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comparison drmutations.xml @ 7:dcd43b402eb3 draft

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planemo upload for repository https://github.com/phac-nml/quasitools commit ce3f1b19e7e110ff47365c672bc6fa17cce0a314
author nml
date Fri, 23 Nov 2018 15:43:16 -0500
parents b69e898b8109
children 9def47f3c1e4
comparison
equal deleted inserted replaced
6:9fb9fed71486 7:dcd43b402eb3
1 <tool id="drmutations" name="Drug Resistance Mutations" version="0.4.2"> 1 <tool id="drmutations" name="Drug Resistance Mutations" version="0.5.1">
2 <description></description> 2 <description></description>
3 <requirements> 3 <requirements>
4 <requirement type="package" version="0.4.2">quasitools</requirement> 4 <requirement type="package" version="0.5.1">quasitools</requirement>
5 </requirements> 5 </requirements>
6 <command detect_errors="exit_code"><![CDATA[ 6 <command detect_errors="exit_code"><![CDATA[
7 7
8 ln -f -s ${input_bam.metadata.bam_index} ${input_bam}.bai && 8 ln -f -s ${input_bam.metadata.bam_index} ${input_bam}.bai &&
9 quasitools drmutations $input_bam $ref_file $var_file $input_genes 9 quasitools drmutations $input_bam $ref_file $var_file $input_genes
56 Drug Resistance Mutations 56 Drug Resistance Mutations
57 ========================= 57 =========================
58 58
59 Generates a report detailing the drug resistant mutations found, above the reporting threshold (default: 1%). 59 Generates a report detailing the drug resistant mutations found, above the reporting threshold (default: 1%).
60 60
61 ------
62 Inputs
63 ------
64
65 1. A BAM file.
66 2. A reference FASTA file.
67 3. A variants (.vcf) file.
68 4. A genes (.bed) file.
69 5. A mutation database (.tsv) file.
70
71 ----------
72 Parameters
73 ----------
74 1. The minimum required frequency for a variant to be considered. Defaults to 0.01.
75 2. The reporting threshold a mutation must pass to be included in the report.
76
77 -------
78 Outputs
79 -------
80
81 A CSV file containing the drug resistant mutations found.
82
61 ]]></help> 83 ]]></help>
62 <citations> 84 <citations>
63 </citations> 85 <citation type="bibtex">
86 @misc{GitHubquasitoolsdrmutations,
87 title = {quasitools drmutations},
88 publisher = {phac-nml},
89 journal = {GitHub repository},
90 url = {https://github.com/phac-nml/quasitools},
91 }
92 </citation>
93 </citations>
64 </tool> 94 </tool>