--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/generate_tests.sh	Sun Aug 08 11:04:17 2021 +0000
@@ -0,0 +1,59 @@
+#! /usr/bin/bash
+## Generate input data:
+if [ ! -e test-data/small_simplified.gtf ]; then
+  wget http://ftp.ensembl.org/pub/release-102/gtf/mus_musculus/Mus_musculus.GRCm38.102.gtf.gz -O /tmp/Mus_musculus.GRCm38.102.gtf.gz
+  zcat /tmp/Mus_musculus.GRCm38.102.gtf.gz | head -n 5 > test-data/small.gtf
+  zcat /tmp/Mus_musculus.GRCm38.102.gtf.gz | awk -v OFS="\t" -v start=74667792 -v end=74748393 '$1 == "2" && $5 > start && $4 < end{print "chr"$0}' >> test-data/small.gtf
+  # annotatePeaks.pl gives different results all time. I need to simplify the gtf.
+  cat test-data/small.gtf | grep -v -P "ENSMUST00000152027|ENSMUST00000156342|ENSMUST00000139005|ENSMUST00000144544|ENSMUST00000111982|ENSMUST00000140666|ENSMUST00000190553|ENSMUST00000132326|ENSMUST00000047830|ENSMUST00000047904|ENSMUST00000111980|ENSMUSG00000065500|ENSMUSG00000100642" > test-data/small_simplified.gtf
+fi
+if [ ! -e test-data/CTCF_peaks.bed ]; then
+  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; $3-=73740000; print}' > test-data/CTCF_peaks_shifted.bed
+fi
+# chr2_subset.fa was downloaded from UCSC
+# https://genome.ucsc.edu/cgi-bin/hgc?hgsid=1136019667_XgAJOvV4a3CY4ibCu6RrUcvGxLNo&g=htcGetDna2&table=&i=mixed&o=56694975&l=56694975&r=56714605&getDnaPos=chr2%3A73740000-75787000&db=mm10&hgSeq.cdsExon=1&hgSeq.padding5=0&hgSeq.padding3=0&hgSeq.casing=upper&hgSeq.maskRepeats=on&boolshad.hgSeq.maskRepeats=0&hgSeq.repMasking=lower&boolshad.hgSeq.revComp=0&submit=get+DNA
+
+. <(planemo conda_env homer_gtf_to_annotation.xml)
+echo "$(which homer)"
+## homer_gtf_to_annotation
+## First test
+parseGTF.pl test-data/small.gtf ann -features exon start_codon stop_codon > /tmp/annotations.txt
+assignGenomeAnnotation /tmp/annotations.txt /tmp/annotations.txt -prioritize test-data/annotations_default.txt > test-data/annotations_default_stats.txt
+## Second test
+parseGTF.pl test-data/small.gtf ann -features exon start_codon > /tmp/annotations2.txt
+assignGenomeAnnotation /tmp/annotations2.txt /tmp/annotations2.txt -prioritize test-data/annotations_exon_start.txt > test-data/annotations_exon_start_stats.txt
+## Third test
+parseGTF.pl test-data/small.gtf ann -features exon start_codon stop_codon -annTSSstartOffset -50 -annTSSendOffset 50 -annTTSstartOffset -50 -annTTSendOffset 50 > /tmp/annotations3.txt
+assignGenomeAnnotation /tmp/annotations3.txt /tmp/annotations3.txt -prioritize test-data/annotations_small_TSSTTS.txt > test-data/annotations_small_TSSTTS_stats.txt
+
+## For annotatePeaks.pl
+parseGTF.pl test-data/small_simplified.gtf ann -features exon start_codon stop_codon > /tmp/annotations.txt
+assignGenomeAnnotation /tmp/annotations.txt /tmp/annotations.txt -prioritize test-data/annotations_default_simplified.txt
+
+## homer_annotatePeaks
+## First test
+annotatePeaks.pl test-data/CTCF_peaks.bed none -gtf test-data/small_simplified.gtf -ann test-data/annotations_default_simplified.txt > test-data/CTCF_peaks_first.txt
+## Second test
+annotatePeaks.pl test-data/CTCF_peaks.bed none -ann test-data/annotations_default.txt > test-data/CTCF_peaks_second.txt
+## Third test
+annotatePeaks.pl test-data/CTCF_peaks.bed none -gtf test-data/small_simplified.gtf > test-data/CTCF_peaks_third.txt
+## Fourth test
+annotatePeaks.pl test-data/fake_phix_peaks.bed test-data/phiX174.fasta -CpG > test-data/phiXcpg.txt
+## Fifth test
+annotatePeaks.pl test-data/fake_phix_peaks.bed none > test-data/phiX_nothing.txt
+
+## findMotifsGenome
+# ! Genome preparsing is giving different results...
+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
+# 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
+# mv CTCF_peaks_shifted_bed_motif test-data/motif_test3
+# findMotifsGenome.pl test-data/CTCF_peaks_shifted.bed test-data/chr2_subset.fa CTCF_peaks_shifted_bed_motif -mset plants -nomotif
+# mv CTCF_peaks_shifted_bed_motif test-data/motif_test4
+