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changeset 2:a9cb6fb9ea94 draft

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Update to Du Novo 0.7.6.
author nick
date Thu, 24 Aug 2017 02:13:33 -0400
parents ea832c221ec9
children 00dde366870a
files align_families.xml correct_barcodes.xml dunovo.xml make_families.xml tool_dependencies.xml
diffstat 5 files changed, 32 insertions(+), 14 deletions(-) [+]
line wrap: on
line diff
--- 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"/>
--- 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"/>
--- 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)"/>
--- 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'
--- 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>