changeset 25:26ab91de7593 draft

Uploaded

--- a/usearch_fastq_mergepairs.xml	Sat Sep 14 11:53:43 2013 -0400
+++ b/usearch_fastq_mergepairs.xml	Sat Sep 14 11:55:44 2013 -0400
@@ -24,7 +24,11 @@
 #if $minlen.value != 0
     -fastq_minlen $minlen
 #end if
+$allowmergestagger
+-fastq_ascii $ascii
+-fastq_qmin $qmin
 -fastq_qmax $qmax
+-fastq_qmaxout $qmaxout
 -fastqout $output
     </command>
     <inputs>
@@ -37,7 +41,12 @@
         <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&lt;=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">