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annotate drmutations.xml @ 8:9def47f3c1e4 draft

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planemo upload for repository https://github.com/phac-nml/quasitools commit 940b463cac33438233bc7a8a1695ca6d34b31a35
author nml
date Tue, 06 Aug 2019 08:50:28 -0400
parents dcd43b402eb3
children 18aad692772a
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1 <tool id="drmutations" name="Drug Resistance Mutations" version="0.7.0">
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2 <description></description>
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3 <requirements>
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4 <requirement type="package" version="0.7.0">quasitools</requirement>
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5 </requirements>
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6 <command detect_errors="exit_code"><![CDATA[
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8 ln -f -s ${input_bam.metadata.bam_index} ${input_bam}.bai &&
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9 quasitools drmutations $input_bam $ref_file $var_file $input_genes
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10
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11 #if $mutation_db:
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12 $mutation_db
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13 #end if
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15 #if $min_freq:
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16 -f $min_freq
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17 #end if
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19 #if $reporting_thres:
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20 -t $reporting_thres
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21 #end if
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23 -o output.csv
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24
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25 ]]></command>
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26 <inputs>
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27 <param name="input_bam" type="data" format="bam" optional="false" label="Bam file" />
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28 <param name="ref_file" type="data" format="fasta" optional="false" label="Reference file" />
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29 <param name="var_file" type="data" format="vcf" optional="false" label="Variants file" />
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30 <param name="input_genes" type="data" format="bed" optional="false" label="Gene file" />
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31 <param name="mutation_db" type="data" format="tsv" optional="false" label="Mutation DB" />
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32 <param name="min_freq" type="float" optional="true" min="0" max="1" label="Minimum frequency" value="0.01" help="The minimum required frequency. Defaults to 0.01." />
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33 <param name="reporting_thres" type="integer" min="1" max="20" optional="true" label="Reporting threshold" value="1"
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34 help="The minimum percentage required for an entry in the drug resistant report. Defaults to 1."/>
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35 </inputs>
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36 <outputs>
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37 <data format="csv" name="output" from_work_dir="output.csv" />
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38 </outputs>
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39 <tests>
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40 <test>
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41 <param name="input_bam" value="align.bam" />
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42 <param name="ref_file" value="hxb2_pol.fas" />
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43 <param name="var_file" value="nt_variants.vcf" />
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44 <param name="input_genes" ftype="bed" value="hxb2_pol.bed" />
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45 <param name="mutation_db" value="mutation_db.tsv" />
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46 <output name="output" >
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47 <assert_contents>
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48 <has_text text="Chromosome,Gene,Category,Surveillance,Wildtype,Position,Mutation,Mutation Frequency,Coverage" />
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49 <has_text text="hxb2_pol,RT,NNRTI,Yes,K,103,N,7.79,154" />
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50 </assert_contents>
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51 </output>
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52 </test>
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53 </tests>
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54 <help><![CDATA[
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55
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56 Drug Resistance Mutations
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57 =========================
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58
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59 Generates a report detailing the drug resistant mutations found, above the reporting threshold (default: 1%).
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60
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61 ------
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62 Inputs
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63 ------
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64
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65 1. A BAM file.
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66 2. A reference FASTA file.
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67 3. A variants (.vcf) file.
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68 4. A genes (.bed) file.
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69 5. A mutation database (.tsv) file.
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70
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71 ----------
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72 Parameters
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73 ----------
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74 1. The minimum required frequency for a variant to be considered. Defaults to 0.01.
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75 2. The reporting threshold a mutation must pass to be included in the report.
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76
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77 -------
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78 Outputs
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79 -------
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80
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81 A CSV file containing the drug resistant mutations found.
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82
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83 ]]></help>
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84 <citations>
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85 <citation type="bibtex">
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86 @misc{GitHubquasitoolsdrmutations,
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87 title = {quasitools drmutations},
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88 publisher = {phac-nml},
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89 journal = {GitHub repository},
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90 url = {https://github.com/phac-nml/quasitools},
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91 }
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92 </citation>
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93 </citations>
0
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94 </tool>