diff tests.sh @ 7:c33d6583e548 draft

"planemo upload commit 50884f7f0269a0bbde078f24fe5020975693bcd9"

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tests.sh	Fri Jun 24 14:19:48 2022 +0000
@@ -0,0 +1,30 @@
+#!/bin/bash
+# set to stop in case of error
+set -e
+# first argument is cpu number
+NCPU_TO_USE=$1
+eval "$(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 \
+-g test_data/sample_DANTE.gff3 -o tmp/test_output1 -c $NCPU_TO_USE
+
+
+cat tmp/test_output1_statistics.csv
+
+echo "Running tests 2, filtering gff"
+./clean_ltr.R -g tmp/test_output1.gff3 -s test_data/sample_genome.fasta \
+-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 \
+-g test_data/sample_DANTE.gff3 -o tmp/test_output3 -c $NCPU_TO_USE -M 2
+
+
+cat tmp/test_output3_statistics.csv
+
+echo "Running tests 4, filtering gff"
+./clean_ltr.R -g tmp/test_output3.gff3 -s test_data/sample_genome.fasta \
+-o tmp/test_output4 -c $NCPU_TO_USE
+
+