diff barcode_sort.xml @ 7:2c843c8df821 draft

planemo upload commit 1af8d398aa035883718d02bb1b9051edb5d10c48

--- a/barcode_sort.xml	Tue Mar 29 12:45:39 2016 -0400
+++ b/barcode_sort.xml	Thu Mar 31 10:32:59 2016 -0400
@@ -7,14 +7,16 @@
 
 <command interpreter="perl">
 
-barcode_sort.pl $barcode $f1 $f2 $barcoded $nonbarcoded
+barcode_sort.pl $barcode $f1 $f2 $barcoded $nonbarcoded $barcode_length $cut_site
 
 </command>
 
 <inputs>
-  <param name="barcode" format="txt" type="data" label="Barcode file 1" />
-  <param name="f1" type="data" format="fastq" label="First reads" />
-  <param name="f2" type="data" format="fastq" label="Second reads" />
+  <param name="barcode" format="txt" type="data" label="Barcode file" />
+  <param name="barcode_length" type="integer" value="6" label="Barcode length" />
+  <param name="f1" type="data" format="fastq" label="First read FASTQ" />
+  <param name="f2" type="data" format="fastq" label="Second read FASTQ" />
+  <param name="cut_site" type="txt" value="TGCA" label="Cut site" />
 </inputs>
 <outputs>
   <data format="fastq" name="barcoded" label="Barcoded sequences"/>
@@ -27,7 +29,11 @@
 
 **What it does**
 
-This program takes 2 input sequence files where the barcode can be on either the 1st or 2nd read (but not both) and sorts all barcoded reads into a single file and all non-barcoded files into a second file. This separation is needed for the STACKs program as it does not handle sequences where the barcode is arbitrarily on the 1st or 2nd read.
+This program takes 2 input sequence files where the barcode can be on either
+the 1st or 2nd read (but not both) and sorts all barcoded reads into a single
+file and all non-barcoded files into a second file. This separation is needed
+for the STACKs program as it does not handle sequences where the barcode is
+arbitrarily on the 1st or 2nd read.
 
 --------
 
@@ -43,4 +49,3 @@
 </help>
 
 </tool>
-