile.xml |
| b |
| diff -r f7f32674f751 -r 200c378d85f3 tb_profiler_profile.xml --- a/tb_profiler_profile.xml Wed Jan 22 14:54:08 2020 -0500 +++ b/tb_profiler_profile.xml Thu Jan 23 03:44:33 2020 -0500 |
| [ |
| @@ -1,4 +1,4 @@ -<tool id="tb_profiler_profile" name="TB-Profiler Profile" version="@TOOL_VERSION@+galaxy0"> +<tool id="tb_profiler_profile" name="TB-Profiler Profile" version="@TOOL_VERSION@+galaxy1"> <description>Infer strain types and drug resistance markers from sequences</description> <macros> <import>macros.xml</import> @@ -41,13 +41,10 @@ --threads "\${GALAXY_SLOTS:-1}" #if $advanced.options == 'yes' - '${advanced.call_whole_genome}' - --call_method '${advanced.call_method}' - --min_gene_frac '${advanced.min_gene_frac}' --mapper '${advanced.mapper}' --min_depth '${advanced.min_depth}' - --af '${min_allel_freq}' - --reporting_af '${min_allel_freq_reporting}' + --af '${advanced.min_allele_freq}' + --reporting_af '${advanced.min_allele_freq_reporting}' #end if #if $output_format == "pdf" @@ -105,24 +102,14 @@ <when value="no"> </when> <when value="yes"> - <param label="Quality required for calls to be accepted" type="select" argument="--call_method"> - <option value="low" selected="true">Low</option> - <option value="high">High</option> - <option value="optimise">Optimise</option> - </param> - <param label="Call variants on the whole genome" type="boolean" argument="--call_whole_genome" - truevalue="--call_whole_genome" falsevalue="" help="Call variants on whole genome (Useful if you need to use whole genome variants later)" /> - <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)"> <option value="bwa" selected="true">bwa</option> <option value="minimap2">minimap2</option> <option value="bowtie2">bowtie2</option> </param> - <param name="min_gene_frac" label="Minimum Gene Fraction" type="float" value="0.9" help="Used to infer a deletion if the fraction of a gene covered falls below this value. Also used to see if sample is high quality to continue by checking the fraction for rpoB (where deletion should not occur). (default: 0.9)" /> - <param name="min_allel_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)" /> - <param name="min_allel_freq_reporting" argument="--reporting_af" value="0.1" label="Reporting Minimum allele frequency to call variants" type="float" help=" Minimum allele frequency to call variants (default: 0.1)"/> + <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)" /> + <param name="min_allele_freq_reporting" argument="--reporting_af" value="0.1" label="Reporting Minimum allele frequency to call variants" type="float" help=" Minimum allele frequency to call variants (default: 0.1)"/> </when> </conditional> </inputs> @@ -171,6 +158,24 @@ </assert_contents> </output> </test> + <test> + <param name="input_select" value="single_fastq"/> + <param name="fastq" ftype="fastq.gz" value="rif_resistant.fastq.gz" /> + <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: 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	rpoB	c.3225T>C	1.000" /> + </assert_contents> + </output> + </test> </tests> <help><![CDATA[ Summary |