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changeset 28:dcad0a24bafa draft

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Uploaded
author serranop
date Sat, 14 Sep 2013 12:20:18 -0400
parents 4c11ec2ae1c0
children 29cb532fc1ee
files usearch_fastq_mergepairs.xml
diffstat 1 files changed, 7 insertions(+), 3 deletions(-) [+]
line wrap: on
line diff
--- a/usearch_fastq_mergepairs.xml	Sat Sep 14 12:05:14 2013 -0400
+++ b/usearch_fastq_mergepairs.xml	Sat Sep 14 12:20:18 2013 -0400
@@ -43,8 +43,8 @@
         <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&lt;=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="truncqual" 		type="integer" value="0" label="7. 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 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" />
@@ -62,7 +62,11 @@
         </conditional>
    </inputs>
     <outputs>
-        <data name="output" format="${output_format.format}" label="Merge result" />
+		<data format="fastq" name="output" label="Merge output">
+			<change_format>
+				<when input="format" value="fasta" format="fasta" />
+			</change_format>
+		</data>
     </outputs>
     <tests>
         <test>