Mercurial > repos > serranop > usearch
changeset 21:a1731593bc94 draft
Testing
author | serranop |
---|---|
date | Sat, 14 Sep 2013 11:37:24 -0400 |
parents | acaab750b5fb |
children | 8aae82cf927b |
files | usearch_fastq_mergepairs.xml |
diffstat | 1 files changed, 2 insertions(+), 35 deletions(-) [+] |
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--- a/usearch_fastq_mergepairs.xml Fri Sep 13 17:28:01 2013 -0400 +++ b/usearch_fastq_mergepairs.xml Sat Sep 14 11:37:24 2013 -0400 @@ -9,48 +9,15 @@ #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 $minlen -#end if -$allowmergestagger --fastq_ascii $ascii --fastq_qmin $qmin -fastq_qmax $qmax --fastq_qmaxout $qmaxout -#if $output_format.format == "fastq" - -fastqout $output -#else - -fastaout $output -#end if +-fastqout $output </command> <inputs> <!-- INPUT OPTIONS --> <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="allowmergestagger" type="boolean" truevalue="-fastq_allowmergestagger" falsevalue="" checked="false" label="Allow merge of a pair where the alignment is staggered like this: --FORWARD - REVERSE--" help="By default, pairs with staggered alignments are discarded." /> - <param name="ascii" type="integer" value="33" label="ASCII_BASE constant" help="See http://drive5.com/usearch/manual/fastq_params.html" /> - <param name="qmin" type="integer" value="0" label="Minimum Q score" /> <param name="qmax" type="integer" value="41" label="Maximum Q score for input files" /> - <param name="qmaxout" type="integer" value="41" label="Maximum Q score for output files" /> <!-- OUTPUT OPTIONS --> <conditional name="output_format"> @@ -63,7 +30,7 @@ </conditional> </inputs> <outputs> - <data name="output" format="${output_format.format}" label="Merge result" /> + <data name="output" format="fastq" label="Merge result" /> </outputs> <tests> <test>