Mercurial > repos > nml > quasitools
comparison hydra.xml @ 1:1abf6b32ecfd draft
planemo upload for repository https://github.com/phac-nml/quasitools commit 1a2c7bac09d21d92533bc2ef31dd05c7ac41b39f
| author | nml |
|---|---|
| date | Wed, 13 Dec 2017 10:28:31 -0500 |
| parents | 71976cfc9022 |
| children | a7093d5933a8 |
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| 0:71976cfc9022 | 1:1abf6b32ecfd |
|---|---|
| 3 <requirements> | 3 <requirements> |
| 4 <requirement type="package" version="0.2.2">quasitools</requirement> | 4 <requirement type="package" version="0.2.2">quasitools</requirement> |
| 5 </requirements> | 5 </requirements> |
| 6 <command detect_errors="exit_code"><![CDATA[ | 6 <command detect_errors="exit_code"><![CDATA[ |
| 7 | 7 |
| 8 quasitools hydra '$forward' | 8 quasitools hydra |
| 9 | 9 |
| 10 #if $reverse: | 10 ## Preparing file input. |
| 11 '$reverse' | 11 #if $data_type.type == "paired": |
| 12 | |
| 13 '$data_type.fastq_input1' | |
| 14 '$data_type.fastq_input2' | |
| 15 | |
| 16 #elif $data_type.type == "collection": | |
| 17 | |
| 18 '$data_type.fastq_input1.forward' | |
| 19 '$data_type.fastq_input1.reverse' | |
| 20 | |
| 21 #elif $data_type.type == "single": | |
| 22 | |
| 23 '$data_type.fastq_input1' | |
| 24 | |
| 12 #end if | 25 #end if |
| 13 | 26 |
| 14 #if $mutation_db: | 27 #if $mutation_db: |
| 15 -m '$mutation_db' | 28 -m '$mutation_db' |
| 16 #end if | 29 #end if |
| 61 | 74 |
| 62 -o output | 75 -o output |
| 63 | 76 |
| 64 ]]></command> | 77 ]]></command> |
| 65 <inputs> | 78 <inputs> |
| 66 <param name="forward" type="data" format="fastq" optional="false" label="Forward read" /> | 79 <conditional name="data_type"> |
| 67 <param name="reverse" type="data" format="fastq" optional="true" label="Reverse read" help="Not required."/> | 80 <param name="type" type="select" label="Specify the read type."> |
| 81 <option value="single">Single-end Data</option> | |
| 82 <option value="paired">Paired-end Data</option> | |
| 83 <option value="collection">Collection Paired-end Data</option> | |
| 84 </param> | |
| 85 <when value="single"> | |
| 86 <param name="fastq_input1" type="data" format="fastq" label="Single end read file(s)"/> | |
| 87 </when> | |
| 88 <when value="paired"> | |
| 89 <param name="fastq_input1" type="data" format="fastq" label="Forward paired-end read file"/> | |
| 90 <param name="fastq_input2" type="data" format="fastq" label="Reverse paired-end read file"/> | |
| 91 </when> | |
| 92 <when value="collection"> | |
| 93 <param name="fastq_input1" type="data_collection" label="Paired-end reads collection" optional="false" format="fastq" collection_type="paired" /> | |
| 94 </when> | |
| 95 </conditional> | |
| 68 <param name="mutation_db" type="data" format="tsv" optional="true" label="Mutation DB" help="Defaults to HIV mutation database." /> | 96 <param name="mutation_db" type="data" format="tsv" optional="true" label="Mutation DB" help="Defaults to HIV mutation database." /> |
| 69 <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." /> | 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." /> |
| 70 <param name="consensus_pct" type="integer" optional="true" min="1" max="20" value="20" label="Reporting threshold" help="Minimum mutation frequency to report. Defaults to 20." /> | 98 <param name="consensus_pct" type="integer" optional="true" min="1" max="20" value="20" label="Reporting threshold" help="Minimum mutation frequency to report. Defaults to 20." /> |
| 71 <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." /> | 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." /> |
| 72 <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." /> | 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." /> |
| 88 <data format="vcf" label="HyDRA: aa mutations output" name="output_aa_mt" from_work_dir="output/mutation_report.hmcf" /> | 116 <data format="vcf" label="HyDRA: aa mutations output" name="output_aa_mt" from_work_dir="output/mutation_report.hmcf" /> |
| 89 <data format="txt" label="HyDRA: stats output" name="output_stats" from_work_dir="output/stats.txt" /> | 117 <data format="txt" label="HyDRA: stats output" name="output_stats" from_work_dir="output/stats.txt" /> |
| 90 </outputs> | 118 </outputs> |
| 91 <tests> | 119 <tests> |
| 92 <test> | 120 <test> |
| 93 <param name="forward" value="forward.fastq" /> | 121 <param name="type" value="single"/> |
| 122 <param name="fastq_input1" value="forward.fastq" /> | |
| 94 <output name="output_coverage"> | 123 <output name="output_coverage"> |
| 95 <assert_contents> | 124 <assert_contents> |
| 96 <has_text text="frame: 0" /> | 125 <has_text text="frame: 0" /> |
| 97 <has_text text="1,0" /> | 126 <has_text text="1,0" /> |
| 98 <has_text text="948,0" /> | 127 <has_text text="948,0" /> |