| Previous changeset 0:bc594df2aba3 (2018-02-15) Next changeset 2:49a5a2e86c84 (2019-01-16) |
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Commit message:
planemo upload for repository https://github.com/tbischler/PEAKachu commit 172dab2fc73fcce3ae7df19286b48848af9033d2-dirty |
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modified:
peakachu.xml |
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added:
test-data/test1_peak_annotations.gff |
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| diff -r bc594df2aba3 -r 68656d100a7f peakachu.xml --- a/peakachu.xml Thu Feb 15 15:59:41 2018 -0500 +++ b/peakachu.xml Tue May 22 11:47:18 2018 -0400 |
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| @@ -1,4 +1,4 @@ -<tool id="peakachu" name="PEAKachu" version="0.1.0.0"> +<tool id="peakachu" name="PEAKachu" version="0.1.0.1"> <description>Calls Peaks in CLIP data</description> <requirements> <requirement type="package" version="3.6">python</requirement> @@ -65,10 +65,18 @@ --padj_threshold $padj_threshold && - head -n 1 -q ./tmp_output/peak_tables/*.csv | head -n 1 > peaks.tsv && - tail -n +2 -q ./tmp_output/peak_tables/*.csv >> peaks.tsv && - mv peaks.tsv '$peak_tables' && - mv ./tmp_output/plots/Initial*.png '$MA_plot' + if ls ./tmp_output/peak_tables/*.csv > /dev/null; + then + head -n 1 -q ./tmp_output/peak_tables/*.csv | head -n 1 > peaks.tsv && + tail -n +2 -q ./tmp_output/peak_tables/*.csv >> peaks.tsv && + mv peaks.tsv '$peak_tables' && + cat ./tmp_output/peak_annotations/*.gff | awk '/peak/ {print $0}' > peak_annotations.gff && + mv peak_annotations.gff '$peak_annotations' && + mv ./tmp_output/plots/Initial*.png '$MA_plot'; + else + echo "No Peaks Found" >&2; + fi + ]]> </command> @@ -157,6 +165,7 @@ </inputs> <outputs> <data format="tabular" name="peak_tables" label="${tool.name} ${mode.mode_selector} on ${on_string}: peaks"/> + <data format="gff" name="peak_annotations" label="${tool.name} ${mode.mode_selector} on ${on_string}: peak_annotations"/> <data format="png" name="MA_plot" label="${tool.name} ${mode.mode_selector} on ${on_string}: MA plot"/> </outputs> <tests> @@ -164,7 +173,7 @@ <param name="experimentLibs" value="test1_+xl.bam"/> <param name="controlLibs" value="test1_-xl.bam"/> <output name="peak_tables" ftype="tabular" file="test1_peaks.tsv"/> - <output name="MA_plot" ftype="png" file="test1_MA.png"/> + <output name="peak_annotations" ftype="gff" file="test1_peak_annotations.gff"/> </test> </tests> <help> |
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| diff -r bc594df2aba3 -r 68656d100a7f test-data/test1_peak_annotations.gff --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test1_peak_annotations.gff Tue May 22 11:47:18 2018 -0400 |
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| @@ -0,0 +1,2 @@ +NC_016810.1 PEAKachu peak_region 514559 514582 . - . ID=NC_016810.1:peak_1 +NC_016810.1 PEAKachu peak_region 514559 514584 . + . ID=NC_016810.1:peak_2 |