# HG changeset patch
# User iuc
# Date 1625902825 0
# Node ID 80adce82354c8857c7d5b918dcce860e45006f1f
# Parent  21f2361c32c93642cf201e78070975628daf451b
"planemo upload for repository https://github.com/arq5x/lumpy-sv commit 41cb10683d89fa20e122f4c60b8f5bf0e3c390d8"

diff -r 21f2361c32c9 -r 80adce82354c lumpy_preprocessing.xml
--- a/lumpy_preprocessing.xml	Thu Nov 12 16:48:34 2020 +0000
+++ b/lumpy_preprocessing.xml	Sat Jul 10 07:40:25 2021 +0000
@@ -1,4 +1,4 @@
-<tool id="lumpy_prep" name="LUMPY preprocessing" version="@WRAPPER_VERSION@">
+<tool id="lumpy_prep" name="LUMPY preprocessing" version="@WRAPPER_VERSION@" profile="20.05">
     <description>extracts discordant read pairs and split-read alignments from a BAM dataset</description>
     <macros>
         <import>macros.xml</import>
@@ -7,6 +7,8 @@
         <requirement type="package" version="@TOOL_VERSION@">lumpy-sv</requirement>
     </requirements>
     <command detect_errors="exit_code"><![CDATA[
+set -o pipefail;
+
 samtools collate -O --output-fmt sam '$bam_in' | samblaster $dup_handling --addMateTags | samtools view -bS - > blasted.bam &&
 
 samtools view -b -F 1294 blasted.bam > discordants.unsorted.bam &&
@@ -34,9 +36,9 @@
         <test>
             <param name="bam_in" ftype="bam" value="sample.bam" />
             <param name="dup_handling" value="" />
-            <output name="blasted_bam" ftype="qname_sorted.bam" file="blasted.bam" />
-            <output name="discordants_bam" ftype="bam" file="discordants.bam" />
-            <output name="splitters_bam" ftype="bam" file="splitters.bam" />
+            <output name="blasted_bam" ftype="qname_sorted.bam" file="blasted.bam" lines_diff="2"/>
+            <output name="discordants_bam" ftype="bam" file="discordants.bam" lines_diff="2"/>
+            <output name="splitters_bam" ftype="bam" file="splitters.bam" lines_diff="2"/>
         </test>
     </tests>
     <help><![CDATA[
diff -r 21f2361c32c9 -r 80adce82354c macros.xml
--- a/macros.xml	Thu Nov 12 16:48:34 2020 +0000
+++ b/macros.xml	Sat Jul 10 07:40:25 2021 +0000
@@ -1,5 +1,5 @@
 <macros>
-    <token name="@WRAPPER_VERSION@">@TOOL_VERSION@+galaxy0</token>
+    <token name="@WRAPPER_VERSION@">@TOOL_VERSION@+galaxy1</token>
     <token name="@TOOL_VERSION@">0.3.1</token>
     <xml name="citations">
         <citations>