Mercurial > repos > nick > duplex
comparison align_families.xml @ 0:d2e46adc199e draft
planemo upload commit 35b743e6492923c0e2b1e5e434eaf4e56d268108
| author | nick |
|---|---|
| date | Mon, 23 Nov 2015 22:06:21 -0500 |
| parents | |
| children | b63d6673f883 |
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| -1:000000000000 | 0:d2e46adc199e |
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| 1 <?xml version="1.0"?> | |
| 2 <tool id="align_families" name="Align families" version="0.1"> | |
| 3 <description>from duplex sequencing data</description> | |
| 4 <requirements> | |
| 5 <requirement type="package" version="7.221">mafft</requirement> | |
| 6 <requirement type="package" version="0.1">duplex</requirement> | |
| 7 <requirement type="set_environment">DUPLEX_DIR</requirement> | |
| 8 </requirements> | |
| 9 <command detect_errors="exit_code">python \$DUPLEX_DIR/align_families.py $input > $output | |
| 10 </command> | |
| 11 <inputs> | |
| 12 <param name="input" type="data" format="tabular" label="Input reads" help="with barcodes, grouped by family"/> | |
| 13 </inputs> | |
| 14 <outputs> | |
| 15 <data name="output" format="tabular"/> | |
| 16 </outputs> | |
| 17 <tests> | |
| 18 <test> | |
| 19 <param name="input" value="smoke.families.tsv"/> | |
| 20 <output name="output" file="smoke.families.aligned.tsv"/> | |
| 21 </test> | |
| 22 <test> | |
| 23 <param name="input" value="families.in.tsv"/> | |
| 24 <output name="output" file="families.sort.tsv"/> | |
| 25 </test> | |
| 26 </tests> | |
| 27 <help> | |
| 28 | |
| 29 **What it does** | |
| 30 | |
| 31 This is for processing duplex sequencing data. It does a multiple sequence alignment on each (single-stranded) family of reads. | |
| 32 | |
| 33 ----- | |
| 34 | |
| 35 **Input** | |
| 36 | |
| 37 This expects the output format of the "Make families" tool. | |
| 38 | |
| 39 ----- | |
| 40 | |
| 41 **Output** | |
| 42 | |
| 43 The output is a tabular file where each line corresponds to a (single) read. | |
| 44 | |
| 45 The columns are:: | |
| 46 | |
| 47 1: barcode (both tags) | |
| 48 2: tag order in barcode ("ab" or "ba") | |
| 49 3: read mate ("1" or "2") | |
| 50 4: read name | |
| 51 5: read sequence, aligned ("-" for gaps) | |
| 52 6: read quality scores, aligned (" " for gaps) | |
| 53 | |
| 54 ----- | |
| 55 | |
| 56 **Alignments** | |
| 57 | |
| 58 The alignments are done using MAFFT, specifically the command | |
| 59 :: | |
| 60 | |
| 61 $ mafft --nuc --quiet family.fa > family.aligned.fa | |
| 62 | |
| 63 </help> | |
| 64 </tool> |