changeset 31:38e5953ca25f draft

Uploaded

--- a/usearch_fastq_mergepairs.xml	Sat Sep 14 12:33:28 2013 -0400
+++ b/usearch_fastq_mergepairs.xml	Sat Sep 14 12:41:19 2013 -0400
@@ -1,4 +1,4 @@
-<tool id="usearch_fastq_mergepairs" name="usearch fastq_mergepairs" version="0.0.2">
+<tool id="usearch_fastq_mergepairs" name="usearch fastq_mergepairs" version="0.0.1">
     <description>merging of paired reads</description>
     <version_command>usearch -version</version_command>
     <command interpreter='bash'>usearch_wrapper.sh
@@ -29,7 +29,7 @@
 -fastq_qmin $qmin
 -fastq_qmax $qmax
 -fastq_qmaxout $qmaxout
-#if $output_format.format == "fastq"
+#if $cond_format.out_format == "fastq"
     -fastqout $output
 #else
     -fastaout $output
@@ -51,10 +51,8 @@
         <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">
-            <param name="format" type="select" label="Output format">
+        <conditional name="cond_format">
+            <param name="out_format" type="select" label="Output format">
                 <option value="fastq" selected="true">FASTQ</option>
                 <option value="fasta">FASTA</option>
             </param>
@@ -65,7 +63,7 @@
     <outputs>
 		<data format="fastq" name="output" label="Merge output">
 			<change_format>
-				<when input="format" value="fasta" format="fasta" />
+				<when input="out_format" value="fasta" format="fasta" />
 			</change_format>
 		</data>
     </outputs>
@@ -82,9 +80,10 @@
 
 Performs merging of paired reads.
 
-The FASTQ filename for the forward reads is specified by the -fastq_mergepairs option, and the reverse read filename is specified by the -reverse option. Output files are specified by -fastqout (for FASTQ) and / or -fastaout (for FASTA).
-
-Forward and reverse must be in 1:1 correspondence and must appear in the same order in both files. The labels for the forward and reverse read in a given pair must be identical except for a single position where a '1' appears in the forward read label and a '2' appears in the reverse read label.
+Forward and reverse must be in 1:1 correspondence and must appear in the same
+order in both files. The labels for the forward and reverse read in a given
+pair must be identical except for a single position where a '1' appears in the
+forward read label and a '2' appears in the reverse read label.
 
 -----