--- a/UMI_riboseq_tool/UMI.py	Mon Jul 25 12:22:53 2022 +0000
+++ b/UMI_riboseq_tool/UMI.py	Fri Sep 30 09:07:04 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'):

--- a/UMI_riboseq_tool/UMI_riboseq.xml	Mon Jul 25 12:22:53 2022 +0000
+++ b/UMI_riboseq_tool/UMI_riboseq.xml	Fri Sep 30 09:07:04 2022 +0000
@@ -3,17 +3,17 @@
     <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 $5_prime_UMI_length $3_prime_UMI_length]]>
 </command>
 <inputs>
     <param format="fastqsanger,fastqsanger.gz" name="reads" type="data" label="fastqsanger,fastqsanger.gz"/>
     <param name="gzip" type="boolean" truevalue="true" falsevalue="false" checked="True" label="Gzip the outputted FASTQ" />
-    <param name="five_prime_UMI_length" type="integer" value=2 label="Number of UMI bases at the 5' end" help="2 for McGlincy Ingolia Protocol" />
-    <param name="three_prime_UMI_length" type="integer" value=5 label="Number of UMI bases at the 3' end)" help="5 for McGlincy Ingolia Protocol" />
+    <param name="5_prime_UMI_length" type="integer" value="2" label="Number of UMI bases at the 5' end" help="2 for McGincy Ingolia Protocol" />
+    <param name="3_prime_UMI_length" type="integer" value="5" label="Number of UMI bases at the 3' end)" help="5 for McGincy Ingolia Protocol" />
 
 </inputs>
 <outputs>
-    <data format="fastqsanger" name="output"/>
+    <data format="fastqsanger,fastqsanger.gz" name="output"/>
 </outputs>
 <tests>
     <test>
@@ -30,7 +30,7 @@
           The output of the script is fastq/fastq.gz file where UMIs (7nt in total, 5'NN and 3'NNNNN preceding barcode consisting of 5nt) are in header of the read. It is designed for protocol: McGlincy NJ, Ingolia NT. Transcriptome-wide measurement of translation by ribosome profiling. Methods. 2017;126:112-129. doi:10.1016/j.ymeth.2017.05.028 ]]>
 </help>
 <citations>
-<citation type="bibtex"> @misc{FedorovaAD2022, author = {Fedorova Alla}, year = {2022}, title = {UMI_for_riboseq}, publisher = {GitHub}, journal = {GitHub repository}, url = {https://github.com/triasteran/RiboGalaxy_with_ansible/blob/main/toolshed_tools/UMI_riboseq_tool/UMI.py}, }
+<citation type="bibtex"> @misc{FedorovaAD2022 and TierneyJack2022, author = {Fedorova Alla, Tierney Jack}, year = {2022}, title = {UMI_for_riboseq}, publisher = {GitHub}, journal = {GitHub repository}, url = {https://github.com/triasteran/RiboGalaxy_with_ansible/blob/main/toolshed_tools/UMI_riboseq_tool/UMI.py}, }
 </citation>
 </citations>
 </tool>