Mercurial > repos > petr-novak > re_utils
comparison pairScan.xml @ 9:c2c69c6090f0 draft
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| author | petr-novak |
|---|---|
| date | Fri, 31 Jan 2020 06:55:23 -0500 |
| parents | e320ef2d105a |
| children | f4ed6a65a2ff |
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| 8:99569eccc583 | 9:c2c69c6090f0 |
|---|---|
| 1 | 1 |
| 2 <tool id="pairScan" name="Scan paired reads for overlap" version="1.0.0"> | 2 <tool id="pairScan" name="Scan paired-end reads for overlap" version="1.0.0"> |
| 3 <description> Scan paired reads for overlap </description> | 3 <description> Scan paired-end reads for overlap </description> |
| 4 <requirements> | 4 <requirements> |
| 5 <requirement type="package">python-levenshtein</requirement> | 5 <requirement type="package">python-levenshtein</requirement> |
| 6 </requirements> | 6 </requirements> |
| 7 <command interpreter="python"> | 7 <command interpreter="python"> |
| 8 pairScan.py -f $fasta_input -o $min_overlap -m $max_mismatch -p $pass -b $bad -s $offset | 8 pairScan.py -f $fasta_input -o $min_overlap -m $max_mismatch -p $pass -b $bad -s $offset |
| 9 </command> | 9 </command> |
| 10 | 10 |
| 11 <inputs> | 11 <inputs> |
| 12 <param format="fasta" type="data" name="fasta_input" label="sequences in fasta format" /> | 12 <param format="fasta" type="data" name="fasta_input" label="Reads in FASTA format" /> |
| 13 <param name="min_overlap" type="integer" size="3" value="30" min="20" max="100" label="minimum overlap length [nt] " /> | 13 <param name="min_overlap" type="integer" size="3" value="30" min="20" max="100" label="Minimum overlap length [nt] " /> |
| 14 <param name="max_mismatch" type="select" label="Maximum number of mismatches per 100 bp"> | 14 <param name="max_mismatch" type="select" label="Maximum number of mismatches per 100 bp"> |
| 15 <option value="0">0</option> | 15 <option value="0">0</option> |
| 16 <option value="1" selected="true">1</option> | 16 <option value="1" selected="true">1</option> |
| 17 <option value="2">2</option> | 17 <option value="2">2</option> |
| 18 <option value="3">3</option> | 18 <option value="3">3</option> |
| 36 | 36 |
| 37 </inputs> | 37 </inputs> |
| 38 | 38 |
| 39 | 39 |
| 40 <outputs> | 40 <outputs> |
| 41 <data format="fasta" name="pass" label="pairs with no overlap from dataset ${fasta_input.hid}"/> | 41 <data format="fasta" name="pass" label="Pairs with no overlap from dataset ${fasta_input.hid}"/> |
| 42 <data format="fasta" name="bad" label="overlaping pairs from dataset ${fasta_input.hid}"/> | 42 <data format="fasta" name="bad" label="Overlaping pairs from dataset ${fasta_input.hid}"/> |
| 43 </outputs> | 43 </outputs> |
| 44 | 44 |
| 45 <help> | 45 <help> |
| 46 **Scan paired reads for overlap** | 46 **Scan paired reads for overlap** |
| 47 | 47 |