Mercurial > repos > nikhil-joshi > scythe
comparison scythe/scythe.xml @ 8:0a70eb1e6432 draft
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| author | nikhil-joshi |
|---|---|
| date | Tue, 10 Mar 2015 20:37:06 -0400 |
| parents | 8e5357ca8ebd |
| children |
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| 7:e01c19b11261 | 8:0a70eb1e6432 |
|---|---|
| 1 <tool id="scythe" name="Scythe"> | 1 <tool id="scythe" name="Scythe" version="0.991"> |
| 2 <description>Trimming adapters/contaminants using a Naive Bayesian classifier</description> | 2 <description>Trimming adapters/contaminants using a Naive Bayesian classifier</description> |
| 3 | 3 |
| 4 <command> | 4 <command> |
| 5 scythe --quiet -a $adapter_file | 5 scythe -a $adapter_file |
| 6 | 6 |
| 7 #if $input_fastq.ext == "fastq": | 7 #if $input_fastq.ext == "fastq": |
| 8 -q sanger | 8 -q sanger |
| 9 #else if $input_fastq.ext == "fastqsanger": | 9 #else if $input_fastq.ext == "fastqsanger": |
| 10 -q sanger | 10 -q sanger |
| 32 | 32 |
| 33 #if str($matches_file) == "matches_file_true": | 33 #if str($matches_file) == "matches_file_true": |
| 34 -m $output_matches | 34 -m $output_matches |
| 35 #end if | 35 #end if |
| 36 | 36 |
| 37 -o $output_trimmed $input_fastq 2> /dev/null | 37 -o $output_trimmed $input_fastq 2>&1 |
| 38 </command> | 38 </command> |
| 39 | 39 |
| 40 <inputs> | 40 <inputs> |
| 41 <param format="fastq, fastqsanger, fastqillumina, fastqsolexa" name="input_fastq" type="data" optional="false" label="FastQ Reads" help="Note: Scythe will infer the quality type of the file from its datatype. I.e., if the datatype is fastqsanger, then the quality type is sanger. The default is fastqsanger."/> | 41 <param format="fastq, fastqsanger, fastqillumina, fastqsolexa" name="input_fastq" type="data" optional="false" label="FastQ Reads" help="Note: Scythe will infer the quality type of the file from its datatype. I.e., if the datatype is fastqsanger, then the quality type is sanger. The default is fastqsanger."/> |
| 42 | 42 |