Mercurial > repos > serranop > usearch
changeset 27:4c11ec2ae1c0 draft
Uploaded
| author | serranop |
|---|---|
| date | Sat, 14 Sep 2013 12:05:14 -0400 |
| parents | aa3acde7621c |
| children | dcad0a24bafa |
| files | usearch_fastq_mergepairs.xml |
| diffstat | 1 files changed, 13 insertions(+), 14 deletions(-) [+] |
line wrap: on
line diff
--- a/usearch_fastq_mergepairs.xml Sat Sep 14 11:57:09 2013 -0400 +++ b/usearch_fastq_mergepairs.xml Sat Sep 14 12:05:14 2013 -0400 @@ -37,20 +37,19 @@ </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" /> + <param name="input_forward" type="data" format="fastq,fastqsanger,fastqcssanger" label="1. File with forward reads" /> + <param name="input_reverse" type="data" format="fastq,fastqsanger,fastqcssanger" label="2. File with reverse reads" /> + <param name="minovlen" type="integer" value="0" label="3. Minimum length of the overlap" help="'0' means no minimum." /> + <param name="minmergelen" type="integer" value="0" label="4. Minimum length of the merged read" help="'0' means no minimum." /> + <param name="maxmergelen" type="integer" value="0" label="5. Maximum length of the merged read" help="'0' means no maximum." /> + <param name="maxdiffs" type="integer" value="0" label="6. 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="7. 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 set this to 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="8. Minimum length of the forward and reverse read, after truncating per option 7 if applicable." help="'0' means no minimum." /> + <param name="allowmergestagger" type="boolean" truevalue="-fastq_allowmergestagger" falsevalue="" checked="false" label="9. Allow merge of a pair where the alignment is staggered" help="By default, pairs with staggered alignments are discarded." /> + <param name="ascii" type="integer" value="33" label="10. ASCII_BASE constant" help="See http://drive5.com/usearch/manual/fastq_params.html" /> + <param name="qmin" type="integer" value="0" label="11. Minimum Q score" /> + <param name="qmax" type="integer" value="41" label="12. Maximum Q score for input files" /> + <param name="qmaxout" type="integer" value="41" label="13. Maximum Q score for output files" /> <!-- OUTPUT OPTIONS --> <conditional name="output_format">