Mercurial > repos > serranop > usearch
changeset 22:8aae82cf927b draft
More testing
| author | serranop |
|---|---|
| date | Sat, 14 Sep 2013 11:50:18 -0400 |
| parents | a1731593bc94 |
| children | 8e0b348cb80c |
| files | usearch_fastq_mergepairs.xml |
| diffstat | 1 files changed, 20 insertions(+), 0 deletions(-) [+] |
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--- a/usearch_fastq_mergepairs.xml Sat Sep 14 11:37:24 2013 -0400 +++ b/usearch_fastq_mergepairs.xml Sat Sep 14 11:50:18 2013 -0400 @@ -9,6 +9,21 @@ #if $minovlen.value != 0 -fastq_minovlen $minovlen #end if +#if $minmergelen.value != 0 + -fastq_minmergelen $minmergelen +#end if +#if $maxmergelen.value != 0 + -fastq_maxmergelen $maxmergelen +#end if +#if $maxdiffs.value != 0 + -fastq_maxdiffs $maxdiffs +#end if +#if $truncqual.value != 0 + -fastq_truncqual $truncqual +#end if +#if $minlen.value != 0 + -fastq_minlen $minlen +#end if -fastq_qmax $qmax -fastqout $output </command> @@ -17,6 +32,11 @@ <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="0" label="Minimum length of the overlap" help="'0' means no minimum." /> + <param name="minmergelen" type="integer" value="0" label="Minimum length of the merged read" help="'0' means no minimum." /> + <param name="maxmergelen" type="integer" value="0" label="Maximum length of the merged read" help="'0' means no maximum." /> + <param name="maxdiffs" type="integer" value="0" label="Maximum number of mismatches allowed in the overlap region" help="'0' means any number of mismatches allowed" /> + <param name="truncqual" type="integer" value="0" label="Truncate the forward and reverse reads at the first Q<=q, if present. This truncation is performed before aligning the pair. With Illumina paired reads, it is recommended to use ‑fastq_trunqual 2 or higher, as low-quality tails will otherwise often cause alignment of the pair to fail." help="'0' means no quality truncation." /> + <param name="minlen" type="integer" value="0" label="Minimum length of the forward and reverse read, after truncating per ‑fastq_truncqual if applicable." help="'0' means no minimum." /> <param name="qmax" type="integer" value="41" label="Maximum Q score for input files" /> <!-- OUTPUT OPTIONS -->