Mercurial > repos > petr-novak > re_utils

comparison test_run2.sh @ 0:a4cd8608ef6b draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded
author petr-novak
date Mon, 01 Apr 2019 07:56:36 -0400
parents
children 378565f5a875
comparison
equal deleted inserted replaced
-1:000000000000 0:a4cd8608ef6b
1 #!/bin/sh
2 ## same as galaxy terst
3 ./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
4
5 echo "paired fastq filtering with defaults"
6 ./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
7
8 echo "paired fastq filtering with with sampling"
9 ./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
10
11 echo "paired fastq filtering with contaminant removing"
12 ./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
13
14 echo "paired fastq filtering with contaminant removing + trimming"
15 ./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
16
17
18 echo "paired fastq filtering with contaminant removing - full run"
19 ./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
20