Mercurial > repos > iuc > tbprofiler

comparison tb_profiler_profile.xml @ 4:c2656b729ee9 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/tb-profiler commit a51548708ea975c0a7b135a2cbaa5d094f3c5602"
author iuc
date Tue, 15 Oct 2019 14:35:47 -0400
parents 19793eecc9f0
children 4272bd430a01
comparison
equal deleted inserted replaced
3:19793eecc9f0 4:c2656b729ee9
39 --bam input.bam 39 --bam input.bam
40 #end if 40 #end if
41 41
42 --threads "\${GALAXY_SLOTS:-1}" 42 --threads "\${GALAXY_SLOTS:-1}"
43 #if $advanced.options == 'yes' 43 #if $advanced.options == 'yes'
44 '${advanced.call_whole_genome}'
44 --call_method '${advanced.call_method}' 45 --call_method '${advanced.call_method}'
45 --min_gene_frac '${advanced.min_gene_frac}' 46 --min_gene_frac '${advanced.min_gene_frac}'
46 --mapper '${advanced.mapper}' 47 --mapper '${advanced.mapper}'
47 --min_depth '${advanced.min_depth}' 48 --min_depth '${advanced.min_depth}'
48 --af '${min_allel_freq}' 49 --af '${min_allel_freq}'
56 #end if 57 #end if
57 && mv results/tbprofiler.results.json $results_json 58 && mv results/tbprofiler.results.json $results_json
58 #if str($fastq_or_bam.input_select) != "bam" 59 #if str($fastq_or_bam.input_select) != "bam"
59 && mv bam/tbprofiler.bam '${output_bam}' 60 && mv bam/tbprofiler.bam '${output_bam}'
60 #end if 61 #end if
61 && bcftools view -Ov -o'${output_vcf}' vcf/tbprofiler.targets.csq.bcf 62 && bcftools view -Ov -o'${output_vcf}' vcf/tbprofiler.targets.csq.vcf.gz
62 #if $output_format == "pdf" 63 #if $output_format == "pdf"
63 && mv results/tbprofiler.results.pdf '${output_pdf}' 64 && mv results/tbprofiler.results.pdf '${output_pdf}'
64 #else if $output_format == "txt" 65 #else if $output_format == "txt"
65 && mv results/tbprofiler.results.txt '${output_txt}' 66 && mv results/tbprofiler.results.txt '${output_txt}'
66 #end if 67 #end if
107 <param label="Quality required for calls to be accepted" type="select" argument="--call_method"> 108 <param label="Quality required for calls to be accepted" type="select" argument="--call_method">
108 <option value="low" selected="true">Low</option> 109 <option value="low" selected="true">Low</option>
109 <option value="high">High</option> 110 <option value="high">High</option>
110 <option value="optimise">Optimise</option> 111 <option value="optimise">Optimise</option>
111 </param> 112 </param>
113 <param label="Call variants on the whole genome" type="boolean" argument="--call_whole_genome"
114 truevalue="--call_whole_genome" falsevalue="" help="Call variants on whole genome (Useful if you need to use whole genome variants later)" />
112 <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" /> 115 <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" />
113 116
114 <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)"/> 117 <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)"/>
115 <param name="mapper" label="Mapper" type="select" help="Mapping tools to use (default: bwa)"> 118 <param name="mapper" label="Mapper" type="select" help="Mapping tools to use (default: bwa)">
116 <option value="bwa" selected="true">bwa</option> 119 <option value="bwa" selected="true">bwa</option>
171 </tests> 174 </tests>
172 <help><![CDATA[ 175 <help><![CDATA[
173 Summary 176 Summary
174 ======= 177 =======
175 178
176 The pipeline aligns reads to the H37Rv reference using bowtie2, BWA or minimap2 and then calls variants using SAMtools. These variants are then compared to a drug-resistance database. We also predict the number of reads supporting drug resistance variants as an insight into hetero-resistance (not applicable for minION data). 179 The pipeline aligns reads to the H37Rv reference using bowtie2, BWA or minimap2 and then calls variants using GATK. These variants are then compared to a drug-resistance database. We also predict the number of reads supporting drug resistance variants as an insight into hetero-resistance (not applicable for minION data).
177 180
178 Produces a JSON output file by default. 181 Produces a JSON output file by default.
179 182
180 ]]> </help> 183 ]]> </help>
181 <citations> 184 <citations>