Mercurial > repos > serranop > usearch
changeset 7:94cda55f1bbb draft
Added -fastq_minovlen option
| author | serranop |
|---|---|
| date | Fri, 13 Sep 2013 14:42:10 -0400 |
| parents | d0974e1ff717 |
| children | 2ef1c29e783d |
| files | usearch_fastq_mergepairs.xml |
| diffstat | 1 files changed, 12 insertions(+), 8 deletions(-) [+] |
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--- a/usearch_fastq_mergepairs.xml Fri Sep 13 14:13:31 2013 -0400 +++ b/usearch_fastq_mergepairs.xml Fri Sep 13 14:42:10 2013 -0400 @@ -2,16 +2,20 @@ <description>merging of paired reads</description> <version_command>usearch -version</version_command> <command>usearch - -quiet - -fastq_mergepairs '$input_forward' - -reverse '$input_reverse' - -fastq_qmax $qmax - -fastqout '$output' +-quiet +-fastq_mergepairs '$input_forward' +-reverse '$input_reverse' +#if $minovlen != '-1': +-fastq_minovlen $minovlen +#end if +-fastq_qmax $qmax +-fastqout '$output' </command> <inputs> - <param name='input_forward' type='data' format='fastq,fastqsanger,fastqcssanger' label='The FASTQ filename for the forward reads' /> - <param name='input_reverse' type='data' format='fastq,fastqsanger,fastqcssanger' label='The FASTQ filename for the reverse reads' /> - <param name='qmax' type='integer' value='41' label='Maximum Q score (input files).' /> + <param name="input_forward" type="data" format="fastq,fastqsanger,fastqcssanger" label="File with forward reads" /> + <param name="input_reverse" type="data" format="fastq,fastqsanger,fastqcssanger" label="File with reverse reads" /> + <param name="minovlen" type="integer" value="-1" label="Minimum length of the overlap" help="'-1' means no minimum." /> + <param name="qmax" type="integer" value="41" label="Maximum Q score (input files)." /> </inputs> <outputs> <data name='output' format='fastq' label="Merge result" />