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changeset 5:4bc49a5769ee draft

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Version 0.5: Split interleaved SSCS output file into two paired files.
author nick
date Thu, 01 Dec 2016 23:22:52 -0500
parents 7f513b9b1b1e
children 9a0bee12b583
files align_families.xml dunovo.xml make_families.xml tool_dependencies.xml
diffstat 4 files changed, 23 insertions(+), 18 deletions(-) [+]
line wrap: on
line diff
--- a/align_families.xml	Mon Dec 21 14:47:48 2015 -0500
+++ b/align_families.xml	Thu Dec 01 23:22:52 2016 -0500
@@ -1,9 +1,9 @@
 <?xml version="1.0"?>
-<tool id="align_families" name="Du Novo: Align families" version="0.3">
+<tool id="align_families" name="Du Novo: Align families" version="0.5">
   <description>of duplex sequencing reads</description>
   <requirements>
     <requirement type="package" version="7.221">mafft</requirement>
-    <requirement type="package" version="0.3">duplex</requirement>
+    <requirement type="package" version="0.5">duplex</requirement>
     <requirement type="set_environment">DUPLEX_DIR</requirement>
     <!-- TODO: require Python 2.7 -->
   </requirements>
--- a/dunovo.xml	Mon Dec 21 14:47:48 2015 -0500
+++ b/dunovo.xml	Thu Dec 01 23:22:52 2016 -0500
@@ -1,19 +1,21 @@
 <?xml version="1.0"?>
-<tool id="duplex" name="Du Novo: Make consensus reads" version="0.3">
+<tool id="duplex" name="Du Novo: Make consensus reads" version="0.5">
   <description>from duplex sequencing alignments</description>
   <requirements>
-    <requirement type="package" version="0.3">duplex</requirement>
+    <requirement type="package" version="0.5">duplex</requirement>
     <requirement type="set_environment">DUPLEX_DIR</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
     #if $keep_sscs:
-      --sscs-file $sscs
+      --sscs-file sscs.fa
     #end if
     > duplex.fa
-    && awk -f \$DUPLEX_DIR/utils/outconv.awk -v target=1 duplex.fa > $output1
-    && awk -f \$DUPLEX_DIR/utils/outconv.awk -v target=2 duplex.fa > $output2
+    && 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 $sscs2
+    #end if
   ]]>
   </command>
   <inputs>
@@ -24,20 +26,23 @@
       <option value="sanger" selected="true">Sanger (PHRED 0 = &quot;!&quot;)</option>
       <option value="solexa">Solexa (PHRED 0 = &quot;@&quot;)</option>
     </param>
-    <param name="keep_sscs" type="boolean" truevalue="true" falsevalue="" label="Output single-strand consensus sequences" />
+    <param name="keep_sscs" type="boolean" truevalue="true" falsevalue="" label="Output single-strand consensus sequences as well" />
   </inputs>
   <outputs>
-    <data name="output1" format="fasta" label="$tool.name on $on_string (mate 1)"/>
-    <data name="output2" format="fasta" label="$tool.name on $on_string (mate 2)"/>
-    <data name="sscs" format="fasta" label="$tool.name on $on_string (SSCS)">
+    <data name="dcs1" format="fasta" label="$tool.name on $on_string (mate 1)"/>
+    <data name="dcs2" format="fasta" label="$tool.name on $on_string (mate 2)"/>
+    <data name="sscs1" format="fasta" label="$tool.name on $on_string (SSCS mate 1)">
+      <filter>keep_sscs</filter>
+    </data>
+    <data name="sscs2" format="fasta" label="$tool.name on $on_string (SSCS mate 2)">
       <filter>keep_sscs</filter>
     </data>
   </outputs>
   <tests>
     <test>
       <param name="input" value="families.msa.tsv"/>
-      <output name="output1" file="families.cons_1.fa"/>
-      <output name="output2" file="families.cons_2.fa"/>
+      <output name="dcs1" file="families.cons_1.fa"/>
+      <output name="dcs2" file="families.cons_2.fa"/>
     </test>
   </tests>
   <help>
--- a/make_families.xml	Mon Dec 21 14:47:48 2015 -0500
+++ b/make_families.xml	Thu Dec 01 23:22:52 2016 -0500
@@ -1,8 +1,8 @@
 <?xml version="1.0"?>
-<tool id="make_families" name="Du Novo: Make families" version="0.3">
+<tool id="make_families" name="Du Novo: Make families" version="0.5">
   <description>of duplex sequencing reads</description>
   <requirements>
-    <requirement type="package" version="0.3">duplex</requirement>
+    <requirement type="package" version="0.5">duplex</requirement>
     <requirement type="set_environment">DUPLEX_DIR</requirement>
   </requirements>
   <!-- TODO: Add dependency on coreutils to get paste? -->
--- a/tool_dependencies.xml	Mon Dec 21 14:47:48 2015 -0500
+++ b/tool_dependencies.xml	Thu Dec 01 23:22:52 2016 -0500
@@ -1,12 +1,12 @@
 <?xml version="1.0"?>
 <tool_dependency>
   <package name="mafft" version="7.221">
-    <repository changeset_revision="d71e007323d4" name="mafft" owner="rnateam" toolshed="https://toolshed.g2.bx.psu.edu" />
+    <repository changeset_revision="15974dd17515" name="mafft" owner="rnateam" toolshed="https://toolshed.g2.bx.psu.edu" />
   </package>
-  <package name="duplex" version="0.3">
+  <package name="duplex" version="0.5">
     <install version="1.0">
       <actions>
-        <action type="download_by_url">https://github.com/makrutenko/dunovo/archive/v0.3.tar.gz</action>
+        <action type="download_by_url">https://github.com/galaxyproject/dunovo/archive/v0.5.tar.gz</action>
         <action type="shell_command">make</action>
         <action type="move_directory_files">
           <source_directory>.</source_directory>