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changeset 3:00dde366870a draft

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planemo upload for repository https://github.com/galaxyproject/dunovo commit b'a3ad9fbb3f010253808fc0c7329897a741ec9feb\n'
author nick
date Mon, 11 Sep 2017 16:59:44 -0400
parents a9cb6fb9ea94
children 5fbeaa41b223
files align_families.xml correct_barcodes.xml dunovo.xml make_families.xml tool_dependencies.xml
diffstat 5 files changed, 19 insertions(+), 23 deletions(-) [+]
line wrap: on
line diff
--- a/align_families.xml	Thu Aug 24 02:13:33 2017 -0400
+++ b/align_families.xml	Mon Sep 11 16:59:44 2017 -0400
@@ -1,12 +1,12 @@
 <?xml version="1.0"?>
-<tool id="align_families" name="Du Novo: Align families" version="0.7.6">
+<tool id="align_families" name="Du Novo: Align families" version="0.8.1">
   <description>of duplex sequencing reads</description>
   <requirements>
     <requirement type="package" version="7.221">mafft</requirement>
-    <requirement type="package" version="0.7.6">dunovo</requirement>
+    <requirement type="package" version="0.8.1">dunovo</requirement>
     <!-- TODO: require Python 2.7 -->
   </requirements>
-  <command detect_errors="exit_code">align_families.py --galaxy $phone -p \${GALAXY_SLOTS:-1} '$input' &gt; '$output'
+  <command detect_errors="exit_code">align_families.py --galaxy $phone --processes \${GALAXY_SLOTS:-1} '$input' &gt; '$output'
   </command>
   <inputs>
     <param name="input" type="data" format="tabular" label="Input reads" help="with barcodes, grouped by family"/>
--- a/correct_barcodes.xml	Thu Aug 24 02:13:33 2017 -0400
+++ b/correct_barcodes.xml	Mon Sep 11 16:59:44 2017 -0400
@@ -1,17 +1,17 @@
 <?xml version="1.0"?>
-<tool id="correct_barcodes" name="Du Novo: Correct barcodes" version="0.7.6">
+<tool id="correct_barcodes" name="Du Novo: Correct barcodes" version="0.8.1">
   <description>of duplex sequencing reads</description>
   <requirements>
     <requirement type="package" version="2.2.5">bowtie2</requirement>
     <requirement type="package" version="0.1.18">samtools</requirement>
     <requirement type="package" version="1.9">networkx</requirement>
-    <requirement type="package" version="0.7.6">dunovo</requirement>
+    <requirement type="package" version="0.8.1">dunovo</requirement>
     <!-- TODO: require Python 2.7 -->
   </requirements>
   <command detect_errors="exit_code"><![CDATA[
     baralign.sh '$input' refdir barcodes.bam
     && samtools view -f 256 barcodes.bam
-    | correct.py --galaxy $phone -d $dist -m $mapq -p $pos '$input' refdir/barcodes.fa
+    | correct.py --galaxy $phone --dist $dist --mapq $mapq --pos $pos '$input' refdir/barcodes.fa
     | sort
     > '$output'
   ]]>
--- a/dunovo.xml	Thu Aug 24 02:13:33 2017 -0400
+++ b/dunovo.xml	Mon Sep 11 16:59:44 2017 -0400
@@ -1,25 +1,21 @@
 <?xml version="1.0"?>
-<tool id="dunovo" name="Du Novo: Make consensus reads" version="0.7.6">
+<tool id="dunovo" name="Du Novo: Make consensus reads" version="0.8.1">
   <description>from duplex sequencing alignments</description>
   <requirements>
-    <requirement type="package" version="0.7.6">dunovo</requirement>
+    <requirement type="package" version="0.8.1">dunovo</requirement>
     <!-- TODO: require Python 2.7 -->
   </requirements>
-  <command detect_errors="exit_code"><![CDATA[
-    dunovo.py --galaxy $phone -r $min_reads -q $qual_thres -F $qual_format '$input'
+  <command detect_errors="exit_code">
+    dunovo.py --galaxy $phone --processes \${GALAXY_SLOTS:-1} --min-reads $min_reads --qual $qual_thres --qual-format $qual_format --cons-thres $cons_thres --min-cons-reads $min_cons_reads '$input' --dcs1 '$dcs1' --dcs2 '$dcs2'
     #if $keep_sscs:
-      --sscs-file sscs.fa
+      --sscs1 '$sscs1' --sscs2 '$sscs2'
     #end if
-    > duplex.fa
-    && outconv.py duplex.fa -1 '$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" />
     <param name="min_reads" type="integer" value="3" min="1" label="Minimum reads per family" help="Single-strand families with fewer than this many reads will be skipped."/>
+    <param name="cons_thres" type="float" value="0.5" min="0.5" max="1.0" label="The threshold to use when making consensus sequences. The consensus base must be present in more than this fraction of the reads, or &quot;N&quot; will be used."/>
+    <param name="min_cons_reads" type="integer" value="0" min="0" label="The minimum number of reads a base must appear in to be used as the consensus base. If no base at the position appears in at least this many reads, &quot;N&quot; will be used."/>
     <param name="qual_thres" type="integer" value="25" min="1" label="Minimum base quality" help="Bases with a PHRED score less than this will not be counted in the consensus making."/>
     <param name="qual_format" type="select" label="FASTQ format" help="Solexa should also work for Illumina 1.3+ and 1.5+, and Sanger should work for Illumina 1.8+">
       <option value="sanger" selected="true">Sanger (PHRED 0 = &quot;!&quot;)</option>
@@ -41,8 +37,8 @@
   <tests>
     <test>
       <param name="input" value="families.msa.tsv"/>
-      <output name="dcs1" file="families.cons_1.fa"/>
-      <output name="dcs2" file="families.cons_2.fa"/>
+      <output name="dcs1" file="families.dcs_1.fa"/>
+      <output name="dcs2" file="families.dcs_2.fa"/>
     </test>
   </tests>
   <citations>
--- a/make_families.xml	Thu Aug 24 02:13:33 2017 -0400
+++ b/make_families.xml	Mon Sep 11 16:59:44 2017 -0400
@@ -1,8 +1,8 @@
 <?xml version="1.0"?>
-<tool id="make_families" name="Du Novo: Make families" version="0.7.6">
+<tool id="make_families" name="Du Novo: Make families" version="0.8.1">
   <description>of duplex sequencing reads</description>
   <requirements>
-    <requirement type="package" version="0.7.6">dunovo</requirement>
+    <requirement type="package" version="0.8.1">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	Thu Aug 24 02:13:33 2017 -0400
+++ b/tool_dependencies.xml	Mon Sep 11 16:59:44 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="0.7.6">
+  <package name="dunovo" version="0.8.1">
     <install version="1.0">
       <actions>
-        <action sha256sum="d184d192f7b7577826c240ee8f0488046b0b38e032325dcf9aa3f6c730f8ea0d" type="download_by_url">https://github.com/galaxyproject/dunovo/archive/v0.7.6.tar.gz</action>
+        <action sha256sum="f85fd35ef67c8f76af0d556a4babe9acf7b8abdd8a77232d4f4763cc7de60eed" type="download_by_url">https://github.com/galaxyproject/dunovo/archive/v0.8.1.tar.gz</action>
         <action type="shell_command">make</action>
         <action type="move_directory_files">
           <source_directory>.</source_directory>