# HG changeset patch
# User nick
# Date 1486154238 18000
# Node ID 8ef925264516a527bcfe582f3f618ff625755c98
# Parent  53cf867b305b2d52d1e5f5d95df76d8655d3c8e8
planemo upload for repository https://github.com/galaxyproject/dunovo commit b'3eab56b30cc9d644798a290017bcc1188f028af8\n'-dirty

diff -r 53cf867b305b -r 8ef925264516 align_families.xml
--- a/align_families.xml	Thu Feb 02 19:50:18 2017 -0500
+++ b/align_families.xml	Fri Feb 03 15:37:18 2017 -0500
@@ -1,9 +1,9 @@
 <?xml version="1.0"?>
-<tool id="align_families" name="Du Novo: Align families" version="0.5">
+<tool id="align_families" name="Du Novo: Align families" version="0.6">
   <description>of duplex sequencing reads</description>
   <requirements>
     <requirement type="package" version="7.221">mafft</requirement>
-    <requirement type="package" version="0.5">duplex</requirement>
+    <requirement type="package" version="0.6">duplex</requirement>
     <requirement type="set_environment">DUPLEX_DIR</requirement>
     <!-- TODO: require Python 2.7 -->
   </requirements>
diff -r 53cf867b305b -r 8ef925264516 correct_barcodes.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/correct_barcodes.xml	Fri Feb 03 15:37:18 2017 -0500
@@ -0,0 +1,60 @@
+<?xml version="1.0"?>
+<tool id="correct_barcodes" name="Du Novo: Correct barcodes" version="0.6">
+  <description>of duplex sequencing reads</description>
+  <requirements>
+    <requirement type="package" version="2.1.0">bowtie2</requirement>
+    <requirement type="package" version="0.1.18">samtools</requirement>
+    <requirement type="package" version="0.6">duplex</requirement>
+    <requirement type="set_environment">DUPLEX_DIR</requirement>
+    <!-- TODO: require Python 2.7 -->
+  </requirements>
+  <command detect_errors="exit_code">bash "\$DUPLEX_DIR/baralign.sh" '$input' refdir barcodes.bam
+    &amp;&amp; samtools view -f 256 barcodes.bam
+    | python "\$DUPLEX_DIR/correct.py" -d $dist -m $mapq -p $pos '$input' refdir/barcodes.fa
+    | sort &gt; '$output'
+  </command>
+  <inputs>
+    <param name="input" type="data" format="tabular" label="Input reads" help="with barcodes, grouped by family"/>
+    <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."/>
+  </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**
+
+This is for processing duplex sequencing data. This will correct duplex barcodes and create new, larger families. Errors in barcodes normally prevent them from being recognized as the same as the other barcodes in their family. Correcting these errors allows the original, full families to be reconstructed, saving reads which would otherwise be lost. This tool accomplishes this by doing an all vs. all alignment between the barcodes with bowtie2. This identifies ones which are identical except a few, small differences.
+
+-----
+
+**Input**
+
+This expects the output format of the "Make families" tool.
+
+-----
+
+**Output**
+
+The output format is the same as the input format, ready to be consumed by the "Align families" tool.
+
+    </help>
+</tool>
diff -r 53cf867b305b -r 8ef925264516 dunovo.xml
--- a/dunovo.xml	Thu Feb 02 19:50:18 2017 -0500
+++ b/dunovo.xml	Fri Feb 03 15:37:18 2017 -0500
@@ -1,8 +1,8 @@
 <?xml version="1.0"?>
-<tool id="duplex" name="Du Novo: Make consensus reads" version="0.5">
+<tool id="duplex" name="Du Novo: Make consensus reads" version="0.6">
   <description>from duplex sequencing alignments</description>
   <requirements>
-    <requirement type="package" version="0.5">duplex</requirement>
+    <requirement type="package" version="0.6">duplex</requirement>
     <requirement type="set_environment">DUPLEX_DIR</requirement>
     <!-- TODO: require Python 2.7 -->
   </requirements>
diff -r 53cf867b305b -r 8ef925264516 make_families.xml
--- a/make_families.xml	Thu Feb 02 19:50:18 2017 -0500
+++ b/make_families.xml	Fri Feb 03 15:37:18 2017 -0500
@@ -1,8 +1,8 @@
 <?xml version="1.0"?>
-<tool id="make_families" name="Du Novo: Make families" version="0.5">
+<tool id="make_families" name="Du Novo: Make families" version="0.6">
   <description>of duplex sequencing reads</description>
   <requirements>
-    <requirement type="package" version="0.5">duplex</requirement>
+    <requirement type="package" version="0.6">duplex</requirement>
     <requirement type="set_environment">DUPLEX_DIR</requirement>
   </requirements>
   <!-- TODO: Add dependency on coreutils to get paste? -->
diff -r 53cf867b305b -r 8ef925264516 tool_dependencies.xml
--- a/tool_dependencies.xml	Thu Feb 02 19:50:18 2017 -0500
+++ b/tool_dependencies.xml	Fri Feb 03 15:37:18 2017 -0500
@@ -3,7 +3,13 @@
   <package name="mafft" version="7.221">
     <repository changeset_revision="dd4a533a0e3c" name="mafft" owner="rnateam" toolshed="https://testtoolshed.g2.bx.psu.edu" />
   </package>
-  <package name="duplex" version="0.5">
+  <package name="bowtie2" version="2.1.0">
+    <repository changeset_revision="606d435a57a4" name="package_bowtie2_2_1_0" owner="devteam" toolshed="https://testtoolshed.g2.bx.psu.edu" />
+  </package>
+  <package name="samtools" version="0.1.18">
+    <repository changeset_revision="f499719dad6e" name="package_samtools_0_1_18" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" />
+  </package>
+  <package name="duplex" version="0.6">
     <install version="1.0">
       <actions>
         <action sha256sum="bcfe5bc066545888da14779bc48941bd6a2f147d57fd0f851d82e495adade48f" type="download_by_url">https://github.com/galaxyproject/dunovo/archive/v0.5.tar.gz</action>