# HG changeset patch
# User nick
# Date 1503555213 14400
# Node ID a9cb6fb9ea948db33bbfc3c2bddce882ecf8c710
# Parent  ea832c221ec96bdf05d73fada36f0404e3c02815
Update to Du Novo 0.7.6.

diff -r ea832c221ec9 -r a9cb6fb9ea94 align_families.xml
--- a/align_families.xml	Fri Feb 24 03:18:01 2017 -0500
+++ b/align_families.xml	Thu Aug 24 02:13:33 2017 -0400
@@ -1,15 +1,16 @@
 <?xml version="1.0"?>
-<tool id="align_families" name="Du Novo: Align families" version="0.7">
+<tool id="align_families" name="Du Novo: Align families" version="0.7.6">
   <description>of duplex sequencing reads</description>
   <requirements>
     <requirement type="package" version="7.221">mafft</requirement>
-    <requirement type="package" version="0.7.1">dunovo</requirement>
+    <requirement type="package" version="0.7.6">dunovo</requirement>
     <!-- TODO: require Python 2.7 -->
   </requirements>
-  <command detect_errors="exit_code">align_families.py -p \${GALAXY_SLOTS:-1} '$input' &gt; '$output'
+  <command detect_errors="exit_code">align_families.py --galaxy $phone -p \${GALAXY_SLOTS:-1} '$input' &gt; '$output'
   </command>
   <inputs>
     <param name="input" type="data" format="tabular" label="Input reads" help="with barcodes, grouped by family"/>
+    <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."/>
   </inputs>
   <outputs>
     <data name="output" format="tabular"/>
diff -r ea832c221ec9 -r a9cb6fb9ea94 correct_barcodes.xml
--- a/correct_barcodes.xml	Fri Feb 24 03:18:01 2017 -0500
+++ b/correct_barcodes.xml	Thu Aug 24 02:13:33 2017 -0400
@@ -1,20 +1,27 @@
 <?xml version="1.0"?>
-<tool id="correct_barcodes" name="Du Novo: Correct barcodes" version="0.7">
+<tool id="correct_barcodes" name="Du Novo: Correct barcodes" version="0.7.6">
   <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="0.7.1">dunovo</requirement>
+    <requirement type="package" version="0.7.6">dunovo</requirement>
     <!-- TODO: require Python 2.7 -->
   </requirements>
-  <command detect_errors="exit_code">correct-barcodes.sh -d $dist -m $mapq -p $pos '$input' &gt; '$output'
+  <command detect_errors="exit_code"><![CDATA[
+    baralign.sh '$input' refdir barcodes.bam
+    && samtools view -f 256 barcodes.bam
+    | correct.py --galaxy $phone -d $dist -m $mapq -p $pos '$input' refdir/barcodes.fa
+    | sort
+    > '$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."/>
+    <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."/>
   </inputs>
   <outputs>
     <data name="output" format="tabular"/>
diff -r ea832c221ec9 -r a9cb6fb9ea94 dunovo.xml
--- a/dunovo.xml	Fri Feb 24 03:18:01 2017 -0500
+++ b/dunovo.xml	Thu Aug 24 02:13:33 2017 -0400
@@ -1,14 +1,21 @@
 <?xml version="1.0"?>
-<tool id="dunovo" name="Du Novo: Make consensus reads" version="0.7">
+<tool id="dunovo" name="Du Novo: Make consensus reads" version="0.7.6">
   <description>from duplex sequencing alignments</description>
   <requirements>
-    <requirement type="package" version="0.7.1">dunovo</requirement>
+    <requirement type="package" version="0.7.6">dunovo</requirement>
     <!-- TODO: require Python 2.7 -->
   </requirements>
-  <command detect_errors="exit_code">dunovo.sh -r $min_reads -q $qual_thres -F $qual_format '$input' '$dcs1' '$dcs2'
+  <command detect_errors="exit_code"><![CDATA[
+    dunovo.py --galaxy $phone -r $min_reads -q $qual_thres -F $qual_format '$input'
     #if $keep_sscs:
-      '$sscs1' '$sscs2'
+      --sscs-file sscs.fa
     #end if
+    > duplex.fa
+    && outconv.py duplex.fa -1 '$dcs1' -2 '$dcs2'
+    #if $keep_sscs:
+      && outconv.py sscs.fa -1 '$sscs1' -2 '$sscs2'
+    #end if
+  ]]>
   </command>
   <inputs>
     <param name="input" type="data" format="tabular" label="Aligned input reads" />
@@ -19,6 +26,7 @@
       <option value="solexa">Solexa (PHRED 0 = &quot;@&quot;)</option>
     </param>
     <param name="keep_sscs" type="boolean" truevalue="true" falsevalue="" label="Output single-strand consensus sequences as well" />
+    <param name="phone" type="boolean" truevalue="--phone-home" falsevalue="" checked="False" label="Send anonymous usage data" help="Report helpful usage data to the developer, to better understand the use cases and performance of the tool. The only data which will be recorded is the name and version of the tool, the size of the input data, the time taken to process it, and the IP address of the machine running it. No parameters or filenames are sent."/>
   </inputs>
   <outputs>
     <data name="dcs1" format="fasta" label="$tool.name on $on_string (mate 1)"/>
diff -r ea832c221ec9 -r a9cb6fb9ea94 make_families.xml
--- a/make_families.xml	Fri Feb 24 03:18:01 2017 -0500
+++ b/make_families.xml	Thu Aug 24 02:13:33 2017 -0400
@@ -1,8 +1,8 @@
 <?xml version="1.0"?>
-<tool id="make_families" name="Du Novo: Make families" version="0.7">
+<tool id="make_families" name="Du Novo: Make families" version="0.7.6">
   <description>of duplex sequencing reads</description>
   <requirements>
-    <requirement type="package" version="0.7.1">dunovo</requirement>
+    <requirement type="package" version="0.7.6">dunovo</requirement>
   </requirements>
   <!-- TODO: Add dependency on coreutils to get paste? -->
   <command detect_errors="exit_code">make-families.sh -t $taglen -i $invariant '$fastq1' '$fastq2' &gt; '$output'
diff -r ea832c221ec9 -r a9cb6fb9ea94 tool_dependencies.xml
--- a/tool_dependencies.xml	Fri Feb 24 03:18:01 2017 -0500
+++ b/tool_dependencies.xml	Thu Aug 24 02:13:33 2017 -0400
@@ -12,10 +12,10 @@
   <package name="networkx" version="1.9">
     <repository changeset_revision="83df321ad85e" name="package_networkx_1_9" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" />
   </package>
-  <package name="dunovo" version="0.7.1">
+  <package name="dunovo" version="0.7.6">
     <install version="1.0">
       <actions>
-        <action sha256sum="c10c54bd2b33929bbd7c78b9d9d98818793f8da3d59bfe4ed7499587bfdef24d" type="download_by_url">https://github.com/galaxyproject/dunovo/archive/v0.7.1.tar.gz</action>
+        <action sha256sum="d184d192f7b7577826c240ee8f0488046b0b38e032325dcf9aa3f6c730f8ea0d" type="download_by_url">https://github.com/galaxyproject/dunovo/archive/v0.7.6.tar.gz</action>
         <action type="shell_command">make</action>
         <action type="move_directory_files">
           <source_directory>.</source_directory>
@@ -24,6 +24,8 @@
         <action type="set_environment">
           <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR</environment_variable>
         </action>
+        <!-- Note: This does not install the submodules.
+        Functionality they provide will not be available. -->
       </actions>
     </install>
   </package>