Mercurial > repos > rnateam > peakachu
changeset 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 |
| files | peakachu.xml test-data/test1_+xl.bam test-data/test1_-xl.bam test-data/test1_minus-xl.bam test-data/test1_plus-xl.bam |
| diffstat | 5 files changed, 5 insertions(+), 4 deletions(-) [+] |
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--- 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>