Mercurial > repos > iuc > homer_annotatepeaks
diff test-data/generate_tests.sh @ 2:35dc2f57d755 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit 186b72f369eb2a11d92f4d63cac2e8ebe386b9bd"
| author | iuc |
|---|---|
| date | Mon, 13 Dec 2021 15:16:02 +0000 |
| parents | adab852c8216 |
| children |
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--- a/test-data/generate_tests.sh Sun Sep 26 12:30:02 2021 +0000 +++ b/test-data/generate_tests.sh Mon Dec 13 15:16:02 2021 +0000 @@ -11,10 +11,10 @@ wget https://raw.githubusercontent.com/lldelisle/scriptsForWilleminEtAl2021/main/CTCF/E12_Limbs_Wt_CTCF_colored.bed -O test-data/CTCF_peaks.bed fi if [ ! -e test-data/CTCF_peaks_shifted.bed ]; then - cat test-data/CTCF_peaks.bed | grep "chr2" | awk -v OFS="\t" '{$1="mm10_dna"; $2-=73740000; $3-=73740000; print}' > test-data/CTCF_peaks_shifted.bed + cat test-data/CTCF_peaks.bed | grep "chr2" | awk -v OFS="\t" '$3<75000000 && $2>73740000{$1="mm10_dna"; $2-=73740000; $3-=73740000; print}' > test-data/CTCF_peaks_shifted.bed fi # chr2_subset.fa was downloaded from UCSC -# https://genome.ucsc.edu/cgi-bin/hgc?hgsid=1136019667_XgAJOvV4a3CY4ibCu6RrUcvGxLNo&g=htcGetDna2&table=&i=mixed&o=56694975&l=56694975&r=56714605&getDnaPos=chr2%3A73740000-75787000&db=mm10&hgSeq.cdsExon=1&hgSeq.padding5=0&hgSeq.padding3=0&hgSeq.casing=upper&hgSeq.maskRepeats=on&boolshad.hgSeq.maskRepeats=0&hgSeq.repMasking=lower&boolshad.hgSeq.revComp=0&submit=get+DNA +# https://genome.ucsc.edu/cgi-bin/hgc?hgsid=1234982067_JnS4z30UVCNarTg26Ztd1Oh6nfu6&g=htcGetDna2&table=&i=mixed&o=56694975&l=56694975&r=56714605&getDnaPos=chr2%3A73740000-75000000&db=mm10&hgSeq.cdsExon=1&hgSeq.padding5=0&hgSeq.padding3=0&hgSeq.casing=upper&hgSeq.maskRepeats=on&boolshad.hgSeq.maskRepeats=0&hgSeq.repMasking=lower&boolshad.hgSeq.revComp=0&submit=get+DNA . <(planemo conda_env homer_gtf_to_annotation.xml) echo "$(which homer)" @@ -50,6 +50,7 @@ findMotifsGenome.pl test-data/fake_phix_peaks.bed test-data/phiX174.fasta fake_phix_peaks_bed_motif mv fake_phix_peaks_bed_motif test-data/motif_test1 # Thus I needed to use has_text for the other outputs +# gunzip -c test-data/chr2_subset.fa.gz > test-data/chr2_subset.fa # findMotifsGenome.pl test-data/CTCF_peaks_shifted.bed test-data/chr2_subset.fa CTCF_peaks_shifted_bed_motif # mv CTCF_peaks_shifted_bed_motif test-data/motif_test2 # findMotifsGenome.pl test-data/CTCF_peaks_shifted.bed test-data/chr2_subset.fa CTCF_peaks_shifted_bed_motif -mask