# HG changeset patch
# User serranop
# Date 1379174714 14400
# Node ID 4c11ec2ae1c0bc8d48a73b124eccb63b900c88f8
# Parent  aa3acde7621c557987b9aedb687d79202a8db0ce
Uploaded

diff -r aa3acde7621c -r 4c11ec2ae1c0 usearch_fastq_mergepairs.xml
--- 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&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" />
+        <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&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" />
+        <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">