# HG changeset patch
# User triasteran
# Date 1664530073 0
# Node ID cf1a0cbe5c346e6238fa56072b04728b0aef2981
# Parent  b90ecf790d5b156a8b457772b03bfb9360738ad3
Uploaded

diff -r b90ecf790d5b -r cf1a0cbe5c34 UMI_riboseq_tool/UMI.py
--- a/UMI_riboseq_tool/UMI.py	Mon Jul 25 12:40:07 2022 +0000
+++ b/UMI_riboseq_tool/UMI.py	Fri Sep 30 09:27:53 2022 +0000
@@ -50,7 +50,7 @@
         print ('file is gzipped fastq')
         with gzip.open(pathToFastaFile, "rt") as handle:
             for i, record in enumerate(SeqIO.parse(handle, "fastq")):
-                process_fastq_record(record, output, UMI_5_prime_length=2, UMI_3_prime_length=5)
+                process_fastq_record(record, output, UMI_5_prime_length, UMI_3_prime_length)
 
     else: 
         for record in SeqIO.parse(pathToFastaFile, 'fastq'):
diff -r b90ecf790d5b -r cf1a0cbe5c34 UMI_riboseq_tool/UMI_riboseq.xml
--- a/UMI_riboseq_tool/UMI_riboseq.xml	Mon Jul 25 12:40:07 2022 +0000
+++ b/UMI_riboseq_tool/UMI_riboseq.xml	Fri Sep 30 09:27:53 2022 +0000
@@ -1,9 +1,9 @@
-<tool id="UMI_riboseq" name="UMIs to Header" version="0.1.8">
+<tool id="UMI_riboseq" name="UMIs to Header" version="0.1.9">
 <requirements>
     <requirement type="package" version="1.75">biopython</requirement>
 </requirements>
 <command detect_errors="exit_code">
-<![CDATA[ python3 $__tool_directory__/UMI.py $reads $output $gzip $five_prime_UMI_length $three_prime_UMI_length]]>
+<![CDATA[ python3 $__tool_directory__/UMI.py $reads $output $gzip ${five_prime_UMI_length} ${three_prime_UMI_length}]]>
 </command>
 <inputs>
     <param format="fastqsanger,fastqsanger.gz" name="reads" type="data" label="fastqsanger,fastqsanger.gz"/>
@@ -13,7 +13,7 @@
 
 </inputs>
 <outputs>
-    <data format="fastqsanger" name="output"/>
+    <data format="fastqsanger,fastqsanger.gz" name="output"/>
 </outputs>
 <tests>
     <test>