Mercurial > repos > nml > quasitools
annotate hydra.xml @ 2:a7093d5933a8 draft
planemo upload for repository https://github.com/phac-nml/quasitools commit de4309426401ce655435d6867b05c3673b9d086f
author | nml |
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date | Mon, 26 Mar 2018 14:23:30 -0400 |
parents | 1abf6b32ecfd |
children | 8cdffc02d2e2 |
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71976cfc9022
planemo upload for repository https://github.com/phac-nml/quasitools commit 8a264400a75945e2e0fdd5a08c007a8b1b7a2f0f
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1 <tool id="hydra" name="Hydra pipeline" version="0.1.0"> |
71976cfc9022
planemo upload for repository https://github.com/phac-nml/quasitools commit 8a264400a75945e2e0fdd5a08c007a8b1b7a2f0f
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2 <description>Identifies drug resistance within an NGS dataset</description> |
71976cfc9022
planemo upload for repository https://github.com/phac-nml/quasitools commit 8a264400a75945e2e0fdd5a08c007a8b1b7a2f0f
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3 <requirements> |
2
a7093d5933a8
planemo upload for repository https://github.com/phac-nml/quasitools commit de4309426401ce655435d6867b05c3673b9d086f
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4 <requirement type="package" version="0.2.3">quasitools</requirement> |
0
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planemo upload for repository https://github.com/phac-nml/quasitools commit 8a264400a75945e2e0fdd5a08c007a8b1b7a2f0f
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5 </requirements> |
71976cfc9022
planemo upload for repository https://github.com/phac-nml/quasitools commit 8a264400a75945e2e0fdd5a08c007a8b1b7a2f0f
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6 <command detect_errors="exit_code"><![CDATA[ |
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planemo upload for repository https://github.com/phac-nml/quasitools commit 8a264400a75945e2e0fdd5a08c007a8b1b7a2f0f
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7 |
1
1abf6b32ecfd
planemo upload for repository https://github.com/phac-nml/quasitools commit 1a2c7bac09d21d92533bc2ef31dd05c7ac41b39f
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8 quasitools hydra |
1abf6b32ecfd
planemo upload for repository https://github.com/phac-nml/quasitools commit 1a2c7bac09d21d92533bc2ef31dd05c7ac41b39f
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9 |
1abf6b32ecfd
planemo upload for repository https://github.com/phac-nml/quasitools commit 1a2c7bac09d21d92533bc2ef31dd05c7ac41b39f
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10 ## Preparing file input. |
1abf6b32ecfd
planemo upload for repository https://github.com/phac-nml/quasitools commit 1a2c7bac09d21d92533bc2ef31dd05c7ac41b39f
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11 #if $data_type.type == "paired": |
1abf6b32ecfd
planemo upload for repository https://github.com/phac-nml/quasitools commit 1a2c7bac09d21d92533bc2ef31dd05c7ac41b39f
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12 |
1abf6b32ecfd
planemo upload for repository https://github.com/phac-nml/quasitools commit 1a2c7bac09d21d92533bc2ef31dd05c7ac41b39f
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13 '$data_type.fastq_input1' |
1abf6b32ecfd
planemo upload for repository https://github.com/phac-nml/quasitools commit 1a2c7bac09d21d92533bc2ef31dd05c7ac41b39f
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14 '$data_type.fastq_input2' |
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planemo upload for repository https://github.com/phac-nml/quasitools commit 8a264400a75945e2e0fdd5a08c007a8b1b7a2f0f
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15 |
1
1abf6b32ecfd
planemo upload for repository https://github.com/phac-nml/quasitools commit 1a2c7bac09d21d92533bc2ef31dd05c7ac41b39f
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16 #elif $data_type.type == "collection": |
1abf6b32ecfd
planemo upload for repository https://github.com/phac-nml/quasitools commit 1a2c7bac09d21d92533bc2ef31dd05c7ac41b39f
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17 |
1abf6b32ecfd
planemo upload for repository https://github.com/phac-nml/quasitools commit 1a2c7bac09d21d92533bc2ef31dd05c7ac41b39f
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18 '$data_type.fastq_input1.forward' |
1abf6b32ecfd
planemo upload for repository https://github.com/phac-nml/quasitools commit 1a2c7bac09d21d92533bc2ef31dd05c7ac41b39f
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19 '$data_type.fastq_input1.reverse' |
1abf6b32ecfd
planemo upload for repository https://github.com/phac-nml/quasitools commit 1a2c7bac09d21d92533bc2ef31dd05c7ac41b39f
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20 |
1abf6b32ecfd
planemo upload for repository https://github.com/phac-nml/quasitools commit 1a2c7bac09d21d92533bc2ef31dd05c7ac41b39f
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21 #elif $data_type.type == "single": |
1abf6b32ecfd
planemo upload for repository https://github.com/phac-nml/quasitools commit 1a2c7bac09d21d92533bc2ef31dd05c7ac41b39f
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22 |
1abf6b32ecfd
planemo upload for repository https://github.com/phac-nml/quasitools commit 1a2c7bac09d21d92533bc2ef31dd05c7ac41b39f
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23 '$data_type.fastq_input1' |
1abf6b32ecfd
planemo upload for repository https://github.com/phac-nml/quasitools commit 1a2c7bac09d21d92533bc2ef31dd05c7ac41b39f
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24 |
0
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planemo upload for repository https://github.com/phac-nml/quasitools commit 8a264400a75945e2e0fdd5a08c007a8b1b7a2f0f
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25 #end if |
71976cfc9022
planemo upload for repository https://github.com/phac-nml/quasitools commit 8a264400a75945e2e0fdd5a08c007a8b1b7a2f0f
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26 |
71976cfc9022
planemo upload for repository https://github.com/phac-nml/quasitools commit 8a264400a75945e2e0fdd5a08c007a8b1b7a2f0f
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27 #if $mutation_db: |
71976cfc9022
planemo upload for repository https://github.com/phac-nml/quasitools commit 8a264400a75945e2e0fdd5a08c007a8b1b7a2f0f
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28 -m '$mutation_db' |
71976cfc9022
planemo upload for repository https://github.com/phac-nml/quasitools commit 8a264400a75945e2e0fdd5a08c007a8b1b7a2f0f
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29 #end if |
71976cfc9022
planemo upload for repository https://github.com/phac-nml/quasitools commit 8a264400a75945e2e0fdd5a08c007a8b1b7a2f0f
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30 |
71976cfc9022
planemo upload for repository https://github.com/phac-nml/quasitools commit 8a264400a75945e2e0fdd5a08c007a8b1b7a2f0f
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31 #if $reporting_threshold: |
71976cfc9022
planemo upload for repository https://github.com/phac-nml/quasitools commit 8a264400a75945e2e0fdd5a08c007a8b1b7a2f0f
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32 -rt '$reporting_threshold' |
71976cfc9022
planemo upload for repository https://github.com/phac-nml/quasitools commit 8a264400a75945e2e0fdd5a08c007a8b1b7a2f0f
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33 #end if |
71976cfc9022
planemo upload for repository https://github.com/phac-nml/quasitools commit 8a264400a75945e2e0fdd5a08c007a8b1b7a2f0f
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34 |
71976cfc9022
planemo upload for repository https://github.com/phac-nml/quasitools commit 8a264400a75945e2e0fdd5a08c007a8b1b7a2f0f
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35 #if $consensus_pct: |
71976cfc9022
planemo upload for repository https://github.com/phac-nml/quasitools commit 8a264400a75945e2e0fdd5a08c007a8b1b7a2f0f
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36 -cp '$consensus_pct' |
71976cfc9022
planemo upload for repository https://github.com/phac-nml/quasitools commit 8a264400a75945e2e0fdd5a08c007a8b1b7a2f0f
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37 #end if |
71976cfc9022
planemo upload for repository https://github.com/phac-nml/quasitools commit 8a264400a75945e2e0fdd5a08c007a8b1b7a2f0f
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38 |
71976cfc9022
planemo upload for repository https://github.com/phac-nml/quasitools commit 8a264400a75945e2e0fdd5a08c007a8b1b7a2f0f
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39 #if $length_cutoff: |
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planemo upload for repository https://github.com/phac-nml/quasitools commit 8a264400a75945e2e0fdd5a08c007a8b1b7a2f0f
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40 -lc '$length_cutoff' |
71976cfc9022
planemo upload for repository https://github.com/phac-nml/quasitools commit 8a264400a75945e2e0fdd5a08c007a8b1b7a2f0f
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41 #end if |
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planemo upload for repository https://github.com/phac-nml/quasitools commit 8a264400a75945e2e0fdd5a08c007a8b1b7a2f0f
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42 |
71976cfc9022
planemo upload for repository https://github.com/phac-nml/quasitools commit 8a264400a75945e2e0fdd5a08c007a8b1b7a2f0f
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43 #if $score_cutoff: |
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planemo upload for repository https://github.com/phac-nml/quasitools commit 8a264400a75945e2e0fdd5a08c007a8b1b7a2f0f
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44 -sc '$score_cutoff' |
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planemo upload for repository https://github.com/phac-nml/quasitools commit 8a264400a75945e2e0fdd5a08c007a8b1b7a2f0f
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45 #end if |
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planemo upload for repository https://github.com/phac-nml/quasitools commit 8a264400a75945e2e0fdd5a08c007a8b1b7a2f0f
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46 |
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planemo upload for repository https://github.com/phac-nml/quasitools commit 8a264400a75945e2e0fdd5a08c007a8b1b7a2f0f
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47 #if $error_rate: |
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planemo upload for repository https://github.com/phac-nml/quasitools commit 8a264400a75945e2e0fdd5a08c007a8b1b7a2f0f
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48 -e '$error_rate' |
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planemo upload for repository https://github.com/phac-nml/quasitools commit 8a264400a75945e2e0fdd5a08c007a8b1b7a2f0f
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49 #end if |
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planemo upload for repository https://github.com/phac-nml/quasitools commit 8a264400a75945e2e0fdd5a08c007a8b1b7a2f0f
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50 |
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planemo upload for repository https://github.com/phac-nml/quasitools commit 8a264400a75945e2e0fdd5a08c007a8b1b7a2f0f
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51 #if $min_qual: |
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52 -mq '$min_qual' |
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planemo upload for repository https://github.com/phac-nml/quasitools commit 8a264400a75945e2e0fdd5a08c007a8b1b7a2f0f
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53 #end if |
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planemo upload for repository https://github.com/phac-nml/quasitools commit 8a264400a75945e2e0fdd5a08c007a8b1b7a2f0f
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54 |
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planemo upload for repository https://github.com/phac-nml/quasitools commit 8a264400a75945e2e0fdd5a08c007a8b1b7a2f0f
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55 #if $min_depth: |
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planemo upload for repository https://github.com/phac-nml/quasitools commit 8a264400a75945e2e0fdd5a08c007a8b1b7a2f0f
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56 -md '$min_depth' |
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planemo upload for repository https://github.com/phac-nml/quasitools commit 8a264400a75945e2e0fdd5a08c007a8b1b7a2f0f
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57 #end if |
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planemo upload for repository https://github.com/phac-nml/quasitools commit 8a264400a75945e2e0fdd5a08c007a8b1b7a2f0f
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58 |
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planemo upload for repository https://github.com/phac-nml/quasitools commit 8a264400a75945e2e0fdd5a08c007a8b1b7a2f0f
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59 #if $min_ac: |
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planemo upload for repository https://github.com/phac-nml/quasitools commit 8a264400a75945e2e0fdd5a08c007a8b1b7a2f0f
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60 -ma '$min_ac' |
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planemo upload for repository https://github.com/phac-nml/quasitools commit 8a264400a75945e2e0fdd5a08c007a8b1b7a2f0f
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61 #end if |
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planemo upload for repository https://github.com/phac-nml/quasitools commit 8a264400a75945e2e0fdd5a08c007a8b1b7a2f0f
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62 |
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planemo upload for repository https://github.com/phac-nml/quasitools commit 8a264400a75945e2e0fdd5a08c007a8b1b7a2f0f
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63 #if $min_freq: |
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64 -mf '$min_freq' |
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65 #end if |
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planemo upload for repository https://github.com/phac-nml/quasitools commit 8a264400a75945e2e0fdd5a08c007a8b1b7a2f0f
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66 |
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67 #if $generate_consensus: |
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68 --generate_consensus |
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69 #end if |
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planemo upload for repository https://github.com/phac-nml/quasitools commit 8a264400a75945e2e0fdd5a08c007a8b1b7a2f0f
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70 |
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71 #if $filter_ns: |
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72 --ns |
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73 #end if |
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74 |
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75 -o output |
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76 |
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77 ]]></command> |
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78 <inputs> |
1
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79 <conditional name="data_type"> |
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80 <param name="type" type="select" label="Specify the read type."> |
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planemo upload for repository https://github.com/phac-nml/quasitools commit 1a2c7bac09d21d92533bc2ef31dd05c7ac41b39f
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81 <option value="single">Single-end Data</option> |
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82 <option value="paired">Paired-end Data</option> |
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83 <option value="collection">Collection Paired-end Data</option> |
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84 </param> |
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85 <when value="single"> |
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86 <param name="fastq_input1" type="data" format="fastq" label="Single end read file(s)"/> |
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planemo upload for repository https://github.com/phac-nml/quasitools commit 1a2c7bac09d21d92533bc2ef31dd05c7ac41b39f
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87 </when> |
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88 <when value="paired"> |
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planemo upload for repository https://github.com/phac-nml/quasitools commit 1a2c7bac09d21d92533bc2ef31dd05c7ac41b39f
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89 <param name="fastq_input1" type="data" format="fastq" label="Forward paired-end read file"/> |
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90 <param name="fastq_input2" type="data" format="fastq" label="Reverse paired-end read file"/> |
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91 </when> |
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92 <when value="collection"> |
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93 <param name="fastq_input1" type="data_collection" label="Paired-end reads collection" optional="false" format="fastq" collection_type="paired" /> |
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94 </when> |
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95 </conditional> |
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96 <param name="mutation_db" type="data" format="tsv" optional="true" label="Mutation DB" help="Defaults to HIV mutation database." /> |
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97 <param name="reporting_threshold" type="integer" optional="true" min="1" max="100" value="1" label="Reporting threshold. Defaults to 1." help="Minimum mutation frequency to report." /> |
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98 <param name="consensus_pct" type="integer" optional="true" min="1" max="20" value="20" label="Consensus percentage" help="Minimum mutation frequency to report. Defaults to 20." /> |
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99 <param name="length_cutoff" type="integer" optional="true" min="0" max="1000" label="Length cutoff" value="100" help="Reads which fall short of the specified length will be filtered out. Defaults to 100." /> |
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100 <param name="score_cutoff" type="integer" optional="true" min="0" max="40" label="Score cutoff" value="30" help="Reads whose average quality score is less than the specified score will be filtered out. Defaults to 30." /> |
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101 <param name="error_rate" type="float" optional="true" min="0" max="1" label="Error rate" value="0.0021" help="Estimated sequencing error rate. Defaults to 0.0021."/> |
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102 <param name="min_qual" type="integer" optional="true" min="1" max="100" label="Minimum quality" value="30" help="Minimum required quality for variant to be considered later on in the pipeline. Defaults to 30." /> |
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103 <param name="min_depth" type="integer" optional="true" min="0" max="5000" label="Minimum depth" value="100" help="Minimum required depth for variant to be considered later on in the pipeline. Defaults to 100." /> |
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104 <param name="min_ac" type="integer" optional="true" min="0" max="5000" label="Minimum allele count" value="5" help="Minimum required allele count for variant to be considered later on in the pipeline. Defaults to 5." /> |
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105 <param name="min_freq" type="float" optional="true" min="0" max="1" label="Minimum frequency" value="0.01" help="Minimum required frequency for variant to be considered later on in the pipeline. Defaults to 0.01." /> |
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106 <param name="generate_consensus" type="boolean" truevalue="--generate_consensus" falsevalue="" checked="False" label="Generate consensus" /> |
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107 <param name="filter_ns" type="boolean" truevalue="--ns" falsevalue="" checked="False" label="Filter out n's" /> |
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108 </inputs> |
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109 <outputs> |
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110 <data format="bam" label="HyDRA: alignment bam output" name="output_bam" from_work_dir="output/align.bam" /> |
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111 <data format="bam" label="HyDRA: bam.bai output" name="output_bam_bai" from_work_dir="output/align.bam.bai" /> |
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112 <data format="csv" label="HyDRA: coverage output" name="output_coverage" from_work_dir="output/coverage_file.csv" /> |
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113 <data format="csv" label="HyDRA: drug resistance output" name="output_dr" from_work_dir="output/dr_report.csv" /> |
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114 <data format="fastq" label="HyDRA: filtered reads output" name="output_filtered" from_work_dir="output/filtered.fastq" /> |
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115 <data format="vcf" label="HyDRA: variants output" name="output_hydra" from_work_dir="output/hydra.vcf" /> |
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116 <data format="vcf" label="HyDRA: aa mutations output" name="output_aa_mt" from_work_dir="output/mutation_report.hmcf" /> |
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117 <data format="txt" label="HyDRA: stats output" name="output_stats" from_work_dir="output/stats.txt" /> |
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118 <data format="fasta" label="HyDRA: consensus output" name="output_consensus" from_work_dir="output/consensus.fasta"> |
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119 <filter>generate_consensus</filter> |
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120 </data> |
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121 </outputs> |
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122 <tests> |
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123 <test> |
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124 <param name="type" value="single"/> |
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125 <param name="fastq_input1" value="forward.fastq" /> |
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126 <output name="output_coverage"> |
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127 <assert_contents> |
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128 <has_text text="frame: 0" /> |
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129 <has_text text="1,0" /> |
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130 <has_text text="948,0" /> |
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131 </assert_contents> |
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132 </output> |
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133 <output name="output_dr"> |
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134 <assert_contents> |
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135 <has_text text="Chromosome,Gene,Category,Surveillance,Wildtype,Position,Mutation,Mutation Frequency,Coverage" /> |
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136 <has_text text="hxb2_pol,RT,NNRTI,Yes,K,101,P,14.23,1574" /> |
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137 <has_text text="hxb2_pol,RT,NNRTI,Yes,K,103,N,5.49,1912" /> |
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138 <has_text text="hxb2_pol,RT,NNRTI,Yes,Y,181,C,24.07,4557" /> |
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139 <has_text text="hxb2_pol,RT,NNRTI,Yes,Y,181,I,18.04,4557" /> |
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140 <has_text text="hxb2_pol,RT,NNRTI,Yes,Y,181,V,20.08,4557" /> |
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141 <has_text text="hxb2_pol,RT,NNRTI,Yes,Y,188,C,2.81,3454" /> |
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142 <has_text text="hxb2_pol,RT,NNRTI,Yes,G,190,A,5.20,3233" /> |
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143 <has_text text="hxb2_pol,RT,NNRTI,Yes,G,190,S,6.68,3233" /> |
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144 </assert_contents> |
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145 </output> |
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146 <output name="output_hydra"> |
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147 <assert_contents> |
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148 <has_text_matching expression="#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO"/> |
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149 <has_text_matching expression="hxb2_pol\s576\s.\sa\sg\s100\sPASS\sDP=805;AC=245;AF=0.3043" /> |
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150 <has_text_matching expression="hxb2_pol\s958\s.\sc\sa\s100\sPASS\sDP=2503;AC=28;AF=0.0112" /> |
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151 </assert_contents> |
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152 </output> |
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153 <output name="output_aa_mt"> |
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154 <assert_contents> |
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155 <has_text_matching expression="#CHROM\sGENE\sTYPE\sWILDTYPE\sPOS\sMUTANT\sFILTER\sMUTANT_FREQ\sCOVERAGE\sINFO"/> |
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156 <has_text_matching expression="hxb2_pol\sRT\smutation\sK\s101\sP\sPASS\s0.1423\s1574\sWC=aaa;MC=CCa;MCF=0.1423;CAT=NNRTI;SRVL=Yes" /> |
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157 <has_text_matching expression="hxb2_pol\sRT\smutation\sH\s221\sN\sPASS\s0.0113\s2475\sWC=cat;MC=Aat;MCF=0.0113;CAT=.;SRVL=." /> |
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158 </assert_contents> |
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159 </output> |
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160 <output name="output_stats"> |
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161 <assert_contents> |
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162 <has_text text="Input Size: 25000"/> |
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163 <has_text text="Number of reads filtered due to length: 15074"/> |
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164 <has_text text="Number of reads filtered due to average quality score: 501"/> |
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165 <has_text text="Number of reads filtered due to presence of Ns: 0"/> |
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166 <has_text text="Number of reads filtered due to excess coverage: 0"/> |
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167 <has_text text="Number of reads filtered due to poor mapping: 12"/> |
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168 <has_text text="Percentage of reads filtered: 62.35"/> |
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169 </assert_contents> |
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170 </output> |
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171 </test> |
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172 </tests> |
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173 <help><![CDATA[ |
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174 |
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175 HyDRA - HIV Drug Resistance Analyzer |
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176 ==================================== |
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177 |
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178 The HyDRA pipeline provides a pipeline for identifying drug resistance within a Next Generation Sequencing dataset. The pipeline takes as input the raw reads produced by a Next Generation Sequencer and produces a report detailing found drug resistance per sample. |
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179 |
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180 Authors |
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181 ------- |
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182 |
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183 The HyDRA pipeline was developed by Eric Enns and David Peddle. |
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184 |
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185 Stages |
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186 ------ |
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187 |
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188 The HyDRA pipleine proceeds through the following stages: |
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189 |
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190 1. Quality Control/Filtering |
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191 2. Reference mapping using bowtie2. |
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192 3. Variant Calling and filtering using a Poisson distribution. |
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193 4. AA Mutation Calling and filtering. |
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194 5. Drug Resistance report generation. |
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195 |
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196 Details |
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197 ------- |
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198 |
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199 The following is an example for running the pipeline, using our included test dataset: |
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200 * Output directory name: "/tmp/hydra_out" |
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201 * Forward reads: "reads_w_K103N.fastq" |
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202 |
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203 ### Output ### |
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204 |
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205 The detailed output directory tree looks as follows: |
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206 |
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207 /tmp/hydra_out/ |
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208 * align.bam |
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209 * align.bam.bai |
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210 * coverage_file.csv |
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211 * dr_report.csv |
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212 * filtered.fastq |
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213 * hydra.vcf |
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214 * mutation_report.hmcf |
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215 * stats.txt |
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216 |
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217 The description of each of these directories/files are as follows: |
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218 |
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219 * __run.conf__: The configuration used when this output was produced. |
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220 * __reads_w_K103N/__: The results directory for the input file reads_w_K103N.fastq |
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221 * __align.bam__: The alignment file in bam format. |
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222 * __align.bam.bai__: The index to the alignment file. |
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223 * __coverage_file.csv__: A file with one entry per line with the AA position and the coverage at the position. |
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224 * __dr_report.csv__: A report detailing the drug resistant mutations found, above the reporting threshold (default: 1%). |
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225 * __filtered.fastq__: The reads remaining after the filtering stage. |
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226 * __hydra.vcf__: The variants found by the pipeline. |
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227 * __mutation_report.hmcf__: The AA mutations found by the pipeline. |
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228 * __stats.txt__: A log file detailing size after filtering and major stages. |
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229 |
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230 The __dr_report.csv__ file lists all found drug resistant mutations (mutations included in the mutation database) which have frequency greater than the reporting threshold. An example of this file is given below. |
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231 |
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232 Example: __dr_report.csv__ |
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233 |
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234 Gene,Category,Surveillance,Wildtype,Position,Mutation,Mutation Frequency,Coverage |
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235 RT,NNRTI,Yes,K,103,N,9.03,155 |
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236 |
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237 The __mutation_report.hmcf__ files is our custom VCF like file which details all of the AA mutations found by the pipeline. An example if this file is given below. |
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238 |
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239 Example: __mutation_report.hmcf__ |
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240 |
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241 ##fileformat=HMCFv1 |
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242 ##fileDate=20150008 |
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243 ##source=HyDRA |
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244 ##reference=/home/ericenns/hydra/var/hxb2_pol.fas |
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245 ##INFO=<ID=MC,Number=.,Description="String"> |
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246 ##INFO=<ID=MCF,Number=.,Description="String"> |
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247 ##INFO=<ID=WC,Number=.,Description="String"> |
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248 ##FILTER=<ID=mf0.01,Description="Mutant freq below 0.01"> |
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249 #GENE CATEGORY SURVEILLANCE TYPE WILDTYPE POS MUTANT FILTER MUTANT_FREQ COVERAGE INFO |
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250 RT NNRTI Yes mutation K 103 N PASS 0.0903 155 WC=aaa;MC=aaC;MCF=0.0903 |
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251 |
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252 ]]></help> |
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planemo upload for repository https://github.com/phac-nml/quasitools commit 8a264400a75945e2e0fdd5a08c007a8b1b7a2f0f
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253 <citations> |
71976cfc9022
planemo upload for repository https://github.com/phac-nml/quasitools commit 8a264400a75945e2e0fdd5a08c007a8b1b7a2f0f
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254 </citations> |
71976cfc9022
planemo upload for repository https://github.com/phac-nml/quasitools commit 8a264400a75945e2e0fdd5a08c007a8b1b7a2f0f
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255 </tool> |