# HG changeset patch
# User rnateam
# Date 1547679230 18000
# Node ID 26304ccaca5726e5f6027cbe8a38aea66cdc1bd5
# Parent  09c51ff142a2fd05170869d512bd7a5c91542010
planemo upload for repository https://github.com/tbischler/PEAKachu commit c5d9e7d26c36c03b485d1a29154018bc9b0fa069

diff -r 09c51ff142a2 -r 26304ccaca57 peakachu.xml
--- a/peakachu.xml	Tue May 22 11:43:54 2018 -0400
+++ b/peakachu.xml	Wed Jan 16 17:53:50 2019 -0500
@@ -1,7 +1,8 @@
-<tool id="peakachu" name="PEAKachu" version="0.1.0.1">
+<tool id="peakachu" name="PEAKachu" version="0.1.0.2">
     <description>Calls Peaks in CLIP data</description>
     <requirements>
         <requirement type="package" version="3.6">python</requirement>
+        <requirement type="package" version="3.4.1">r-base</requirement>
         <requirement type="package" version="0.1.0">peakachu</requirement>
     </requirements>
     <version_command>
@@ -67,7 +68,7 @@
         &&
         if ls ./tmp_output/peak_tables/*.csv > /dev/null;
         then 
-            head -n 1 -q ./tmp_output/peak_tables/*.csv | head -n 1 > peaks.tsv &&
+            cat ./tmp_output/peak_tables/*.csv | head -n 1 > peaks.tsv &&
             tail -n +2 -q ./tmp_output/peak_tables/*.csv >> peaks.tsv &&
             mv peaks.tsv '$peak_tables' &&
             cat ./tmp_output/peak_annotations/*.gff | awk '/peak/ {print $0}' > peak_annotations.gff &&
@@ -170,8 +171,8 @@
     </outputs>
     <tests>
         <test>
-            <param name="experimentLibs" value="test1_+xl.bam"/>
-            <param name="controlLibs" value="test1_-xl.bam"/>
+            <param name="experimentLibs" value="test1_plus-xl.bam"/>
+            <param name="controlLibs" value="test1_minus-xl.bam"/>
             <output name="peak_tables" ftype="tabular" file="test1_peaks.tsv"/>
             <output name="peak_annotations" ftype="gff" file="test1_peak_annotations.gff"/>
         </test>
diff -r 09c51ff142a2 -r 26304ccaca57 test-data/test1_+xl.bam
Binary file test-data/test1_+xl.bam has changed
diff -r 09c51ff142a2 -r 26304ccaca57 test-data/test1_-xl.bam
Binary file test-data/test1_-xl.bam has changed
diff -r 09c51ff142a2 -r 26304ccaca57 test-data/test1_minus-xl.bam
Binary file test-data/test1_minus-xl.bam has changed
diff -r 09c51ff142a2 -r 26304ccaca57 test-data/test1_plus-xl.bam
Binary file test-data/test1_plus-xl.bam has changed