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changeset 5:000969829a5d draft

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correct.py wrapper fix
author nick
date Fri, 27 Oct 2017 12:50:39 -0400
parents 5fbeaa41b223
children 23f5d9316694
files align_families.xml correct_barcodes.xml dunovo.xml make_families.xml
diffstat 4 files changed, 10 insertions(+), 5 deletions(-) [+]
line wrap: on
line diff
--- a/align_families.xml	Wed Oct 25 19:26:43 2017 -0400
+++ b/align_families.xml	Fri Oct 27 12:50:39 2017 -0400
@@ -6,6 +6,7 @@
     <requirement type="package" version="2.0.6">dunovo</requirement>
     <!-- TODO: require Python 2.7 -->
   </requirements>
+  <version_command>align_families.py --version</version_command>
   <command detect_errors="exit_code">align_families.py --aligner $aligner --galaxy $phone --processes \${GALAXY_SLOTS:-1} '$input' &gt; '$output'
   </command>
   <inputs>
--- a/correct_barcodes.xml	Wed Oct 25 19:26:43 2017 -0400
+++ b/correct_barcodes.xml	Fri Oct 27 12:50:39 2017 -0400
@@ -1,5 +1,5 @@
 <?xml version="1.0"?>
-<tool id="correct_barcodes" name="Du Novo: Correct barcodes" version="2.0.6">
+<tool id="correct_barcodes" name="Du Novo: Correct barcodes" version="2.0.6.1">
   <description>of duplex sequencing reads</description>
   <requirements>
     <requirement type="package" version="2.2.5">bowtie2</requirement>
@@ -8,12 +8,14 @@
     <requirement type="package" version="2.0.6">dunovo</requirement>
     <!-- TODO: require Python 2.7 -->
   </requirements>
+  <version_command>correct.py --version</version_command>
   <command detect_errors="exit_code"><![CDATA[
-    baralign.sh '$input' refdir
-    | samtools view -S -f 256 -
+    baralign.sh '$input' refdir correct.sam
+    && samtools view -S -f 256 correct.sam
     | correct.py --galaxy $phone --dist $dist --mapq $mapq --pos $pos '$input' refdir/barcodes.fa
-    | sort
-    > '$output'
+      > families.corrected.tsv
+    && sort families.corrected.tsv
+      > '$output'
   ]]>
   </command>
   <inputs>
--- a/dunovo.xml	Wed Oct 25 19:26:43 2017 -0400
+++ b/dunovo.xml	Fri Oct 27 12:50:39 2017 -0400
@@ -5,6 +5,7 @@
     <requirement type="package" version="2.0.6">dunovo</requirement>
     <!-- TODO: require Python 2.7 -->
   </requirements>
+  <version_command>dunovo.py --version</version_command>
   <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:
--- a/make_families.xml	Wed Oct 25 19:26:43 2017 -0400
+++ b/make_families.xml	Fri Oct 27 12:50:39 2017 -0400
@@ -5,6 +5,7 @@
     <requirement type="package" version="2.0.6">dunovo</requirement>
   </requirements>
   <!-- TODO: Add dependency on coreutils to get paste? -->
+  <version_command>dunovo.py --version</version_command>
   <command detect_errors="exit_code">make-families.sh -t $taglen -i $invariant '$fastq1' '$fastq2' &gt; '$output'
   </command>
   <inputs>