--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test_run2.sh	Mon Apr 01 07:56:36 2019 -0400
@@ -0,0 +1,20 @@
+#!/bin/sh
+## same as galaxy terst
+./paired_fastq_filtering_wrapper.sh -a test_data/ERR215189_1_part.fastq.gz -b test_data/ERR215189_2_part.fastq.gz -o test_data/single_output.fasta -G test_data/single_output.png -c 10 -N 0 -p 95
+
+echo "paired fastq filtering with defaults"
+./paired_fastq_filtering_wrapper.sh -b test_data/ERR215189_2_part.fastq.gz -a test_data/ERR215189_1_part.fastq.gz -o tmp/test2.1.fasta -G tmp/test2.1.png -c 10 -N 0
+
+echo "paired fastq filtering with with sampling"
+./paired_fastq_filtering_wrapper.sh -b test_data/ERR215189_2_part.fastq.gz -a test_data/ERR215189_1_part.fastq.gz -o tmp/test2.2.fasta -G tmp/test2.2.png -c 10 -N 0 -n 500
+
+echo "paired fastq filtering with contaminant removing"
+./paired_fastq_filtering_wrapper.sh -F tool_data/organele_ref_and_phi-X174.fasta -b test_data/ERR215189_2_part.fastq.gz -a test_data/ERR215189_1_part.fastq.gz -o tmp/test2.3.fasta -G tmp/test2.3.png -c 10 -N 0
+
+echo "paired fastq filtering with contaminant removing + trimming"
+./paired_fastq_filtering_wrapper.sh -F tool_data/organele_ref_and_phi-X174.fasta -b test_data/ERR215189_2_part.fastq.gz -a test_data/ERR215189_1_part.fastq.gz -o tmp/test2.3.fasta -G tmp/test2.3.png -c 10 -N 0 -s 10 -e 80
+
+
+echo "paired fastq filtering with contaminant removing - full run"
+./paired_fastq_filtering_wrapper.sh -F tool_data/organele_ref_and_phi-X174.fasta -b test_data/ERR215189_2.fastq.gz -a test_data/ERR215189_1.fastq.gz -o tmp/test2.3.fasta -G tmp/test2.3.png -c 10 -N 0
+