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annotate drmutations.xml @ 0:1f1214983a1c draft default tip

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planemo upload for repository https://github.com/phac-nml/quasitools commit 5a9e4c9a582828654893166caf20576f5e0c418e
author nml
date Mon, 20 Jun 2022 20:05:57 +0000
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1f1214983a1c planemo upload for repository https://github.com/phac-nml/quasitools commit 5a9e4c9a582828654893166caf20576f5e0c418e
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1 <tool id="drmutations" name="Drug Resistance Mutations" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
1f1214983a1c planemo upload for repository https://github.com/phac-nml/quasitools commit 5a9e4c9a582828654893166caf20576f5e0c418e
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2 <description></description>
1f1214983a1c planemo upload for repository https://github.com/phac-nml/quasitools commit 5a9e4c9a582828654893166caf20576f5e0c418e
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
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6 <expand macro="requirements"/>
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7 <command detect_errors="exit_code"><![CDATA[
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9 ln -s $input_bam '${input_bam.name}' &&
1f1214983a1c planemo upload for repository https://github.com/phac-nml/quasitools commit 5a9e4c9a582828654893166caf20576f5e0c418e
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10 ln -s $input_bam.metadata.bam_index '${input_bam.name}.bai' &&
1f1214983a1c planemo upload for repository https://github.com/phac-nml/quasitools commit 5a9e4c9a582828654893166caf20576f5e0c418e
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12 quasitools drmutations '${input_bam.name}' $ref_file $var_file $input_genes
1f1214983a1c planemo upload for repository https://github.com/phac-nml/quasitools commit 5a9e4c9a582828654893166caf20576f5e0c418e
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14 #if $mutation_db:
1f1214983a1c planemo upload for repository https://github.com/phac-nml/quasitools commit 5a9e4c9a582828654893166caf20576f5e0c418e
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15 $mutation_db
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16 #end if
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18 #if $min_freq:
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19 -f $min_freq
1f1214983a1c planemo upload for repository https://github.com/phac-nml/quasitools commit 5a9e4c9a582828654893166caf20576f5e0c418e
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20 #end if
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22 #if $reporting_thres:
1f1214983a1c planemo upload for repository https://github.com/phac-nml/quasitools commit 5a9e4c9a582828654893166caf20576f5e0c418e
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23 -t $reporting_thres
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24 #end if
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26 -o output.csv
1f1214983a1c planemo upload for repository https://github.com/phac-nml/quasitools commit 5a9e4c9a582828654893166caf20576f5e0c418e
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27
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28 ]]></command>
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29 <inputs>
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30 <param name="input_bam" type="data" format="bam" optional="false" label="Bam file" />
1f1214983a1c planemo upload for repository https://github.com/phac-nml/quasitools commit 5a9e4c9a582828654893166caf20576f5e0c418e
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31 <param name="ref_file" type="data" format="fasta" optional="false" label="Reference file" />
1f1214983a1c planemo upload for repository https://github.com/phac-nml/quasitools commit 5a9e4c9a582828654893166caf20576f5e0c418e
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32 <param name="var_file" type="data" format="vcf" optional="false" label="Variants file" />
1f1214983a1c planemo upload for repository https://github.com/phac-nml/quasitools commit 5a9e4c9a582828654893166caf20576f5e0c418e
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33 <param name="input_genes" type="data" format="bed" optional="false" label="Gene file" />
1f1214983a1c planemo upload for repository https://github.com/phac-nml/quasitools commit 5a9e4c9a582828654893166caf20576f5e0c418e
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34 <param name="mutation_db" type="data" format="tsv" optional="false" label="Mutation DB" />
1f1214983a1c planemo upload for repository https://github.com/phac-nml/quasitools commit 5a9e4c9a582828654893166caf20576f5e0c418e
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35 <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." />
1f1214983a1c planemo upload for repository https://github.com/phac-nml/quasitools commit 5a9e4c9a582828654893166caf20576f5e0c418e
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36 <param name="reporting_thres" type="integer" min="1" max="20" optional="true" label="Reporting threshold" value="1"
1f1214983a1c planemo upload for repository https://github.com/phac-nml/quasitools commit 5a9e4c9a582828654893166caf20576f5e0c418e
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37 help="The minimum percentage required for an entry in the drug resistant report. Defaults to 1."/>
1f1214983a1c planemo upload for repository https://github.com/phac-nml/quasitools commit 5a9e4c9a582828654893166caf20576f5e0c418e
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38 </inputs>
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39 <outputs>
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40 <data format="csv" name="output" from_work_dir="output.csv" />
1f1214983a1c planemo upload for repository https://github.com/phac-nml/quasitools commit 5a9e4c9a582828654893166caf20576f5e0c418e
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41 </outputs>
1f1214983a1c planemo upload for repository https://github.com/phac-nml/quasitools commit 5a9e4c9a582828654893166caf20576f5e0c418e
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42 <tests>
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43 <test>
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44 <param name="input_bam" value="align.bam" />
1f1214983a1c planemo upload for repository https://github.com/phac-nml/quasitools commit 5a9e4c9a582828654893166caf20576f5e0c418e
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45 <param name="ref_file" value="hxb2_pol.fas" />
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46 <param name="var_file" value="nt_variants.vcf" />
1f1214983a1c planemo upload for repository https://github.com/phac-nml/quasitools commit 5a9e4c9a582828654893166caf20576f5e0c418e
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47 <param name="input_genes" ftype="bed" value="hxb2_pol.bed" />
1f1214983a1c planemo upload for repository https://github.com/phac-nml/quasitools commit 5a9e4c9a582828654893166caf20576f5e0c418e
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48 <param name="mutation_db" value="mutation_db.tsv" />
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49 <output name="output" >
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50 <assert_contents>
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51 <has_text text="Chromosome,Gene,Category,Surveillance,Wildtype,Position,Mutation,Mutation Frequency,Coverage" />
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52 <has_text text="hxb2_pol,RT,NNRTI,Yes,K,103,N,7.79,154" />
1f1214983a1c planemo upload for repository https://github.com/phac-nml/quasitools commit 5a9e4c9a582828654893166caf20576f5e0c418e
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53 </assert_contents>
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54 </output>
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55 </test>
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56 </tests>
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57 <help><![CDATA[
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58
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59 Drug Resistance Mutations
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60 =========================
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61
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62 Generates a report detailing the drug resistant mutations found, above the reporting threshold (default: 1%).
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63
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64 ------
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65 Inputs
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66 ------
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67
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68 1. A BAM file.
1f1214983a1c planemo upload for repository https://github.com/phac-nml/quasitools commit 5a9e4c9a582828654893166caf20576f5e0c418e
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69 2. A reference FASTA file.
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70 3. A variants (.vcf) file.
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71 4. A genes (.bed) file.
1f1214983a1c planemo upload for repository https://github.com/phac-nml/quasitools commit 5a9e4c9a582828654893166caf20576f5e0c418e
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72 5. A mutation database (.tsv) file.
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73
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74 ----------
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75 Parameters
1f1214983a1c planemo upload for repository https://github.com/phac-nml/quasitools commit 5a9e4c9a582828654893166caf20576f5e0c418e
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76 ----------
1f1214983a1c planemo upload for repository https://github.com/phac-nml/quasitools commit 5a9e4c9a582828654893166caf20576f5e0c418e
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77 1. The minimum required frequency for a variant to be considered. Defaults to 0.01.
1f1214983a1c planemo upload for repository https://github.com/phac-nml/quasitools commit 5a9e4c9a582828654893166caf20576f5e0c418e
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78 2. The reporting threshold a mutation must pass to be included in the report.
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79
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80 -------
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81 Outputs
1f1214983a1c planemo upload for repository https://github.com/phac-nml/quasitools commit 5a9e4c9a582828654893166caf20576f5e0c418e
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82 -------
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83
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84 A CSV file containing the drug resistant mutations found.
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85
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86 ]]></help>
1f1214983a1c planemo upload for repository https://github.com/phac-nml/quasitools commit 5a9e4c9a582828654893166caf20576f5e0c418e
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87 <expand macro="citations" />
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88 </tool>