changeset 23:8e0b348cb80c draft

Uploaded

--- a/usearch_fastq_mergepairs.xml	Sat Sep 14 11:50:18 2013 -0400
+++ b/usearch_fastq_mergepairs.xml	Sat Sep 14 11:52:17 2013 -0400
@@ -12,18 +12,6 @@
 #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>
@@ -33,10 +21,6 @@
         <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 -->