Mercurial > repos > serranop > usearch
changeset 17:cb90b8246ef2 draft
New options
author | serranop |
---|---|
date | Fri, 13 Sep 2013 17:00:10 -0400 |
parents | 3244a7ca3faa |
children | 861744133340 |
files | usearch_fastq_mergepairs.xml |
diffstat | 1 files changed, 47 insertions(+), 9 deletions(-) [+] |
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--- a/usearch_fastq_mergepairs.xml Fri Sep 13 16:11:26 2013 -0400 +++ b/usearch_fastq_mergepairs.xml Fri Sep 13 17:00:10 2013 -0400 @@ -6,20 +6,62 @@ -quiet -fastq_mergepairs '$input_forward' -reverse '$input_reverse' -#if $minovlen == "0" - -fastq_minovlen 1 -#else +#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 $qmax --fastqout '$output' +-fastq_qmaxout $qmaxout +#if $output_format.format == "fastq" + -fastqout $output +#else + -fastaout $output +#end if </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" /> - </inputs> + <param name="qmaxout" type="integer" value="41" label="Maximum Q score for output files" /> + + <!-- OUTPUT OPTIONS --> + <conditional name="output_format"> + <param name="format" type="select" display="radio" label="Output format"> + <option value="fastq">FASTQ</option> + <option value="fasta">FASTA</option> + </param> + <when value="fastq"></when> + <when value="fasta"></when> + </conditional> + </inputs> <outputs> <data name='output' format='fastq' label="Merge result" /> </outputs> @@ -71,10 +113,6 @@ ------ -**Author** - -Robert C. Edgar (robert@drive5.com) - **Manual** http://drive5.com/usearch/manual/fastq_mergepairs.html