# HG changeset patch
# User nick
# Date 1487409019 18000
# Node ID f33b89fe9f82a0b08d9979f155f4e240dbc195e3
# Parent  a2dc1e1c10dbb3eed6f95246ef73873033a31a00
planemo upload for repository https://github.com/galaxyproject/dunovo commit b'e513259f9701a68e53baddaeedfa51406df857bf\n'-dirty

diff -r a2dc1e1c10db -r f33b89fe9f82 align_families.xml
--- a/align_families.xml	Mon Feb 06 23:34:30 2017 -0500
+++ b/align_families.xml	Sat Feb 18 04:10:19 2017 -0500
@@ -3,11 +3,10 @@
   <description>of duplex sequencing reads</description>
   <requirements>
     <requirement type="package" version="7.221">mafft</requirement>
-    <requirement type="package" version="0.6">duplex</requirement>
-    <requirement type="set_environment">DUPLEX_DIR</requirement>
+    <requirement type="package" version="0.6.1">duplex</requirement>
     <!-- TODO: require Python 2.7 -->
   </requirements>
-  <command detect_errors="exit_code">python "\$DUPLEX_DIR/align_families.py" -p \${GALAXY_SLOTS:-1} '$input' &gt; '$output'
+  <command detect_errors="exit_code">align_families.py -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"/>
diff -r a2dc1e1c10db -r f33b89fe9f82 correct_barcodes.xml
--- a/correct_barcodes.xml	Mon Feb 06 23:34:30 2017 -0500
+++ b/correct_barcodes.xml	Sat Feb 18 04:10:19 2017 -0500
@@ -5,14 +5,10 @@
     <requirement type="package" version="2.1.0">bowtie2</requirement>
     <requirement type="package" version="0.1.18">samtools</requirement>
     <requirement type="package" version="1.9">networkx</requirement>
-    <requirement type="package" version="0.6">duplex</requirement>
-    <requirement type="set_environment">DUPLEX_DIR</requirement>
+    <requirement type="package" version="0.6.1">duplex</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 detect_errors="exit_code">correct-barcodes.sh -d $dist -m $mapq -p $pos '$input' &gt; '$output'
   </command>
   <inputs>
     <param name="input" type="data" format="tabular" label="Input reads" help="with barcodes, grouped by family"/>
diff -r a2dc1e1c10db -r f33b89fe9f82 dunovo.xml
--- a/dunovo.xml	Mon Feb 06 23:34:30 2017 -0500
+++ b/dunovo.xml	Sat Feb 18 04:10:19 2017 -0500
@@ -2,21 +2,13 @@
 <tool id="duplex" name="Du Novo: Make consensus reads" version="0.6">
   <description>from duplex sequencing alignments</description>
   <requirements>
-    <requirement type="package" version="0.6">duplex</requirement>
-    <requirement type="set_environment">DUPLEX_DIR</requirement>
+    <requirement type="package" version="0.6.1">duplex</requirement>
     <!-- TODO: require Python 2.7 -->
   </requirements>
-  <command detect_errors="exit_code"><![CDATA[
-    python "\$DUPLEX_DIR/dunovo.py" -r $min_reads -q $qual_thres -F $qual_format '$input'
+  <command detect_errors="exit_code">dunovo.sh -r $min_reads -q $qual_thres -F $qual_format '$input' '$dcs1' '$dcs2'
     #if $keep_sscs:
-      --sscs-file sscs.fa
+      '$sscs1' '$sscs2'
     #end if
-    > duplex.fa
-    && python "\$DUPLEX_DIR/utils/outconv.py" duplex.fa -1 '$dcs1' -2 '$dcs2'
-    #if $keep_sscs:
-      && python "\$DUPLEX_DIR/utils/outconv.py" sscs.fa -1 '$sscs1' -2 '$sscs2'
-    #end if
-  ]]>
   </command>
   <inputs>
     <param name="input" type="data" format="tabular" label="Aligned input reads" />
diff -r a2dc1e1c10db -r f33b89fe9f82 make_families.xml
--- a/make_families.xml	Mon Feb 06 23:34:30 2017 -0500
+++ b/make_families.xml	Sat Feb 18 04:10:19 2017 -0500
@@ -2,15 +2,10 @@
 <tool id="make_families" name="Du Novo: Make families" version="0.6">
   <description>of duplex sequencing reads</description>
   <requirements>
-    <requirement type="package" version="0.6">duplex</requirement>
-    <requirement type="set_environment">DUPLEX_DIR</requirement>
+    <requirement type="package" version="0.6.1">duplex</requirement>
   </requirements>
   <!-- TODO: Add dependency on coreutils to get paste? -->
-  <command>paste '$fastq1' '$fastq2'
-    | paste - - - -
-    | awk -f "\$DUPLEX_DIR/make-barcodes.awk" -v TAG_LEN=$taglen -v INVARIANT=$invariant
-    | sort
-    &gt; '$output'
+  <command detect_errors="exit_code">make-families.sh -v TAG_LEN=$taglen -v INVARIANT=$invariant '$fastq1' '$fastq2' &gt; '$output'
   </command>
   <inputs>
     <param name="fastq1" type="data" format="fastq" label="Sequencing reads, mate 1"/>
diff -r a2dc1e1c10db -r f33b89fe9f82 tool_dependencies.xml
--- a/tool_dependencies.xml	Mon Feb 06 23:34:30 2017 -0500
+++ b/tool_dependencies.xml	Sat Feb 18 04:10:19 2017 -0500
@@ -12,17 +12,16 @@
   <package name="networkx" version="1.9">
     <repository changeset_revision="2ca57555a756" name="package_networkx_1_9" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" />
   </package>
-  <package name="duplex" version="0.6">
+  <package name="duplex" version="0.6.1">
     <install version="1.0">
       <actions>
-        <action sha256sum="a3cc378c22fcfc3bcaa11129f27f61bab5ff51cc9185320d53ece273b56e6214" type="download_by_url">https://github.com/galaxyproject/dunovo/archive/v0.6.tar.gz</action>
+        <action sha256sum="f4ee6ef4db6b97bd96bcfb79b18b2ed87b933c8bbbc26073390597da84683ee0" type="download_by_url">https://github.com/galaxyproject/dunovo/archive/v0.6.1.tar.gz</action>
         <action type="shell_command">make</action>
         <action type="move_directory_files">
           <source_directory>.</source_directory>
           <destination_directory>$INSTALL_DIR</destination_directory>
         </action>
         <action type="set_environment">
-          <environment_variable action="set_to" name="DUPLEX_DIR">$INSTALL_DIR</environment_variable>
           <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR</environment_variable>
         </action>
       </actions>