diff peakachu.xml @ 2:49a5a2e86c84 draft

planemo upload for repository https://github.com/tbischler/PEAKachu commit c5d9e7d26c36c03b485d1a29154018bc9b0fa069
author rnateam
date Wed, 16 Jan 2019 17:52:56 -0500
parents 68656d100a7f
children 886f5adba83d
line wrap: on
line diff
--- a/peakachu.xml	Tue May 22 11:47:18 2018 -0400
+++ b/peakachu.xml	Wed Jan 16 17:52:56 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>