diff tests.sh @ 12:ff01d4263391 draft

"planemo upload commit 414119ad7c44562d2e956b765e97ca113bc35b2b-dirty"

--- a/tests.sh	Wed Jul 13 11:02:55 2022 +0000
+++ b/tests.sh	Thu Jul 21 08:23:15 2022 +0000
@@ -3,10 +3,17 @@
 set -e
 # first argument is cpu number
 NCPU_TO_USE=$1
+
+# test if NCPU_TO_USE is set:
+if [ -z "${NCPU_TO_USE}" ]; then
+    echo "NCPU_TO_USE is not set, using 10"
+    NCPU_TO_USE=10
+fi
+
 eval "$(conda shell.bash hook)"
 conda activate dante_ltr
 echo "Running tests 1, detection of LTRs"
-./extract_putative_ltr.R -s test_data/sample_genome.fasta \
+./detect_putative_ltr.R -s test_data/sample_genome.fasta \
 -g test_data/sample_DANTE.gff3 -o tmp/test_output1 -c $NCPU_TO_USE
 
 
@@ -17,7 +24,7 @@
 -o tmp/test_output2 -c $NCPU_TO_USE
 
 echo "Running tests 3, detection of LTRs, allow missing domains"
-./extract_putative_ltr.R -s test_data/sample_genome.fasta \
+./detect_putative_ltr.R -s test_data/sample_genome.fasta \
 -g test_data/sample_DANTE.gff3 -o tmp/test_output3 -c $NCPU_TO_USE -M 2
 
 
@@ -28,3 +35,12 @@
 -o tmp/test_output4 -c $NCPU_TO_USE
 
 
+echo "Running tests 5, detection of LTRs using python wrapper"
+./detect_putative_ltr_wrapper.py -s test_data/sample_genome.fasta \
+-g test_data/sample_DANTE.gff3 -o tmp/test_output5 -c $NCPU_TO_USE \
+-S 10000000
+cat tmp/test_output5_statistics.csv
+
+echo "Running tests 4, filtering gff"
+./clean_ltr.R -g tmp/test_output5.gff3 -s test_data/sample_genome.fasta \
+-o tmp/test_output6 -c $NCPU_TO_USE