--- a/correct_barcodes.xml	Mon Sep 11 16:59:44 2017 -0400
+++ b/correct_barcodes.xml	Wed Oct 25 19:26:43 2017 -0400
@@ -1,16 +1,16 @@
 <?xml version="1.0"?>
-<tool id="correct_barcodes" name="Du Novo: Correct barcodes" version="0.8.1">
+<tool id="correct_barcodes" name="Du Novo: Correct barcodes" version="2.0.6">
   <description>of duplex sequencing reads</description>
   <requirements>
     <requirement type="package" version="2.2.5">bowtie2</requirement>
     <requirement type="package" version="0.1.18">samtools</requirement>
-    <requirement type="package" version="1.9">networkx</requirement>
-    <requirement type="package" version="0.8.1">dunovo</requirement>
+    <requirement type="package" version="1.11">networkx</requirement>
+    <requirement type="package" version="2.0.6">dunovo</requirement>
     <!-- TODO: require Python 2.7 -->
   </requirements>
   <command detect_errors="exit_code"><![CDATA[
-    baralign.sh '$input' refdir barcodes.bam
-    && samtools view -f 256 barcodes.bam
+    baralign.sh '$input' refdir
+    | samtools view -S -f 256 -
     | correct.py --galaxy $phone --dist $dist --mapq $mapq --pos $pos '$input' refdir/barcodes.fa
     | sort
     > '$output'
@@ -21,27 +21,11 @@
     <param name="dist" type="integer" value="1" min="1" label="Maximum edit distance" help="Only use alignments where the barcodes differ by at most these many errors."/>
     <param name="mapq" type="integer" value="20" min="0" label="Minimum mapping quality" help="Only use alignments whose MAPQ is at least this."/>
     <param name="pos" type="integer" value="2" min="0" label="Minimum start offset" help="Ignore alignments where the start positions differ by more than this."/>
-    <param name="phone" type="boolean" truevalue="--phone-home" falsevalue="" checked="False" label="Send anonymous usage data" help="Report helpful usage data to the developer, to better understand the use cases and performance of the tool. The only data which will be recorded is the name and version of the tool, the size of the input data, the time taken to process it, and the IP address of the machine running it. No parameters or filenames are sent."/>
+    <param name="phone" type="boolean" truevalue="--phone-home" falsevalue="" checked="False" label="Send usage data" help="Report helpful usage data to the developer, to better understand the use cases and performance of the tool. The only data which will be recorded is the name and version of the tool, the size of the input data, the time and memory taken to process it, and the IP address of the machine running it. Also, if the tool fails, it will report the name of the exception thrown and the line of code it occurred in. The parameters and input/output dataset names are not sent. All the reporting and recording code is available at https://github.com/NickSto/ET"/>
   </inputs>
   <outputs>
     <data name="output" format="tabular"/>
   </outputs>
-  <citations>
-    <citation type="bibtex">@article{Stoler2016,
-      author = {Stoler, Nicholas and Arbeithuber, Barbara and Guiblet, Wilfried and Makova, Kateryna D and Nekrutenko, Anton},
-      doi = {10.1186/s13059-016-1039-4},
-      issn = {1474-760X},
-      journal = {Genome biology},
-      number = {1},
-      pages = {180},
-      pmid = {27566673},
-      publisher = {Genome Biology},
-      title = {{Streamlined analysis of duplex sequencing data with Du Novo.}},
-      url = {http://www.ncbi.nlm.nih.gov/pubmed/27566673},
-      volume = {17},
-      year = {2016}
-    }</citation>
-  </citations>
   <help>
 
 **What it does**
@@ -60,5 +44,21 @@
 
 The output format is the same as the input format, ready to be consumed by the "Align families" tool.
 
-    </help>
+  </help>
+  <citations>
+    <citation type="bibtex">@article{Stoler2016,
+      author = {Stoler, Nicholas and Arbeithuber, Barbara and Guiblet, Wilfried and Makova, Kateryna D and Nekrutenko, Anton},
+      doi = {10.1186/s13059-016-1039-4},
+      issn = {1474-760X},
+      journal = {Genome biology},
+      number = {1},
+      pages = {180},
+      pmid = {27566673},
+      publisher = {Genome Biology},
+      title = {{Streamlined analysis of duplex sequencing data with Du Novo.}},
+      url = {http://www.ncbi.nlm.nih.gov/pubmed/27566673},
+      volume = {17},
+      year = {2016}
+    }</citation>
+  </citations>
 </tool>