Mercurial > repos > bebatut > extract_sequence_file

annotate test-data/src/run_tests.sh @ 1:bbde61ab5519 draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/extract_sequence_file/ commit 5c45ed58045ce1686aa069403f8a9426ea20bac5-dirty
author bebatut
date Tue, 12 Apr 2016 02:59:22 -0400
parents 14fd6f3b0898
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
14fd6f3b0898 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/extract_sequence_file/ commit ffb68b2ddd94854a34a2533105f7bc08884c6e38-dirty
bebatut
parents:
diff changeset
1 #!/bin/bash
14fd6f3b0898 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/extract_sequence_file/ commit ffb68b2ddd94854a34a2533105f7bc08884c6e38-dirty
bebatut
parents:
diff changeset
2
14fd6f3b0898 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/extract_sequence_file/ commit ffb68b2ddd94854a34a2533105f7bc08884c6e38-dirty
bebatut
parents:
diff changeset
3 input_data_dir="test-data/data/input/"
14fd6f3b0898 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/extract_sequence_file/ commit ffb68b2ddd94854a34a2533105f7bc08884c6e38-dirty
bebatut
parents:
diff changeset
4 output_sequence_dir="test-data/data/output_sequence_file/"
14fd6f3b0898 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/extract_sequence_file/ commit ffb68b2ddd94854a34a2533105f7bc08884c6e38-dirty
bebatut
parents:
diff changeset
5 output_information_dir="test-data/data/output_information_file/"
14fd6f3b0898 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/extract_sequence_file/ commit ffb68b2ddd94854a34a2533105f7bc08884c6e38-dirty
bebatut
parents:
diff changeset
6 output_report_dir="test-data/data/output_report_file/"
14fd6f3b0898 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/extract_sequence_file/ commit ffb68b2ddd94854a34a2533105f7bc08884c6e38-dirty
bebatut
parents:
diff changeset
7 output_qual_dir="test-data/data/output_qual_file/"
14fd6f3b0898 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/extract_sequence_file/ commit ffb68b2ddd94854a34a2533105f7bc08884c6e38-dirty
bebatut
parents:
diff changeset
8
14fd6f3b0898 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/extract_sequence_file/ commit ffb68b2ddd94854a34a2533105f7bc08884c6e38-dirty
bebatut
parents:
diff changeset
9 ## Fasta format
14fd6f3b0898 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/extract_sequence_file/ commit ffb68b2ddd94854a34a2533105f7bc08884c6e38-dirty
bebatut
parents:
diff changeset
10
14fd6f3b0898 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/extract_sequence_file/ commit ffb68b2ddd94854a34a2533105f7bc08884c6e38-dirty
bebatut
parents:
diff changeset
11 echo "Read and write fasta file"
14fd6f3b0898 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/extract_sequence_file/ commit ffb68b2ddd94854a34a2533105f7bc08884c6e38-dirty
bebatut
parents:
diff changeset
12 test_dir="test-data/data/read_write_fasta_file/"
14fd6f3b0898 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/extract_sequence_file/ commit ffb68b2ddd94854a34a2533105f7bc08884c6e38-dirty
bebatut
parents:
diff changeset
13 python extract_sequence_file.py \
14fd6f3b0898 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/extract_sequence_file/ commit ffb68b2ddd94854a34a2533105f7bc08884c6e38-dirty
bebatut
parents:
diff changeset
14 --input $test_dir/"input_sequence_file.fasta" \
14fd6f3b0898 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/extract_sequence_file/ commit ffb68b2ddd94854a34a2533105f7bc08884c6e38-dirty
bebatut
parents:
diff changeset
15 --custom_extraction_type "no" \
14fd6f3b0898 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/extract_sequence_file/ commit ffb68b2ddd94854a34a2533105f7bc08884c6e38-dirty
bebatut
parents:
diff changeset
16 --output_sequence $test_dir/"output_sequence_file.fasta" \
14fd6f3b0898 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/extract_sequence_file/ commit ffb68b2ddd94854a34a2533105f7bc08884c6e38-dirty
bebatut
parents:
diff changeset
17 --report $test_dir"output_report.txt" \
14fd6f3b0898 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/extract_sequence_file/ commit ffb68b2ddd94854a34a2533105f7bc08884c6e38-dirty
bebatut
parents:
diff changeset
18 --format "fasta"
14fd6f3b0898 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/extract_sequence_file/ commit ffb68b2ddd94854a34a2533105f7bc08884c6e38-dirty
bebatut
parents:
diff changeset
19 python test-data/src/compare_files.py \
14fd6f3b0898 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/extract_sequence_file/ commit ffb68b2ddd94854a34a2533105f7bc08884c6e38-dirty
bebatut
parents:
diff changeset
20 --exp_file $test_dir/"input_sequence_file.fasta" \
14fd6f3b0898 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/extract_sequence_file/ commit ffb68b2ddd94854a34a2533105f7bc08884c6e38-dirty
bebatut
parents:
diff changeset
21 --obs_file $test_dir/"output_sequence_file.fasta" \
14fd6f3b0898 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/extract_sequence_file/ commit ffb68b2ddd94854a34a2533105f7bc08884c6e38-dirty
bebatut
parents:
diff changeset
22 --comparison "Sequence file"
14fd6f3b0898 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/extract_sequence_file/ commit ffb68b2ddd94854a34a2533105f7bc08884c6e38-dirty
bebatut
parents:
diff changeset
23 python test-data/src/compare_files.py \
14fd6f3b0898 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/extract_sequence_file/ commit ffb68b2ddd94854a34a2533105f7bc08884c6e38-dirty
bebatut
parents:
diff changeset
24 --exp_file $test_dir"/expected_output_report.txt" \
14fd6f3b0898 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/extract_sequence_file/ commit ffb68b2ddd94854a34a2533105f7bc08884c6e38-dirty
bebatut
parents:
diff changeset
25 --obs_file $test_dir"output_report.txt" \
14fd6f3b0898 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/extract_sequence_file/ commit ffb68b2ddd94854a34a2533105f7bc08884c6e38-dirty
bebatut
parents:
diff changeset
26 --comparison "Report file"
14fd6f3b0898 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/extract_sequence_file/ commit ffb68b2ddd94854a34a2533105f7bc08884c6e38-dirty
bebatut
parents:
diff changeset
27
14fd6f3b0898 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/extract_sequence_file/ commit ffb68b2ddd94854a34a2533105f7bc08884c6e38-dirty
bebatut
parents:
diff changeset
28 echo "Simple extraction of fasta file"
14fd6f3b0898 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/extract_sequence_file/ commit ffb68b2ddd94854a34a2533105f7bc08884c6e38-dirty
bebatut
parents:
diff changeset
29 test_dir="test-data/data/simple_extraction_fasta_file/"
14fd6f3b0898 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/extract_sequence_file/ commit ffb68b2ddd94854a34a2533105f7bc08884c6e38-dirty
bebatut
parents:
diff changeset
30 python extract_sequence_file.py \
14fd6f3b0898 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/extract_sequence_file/ commit ffb68b2ddd94854a34a2533105f7bc08884c6e38-dirty
bebatut
parents:
diff changeset
31 --input $test_dir/"input_sequence_file.fasta" \
14fd6f3b0898 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/extract_sequence_file/ commit ffb68b2ddd94854a34a2533105f7bc08884c6e38-dirty
bebatut
parents:
diff changeset
32 --custom_extraction_type "yes" \
14fd6f3b0898 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/extract_sequence_file/ commit ffb68b2ddd94854a34a2533105f7bc08884c6e38-dirty
bebatut
parents:
diff changeset
33 --output_information $test_dir"output_information.txt" \
14fd6f3b0898 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/extract_sequence_file/ commit ffb68b2ddd94854a34a2533105f7bc08884c6e38-dirty
bebatut
parents:
diff changeset
34 --report $test_dir"output_report.txt" \
14fd6f3b0898 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/extract_sequence_file/ commit ffb68b2ddd94854a34a2533105f7bc08884c6e38-dirty
bebatut
parents:
diff changeset
35 --to_extract "{id,length}" \
14fd6f3b0898 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/extract_sequence_file/ commit ffb68b2ddd94854a34a2533105f7bc08884c6e38-dirty
bebatut
parents:
diff changeset
36 --format "fasta"
14fd6f3b0898 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/extract_sequence_file/ commit ffb68b2ddd94854a34a2533105f7bc08884c6e38-dirty
bebatut
parents:
diff changeset
37 python test-data/src/compare_files.py \
14fd6f3b0898 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/extract_sequence_file/ commit ffb68b2ddd94854a34a2533105f7bc08884c6e38-dirty
bebatut
parents:
diff changeset
38 --exp_file $test_dir"/expected_output_report.txt" \
14fd6f3b0898 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/extract_sequence_file/ commit ffb68b2ddd94854a34a2533105f7bc08884c6e38-dirty
bebatut
parents:
diff changeset
39 --obs_file $test_dir"output_report.txt" \
14fd6f3b0898 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/extract_sequence_file/ commit ffb68b2ddd94854a34a2533105f7bc08884c6e38-dirty
bebatut
parents:
diff changeset
40 --comparison "Report file"
14fd6f3b0898 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/extract_sequence_file/ commit ffb68b2ddd94854a34a2533105f7bc08884c6e38-dirty
bebatut
parents:
diff changeset
41 python test-data/src/compare_files.py \
14fd6f3b0898 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/extract_sequence_file/ commit ffb68b2ddd94854a34a2533105f7bc08884c6e38-dirty
bebatut
parents:
diff changeset
42 --exp_file $test_dir"expected_output_information.txt" \
14fd6f3b0898 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/extract_sequence_file/ commit ffb68b2ddd94854a34a2533105f7bc08884c6e38-dirty
bebatut
parents:
diff changeset
43 --obs_file $test_dir"output_information.txt" \
14fd6f3b0898 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/extract_sequence_file/ commit ffb68b2ddd94854a34a2533105f7bc08884c6e38-dirty
bebatut
parents:
diff changeset
44 --comparison "Information file"
14fd6f3b0898 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/extract_sequence_file/ commit ffb68b2ddd94854a34a2533105f7bc08884c6e38-dirty
bebatut
parents:
diff changeset
45
14fd6f3b0898 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/extract_sequence_file/ commit ffb68b2ddd94854a34a2533105f7bc08884c6e38-dirty
bebatut
parents:
diff changeset
46 echo "Simple constraint of fasta file"
14fd6f3b0898 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/extract_sequence_file/ commit ffb68b2ddd94854a34a2533105f7bc08884c6e38-dirty
bebatut
parents:
diff changeset
47 test_dir="test-data/data/simple_constraint_fasta_file/"
14fd6f3b0898 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/extract_sequence_file/ commit ffb68b2ddd94854a34a2533105f7bc08884c6e38-dirty
bebatut
parents:
diff changeset
48 python extract_sequence_file.py \
14fd6f3b0898 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/extract_sequence_file/ commit ffb68b2ddd94854a34a2533105f7bc08884c6e38-dirty
bebatut
parents:
diff changeset
49 --input $test_dir/"input_sequence_file.fasta" \
14fd6f3b0898 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/extract_sequence_file/ commit ffb68b2ddd94854a34a2533105f7bc08884c6e38-dirty
bebatut
parents:
diff changeset
50 --custom_extraction_type "yes" \
14fd6f3b0898 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/extract_sequence_file/ commit ffb68b2ddd94854a34a2533105f7bc08884c6e38-dirty
bebatut
parents:
diff changeset
51 --output_information $test_dir"output_information.txt" \
14fd6f3b0898 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/extract_sequence_file/ commit ffb68b2ddd94854a34a2533105f7bc08884c6e38-dirty
bebatut
parents:
diff changeset
52 --report $test_dir"output_report.txt" \
14fd6f3b0898 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/extract_sequence_file/ commit ffb68b2ddd94854a34a2533105f7bc08884c6e38-dirty
bebatut
parents:
diff changeset
53 --to_extract "{id,length}" \
14fd6f3b0898 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/extract_sequence_file/ commit ffb68b2ddd94854a34a2533105f7bc08884c6e38-dirty
bebatut
parents:
diff changeset
54 --constraint "length: greater: 100" \
14fd6f3b0898 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/extract_sequence_file/ commit ffb68b2ddd94854a34a2533105f7bc08884c6e38-dirty
bebatut
parents:
diff changeset
55 --format "fasta"
14fd6f3b0898 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/extract_sequence_file/ commit ffb68b2ddd94854a34a2533105f7bc08884c6e38-dirty
bebatut
parents:
diff changeset
56 python test-data/src/compare_files.py \
14fd6f3b0898 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/extract_sequence_file/ commit ffb68b2ddd94854a34a2533105f7bc08884c6e38-dirty
bebatut
parents:
diff changeset
57 --exp_file $test_dir"/expected_output_report.txt" \
14fd6f3b0898 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/extract_sequence_file/ commit ffb68b2ddd94854a34a2533105f7bc08884c6e38-dirty
bebatut
parents:
diff changeset
58 --obs_file $test_dir"output_report.txt" \
14fd6f3b0898 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/extract_sequence_file/ commit ffb68b2ddd94854a34a2533105f7bc08884c6e38-dirty
bebatut
parents:
diff changeset
59 --comparison "Report file"
14fd6f3b0898 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/extract_sequence_file/ commit ffb68b2ddd94854a34a2533105f7bc08884c6e38-dirty
bebatut
parents:
diff changeset
60 python test-data/src/compare_files.py \
14fd6f3b0898 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/extract_sequence_file/ commit ffb68b2ddd94854a34a2533105f7bc08884c6e38-dirty
bebatut
parents:
diff changeset
61 --exp_file $test_dir"expected_output_information.txt" \
14fd6f3b0898 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/extract_sequence_file/ commit ffb68b2ddd94854a34a2533105f7bc08884c6e38-dirty
bebatut
parents:
diff changeset
62 --obs_file $test_dir"output_information.txt" \
14fd6f3b0898 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/extract_sequence_file/ commit ffb68b2ddd94854a34a2533105f7bc08884c6e38-dirty
bebatut
parents:
diff changeset
63 --comparison "Information file"
14fd6f3b0898 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/extract_sequence_file/ commit ffb68b2ddd94854a34a2533105f7bc08884c6e38-dirty
bebatut
parents:
diff changeset
64
14fd6f3b0898 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/extract_sequence_file/ commit ffb68b2ddd94854a34a2533105f7bc08884c6e38-dirty
bebatut
parents:
diff changeset
65 echo "Double constraints of fasta file"
14fd6f3b0898 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/extract_sequence_file/ commit ffb68b2ddd94854a34a2533105f7bc08884c6e38-dirty
bebatut
parents:
diff changeset
66 test_dir="test-data/data/double_constraint_fasta_file/"
14fd6f3b0898 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/extract_sequence_file/ commit ffb68b2ddd94854a34a2533105f7bc08884c6e38-dirty
bebatut
parents:
diff changeset
67 python extract_sequence_file.py \
14fd6f3b0898 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/extract_sequence_file/ commit ffb68b2ddd94854a34a2533105f7bc08884c6e38-dirty
bebatut
parents:
diff changeset
68 --input $test_dir/"input_sequence_file.fasta" \
14fd6f3b0898 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/extract_sequence_file/ commit ffb68b2ddd94854a34a2533105f7bc08884c6e38-dirty
bebatut
parents:
diff changeset
69 --custom_extraction_type "yes" \
14fd6f3b0898 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/extract_sequence_file/ commit ffb68b2ddd94854a34a2533105f7bc08884c6e38-dirty
bebatut
parents:
diff changeset
70 --output_information $test_dir"output_information.txt" \
14fd6f3b0898 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/extract_sequence_file/ commit ffb68b2ddd94854a34a2533105f7bc08884c6e38-dirty
bebatut
parents:
diff changeset
71 --report $test_dir"output_report.txt" \
14fd6f3b0898 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/extract_sequence_file/ commit ffb68b2ddd94854a34a2533105f7bc08884c6e38-dirty
bebatut
parents:
diff changeset
72 --to_extract "{id,length}" \
14fd6f3b0898 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/extract_sequence_file/ commit ffb68b2ddd94854a34a2533105f7bc08884c6e38-dirty
bebatut
parents:
diff changeset
73 --constraint "length: greater: 100" \
14fd6f3b0898 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/extract_sequence_file/ commit ffb68b2ddd94854a34a2533105f7bc08884c6e38-dirty
bebatut
parents:
diff changeset
74 --constraint "id: in: test-data/data/id_in_list.txt" \
14fd6f3b0898 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/extract_sequence_file/ commit ffb68b2ddd94854a34a2533105f7bc08884c6e38-dirty
bebatut
parents:
diff changeset
75 --format "fasta"
14fd6f3b0898 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/extract_sequence_file/ commit ffb68b2ddd94854a34a2533105f7bc08884c6e38-dirty
bebatut
parents:
diff changeset
76 python test-data/src/compare_files.py \
14fd6f3b0898 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/extract_sequence_file/ commit ffb68b2ddd94854a34a2533105f7bc08884c6e38-dirty
bebatut
parents:
diff changeset
77 --exp_file $test_dir"/expected_output_report.txt" \
14fd6f3b0898 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/extract_sequence_file/ commit ffb68b2ddd94854a34a2533105f7bc08884c6e38-dirty
bebatut
parents:
diff changeset
78 --obs_file $test_dir"output_report.txt" \
14fd6f3b0898 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/extract_sequence_file/ commit ffb68b2ddd94854a34a2533105f7bc08884c6e38-dirty
bebatut
parents:
diff changeset
79 --comparison "Report file"
14fd6f3b0898 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/extract_sequence_file/ commit ffb68b2ddd94854a34a2533105f7bc08884c6e38-dirty
bebatut
parents:
diff changeset
80 python test-data/src/compare_files.py \
14fd6f3b0898 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/extract_sequence_file/ commit ffb68b2ddd94854a34a2533105f7bc08884c6e38-dirty
bebatut
parents:
diff changeset
81 --exp_file $test_dir"expected_output_information.txt" \
14fd6f3b0898 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/extract_sequence_file/ commit ffb68b2ddd94854a34a2533105f7bc08884c6e38-dirty
bebatut
parents:
diff changeset
82 --obs_file $test_dir"output_information.txt" \
14fd6f3b0898 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/extract_sequence_file/ commit ffb68b2ddd94854a34a2533105f7bc08884c6e38-dirty
bebatut
parents:
diff changeset
83 --comparison "Information file"
14fd6f3b0898 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/extract_sequence_file/ commit ffb68b2ddd94854a34a2533105f7bc08884c6e38-dirty
bebatut
parents:
diff changeset
84
14fd6f3b0898 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/extract_sequence_file/ commit ffb68b2ddd94854a34a2533105f7bc08884c6e38-dirty
bebatut
parents:
diff changeset
85 ## Fastq format
14fd6f3b0898 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/extract_sequence_file/ commit ffb68b2ddd94854a34a2533105f7bc08884c6e38-dirty
bebatut
parents:
diff changeset
86
14fd6f3b0898 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/extract_sequence_file/ commit ffb68b2ddd94854a34a2533105f7bc08884c6e38-dirty
bebatut
parents:
diff changeset
87 echo "Read and write fastq file"
14fd6f3b0898 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/extract_sequence_file/ commit ffb68b2ddd94854a34a2533105f7bc08884c6e38-dirty
bebatut
parents:
diff changeset
88 test_dir="test-data/data/read_write_fastq_file/"
14fd6f3b0898 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/extract_sequence_file/ commit ffb68b2ddd94854a34a2533105f7bc08884c6e38-dirty
bebatut
parents:
diff changeset
89 python extract_sequence_file.py \
14fd6f3b0898 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/extract_sequence_file/ commit ffb68b2ddd94854a34a2533105f7bc08884c6e38-dirty
bebatut
parents:
diff changeset
90 --input $test_dir/"input_sequence_file.fastq" \
14fd6f3b0898 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/extract_sequence_file/ commit ffb68b2ddd94854a34a2533105f7bc08884c6e38-dirty
bebatut
parents:
diff changeset
91 --custom_extraction_type "no" \
14fd6f3b0898 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/extract_sequence_file/ commit ffb68b2ddd94854a34a2533105f7bc08884c6e38-dirty
bebatut
parents:
diff changeset
92 --output_sequence $test_dir/"output_sequence_file.fastq" \
14fd6f3b0898 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/extract_sequence_file/ commit ffb68b2ddd94854a34a2533105f7bc08884c6e38-dirty
bebatut
parents:
diff changeset
93 --report $test_dir"output_report.txt" \
14fd6f3b0898 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/extract_sequence_file/ commit ffb68b2ddd94854a34a2533105f7bc08884c6e38-dirty
bebatut
parents:
diff changeset
94 --format "fastq"
14fd6f3b0898 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/extract_sequence_file/ commit ffb68b2ddd94854a34a2533105f7bc08884c6e38-dirty
bebatut
parents:
diff changeset
95 python test-data/src/compare_files.py \
14fd6f3b0898 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/extract_sequence_file/ commit ffb68b2ddd94854a34a2533105f7bc08884c6e38-dirty
bebatut
parents:
diff changeset
96 --exp_file $test_dir/"input_sequence_file.fastq" \
14fd6f3b0898 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/extract_sequence_file/ commit ffb68b2ddd94854a34a2533105f7bc08884c6e38-dirty
bebatut
parents:
diff changeset
97 --obs_file $test_dir/"output_sequence_file.fastq" \
14fd6f3b0898 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/extract_sequence_file/ commit ffb68b2ddd94854a34a2533105f7bc08884c6e38-dirty
bebatut
parents:
diff changeset
98 --comparison "Sequence file"
14fd6f3b0898 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/extract_sequence_file/ commit ffb68b2ddd94854a34a2533105f7bc08884c6e38-dirty
bebatut
parents:
diff changeset
99 python test-data/src/compare_files.py \
14fd6f3b0898 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/extract_sequence_file/ commit ffb68b2ddd94854a34a2533105f7bc08884c6e38-dirty
bebatut
parents:
diff changeset
100 --exp_file $test_dir"/expected_output_report.txt" \
14fd6f3b0898 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/extract_sequence_file/ commit ffb68b2ddd94854a34a2533105f7bc08884c6e38-dirty
bebatut
parents:
diff changeset
101 --obs_file $test_dir"output_report.txt" \
14fd6f3b0898 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/extract_sequence_file/ commit ffb68b2ddd94854a34a2533105f7bc08884c6e38-dirty
bebatut
parents:
diff changeset
102 --comparison "Report file"
14fd6f3b0898 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/extract_sequence_file/ commit ffb68b2ddd94854a34a2533105f7bc08884c6e38-dirty
bebatut
parents:
diff changeset
103
14fd6f3b0898 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/extract_sequence_file/ commit ffb68b2ddd94854a34a2533105f7bc08884c6e38-dirty
bebatut
parents:
diff changeset
104 echo "Read and split fastq file"
14fd6f3b0898 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/extract_sequence_file/ commit ffb68b2ddd94854a34a2533105f7bc08884c6e38-dirty
bebatut
parents:
diff changeset
105 test_dir="test-data/data/split_fastq_file/"
14fd6f3b0898 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/extract_sequence_file/ commit ffb68b2ddd94854a34a2533105f7bc08884c6e38-dirty
bebatut
parents:
diff changeset
106 python extract_sequence_file.py \
14fd6f3b0898 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/extract_sequence_file/ commit ffb68b2ddd94854a34a2533105f7bc08884c6e38-dirty
bebatut
parents:
diff changeset
107 --input $test_dir/"input_sequence_file.fastq" \
14fd6f3b0898 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/extract_sequence_file/ commit ffb68b2ddd94854a34a2533105f7bc08884c6e38-dirty
bebatut
parents:
diff changeset
108 --custom_extraction_type "no" \
14fd6f3b0898 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/extract_sequence_file/ commit ffb68b2ddd94854a34a2533105f7bc08884c6e38-dirty
bebatut
parents:
diff changeset
109 --split "yes" \
14fd6f3b0898 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/extract_sequence_file/ commit ffb68b2ddd94854a34a2533105f7bc08884c6e38-dirty
bebatut
parents:
diff changeset
110 --quality_format "sanger" \
14fd6f3b0898 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/extract_sequence_file/ commit ffb68b2ddd94854a34a2533105f7bc08884c6e38-dirty
bebatut
parents:
diff changeset
111 --output_sequence $test_dir/"output_sequence_file.fasta" \
14fd6f3b0898 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/extract_sequence_file/ commit ffb68b2ddd94854a34a2533105f7bc08884c6e38-dirty
bebatut
parents:
diff changeset
112 --output_quality $test_dir/"output_quality.qual" \
14fd6f3b0898 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/extract_sequence_file/ commit ffb68b2ddd94854a34a2533105f7bc08884c6e38-dirty
bebatut
parents:
diff changeset
113 --report $test_dir"output_report.txt" \
14fd6f3b0898 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/extract_sequence_file/ commit ffb68b2ddd94854a34a2533105f7bc08884c6e38-dirty
bebatut
parents:
diff changeset
114 --format "fastq"
14fd6f3b0898 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/extract_sequence_file/ commit ffb68b2ddd94854a34a2533105f7bc08884c6e38-dirty
bebatut
parents:
diff changeset
115 python test-data/src/compare_files.py \
14fd6f3b0898 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/extract_sequence_file/ commit ffb68b2ddd94854a34a2533105f7bc08884c6e38-dirty
bebatut
parents:
diff changeset
116 --exp_file $test_dir/"expected_output_sequence_file.fasta" \
14fd6f3b0898 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/extract_sequence_file/ commit ffb68b2ddd94854a34a2533105f7bc08884c6e38-dirty
bebatut
parents:
diff changeset
117 --obs_file $test_dir/"output_sequence_file.fasta" \
14fd6f3b0898 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/extract_sequence_file/ commit ffb68b2ddd94854a34a2533105f7bc08884c6e38-dirty
bebatut
parents:
diff changeset
118 --comparison "Sequence file"
14fd6f3b0898 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/extract_sequence_file/ commit ffb68b2ddd94854a34a2533105f7bc08884c6e38-dirty
bebatut
parents:
diff changeset
119 python test-data/src/compare_files.py \
14fd6f3b0898 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/extract_sequence_file/ commit ffb68b2ddd94854a34a2533105f7bc08884c6e38-dirty
bebatut
parents:
diff changeset
120 --exp_file $test_dir/"output_quality.qual" \
14fd6f3b0898 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/extract_sequence_file/ commit ffb68b2ddd94854a34a2533105f7bc08884c6e38-dirty
bebatut
parents:
diff changeset
121 --obs_file $test_dir/"expected_output_quality.qual" \
14fd6f3b0898 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/extract_sequence_file/ commit ffb68b2ddd94854a34a2533105f7bc08884c6e38-dirty
bebatut
parents:
diff changeset
122 --comparison "Quality file"
14fd6f3b0898 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/extract_sequence_file/ commit ffb68b2ddd94854a34a2533105f7bc08884c6e38-dirty
bebatut
parents:
diff changeset
123 python test-data/src/compare_files.py \
14fd6f3b0898 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/extract_sequence_file/ commit ffb68b2ddd94854a34a2533105f7bc08884c6e38-dirty
bebatut
parents:
diff changeset
124 --exp_file $test_dir"/expected_output_report.txt" \
14fd6f3b0898 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/extract_sequence_file/ commit ffb68b2ddd94854a34a2533105f7bc08884c6e38-dirty
bebatut
parents:
diff changeset
125 --obs_file $test_dir"output_report.txt" \
14fd6f3b0898 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/extract_sequence_file/ commit ffb68b2ddd94854a34a2533105f7bc08884c6e38-dirty
bebatut
parents:
diff changeset
126 --comparison "Report file"
14fd6f3b0898 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/extract_sequence_file/ commit ffb68b2ddd94854a34a2533105f7bc08884c6e38-dirty
bebatut
parents:
diff changeset
127
14fd6f3b0898 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/extract_sequence_file/ commit ffb68b2ddd94854a34a2533105f7bc08884c6e38-dirty
bebatut
parents:
diff changeset
128 echo "Simple extraction of fastq file"
14fd6f3b0898 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/extract_sequence_file/ commit ffb68b2ddd94854a34a2533105f7bc08884c6e38-dirty
bebatut
parents:
diff changeset
129 test_dir="test-data/data/simple_extraction_fastq_file/"
14fd6f3b0898 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/extract_sequence_file/ commit ffb68b2ddd94854a34a2533105f7bc08884c6e38-dirty
bebatut
parents:
diff changeset
130 python extract_sequence_file.py \
14fd6f3b0898 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/extract_sequence_file/ commit ffb68b2ddd94854a34a2533105f7bc08884c6e38-dirty
bebatut
parents:
diff changeset
131 --input $test_dir/"input_sequence_file.fastq" \
14fd6f3b0898 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/extract_sequence_file/ commit ffb68b2ddd94854a34a2533105f7bc08884c6e38-dirty
bebatut
parents:
diff changeset
132 --custom_extraction_type "yes" \
14fd6f3b0898 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/extract_sequence_file/ commit ffb68b2ddd94854a34a2533105f7bc08884c6e38-dirty
bebatut
parents:
diff changeset
133 --output_information $test_dir"output_information.txt" \
14fd6f3b0898 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/extract_sequence_file/ commit ffb68b2ddd94854a34a2533105f7bc08884c6e38-dirty
bebatut
parents:
diff changeset
134 --report $test_dir"output_report.txt" \
14fd6f3b0898 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/extract_sequence_file/ commit ffb68b2ddd94854a34a2533105f7bc08884c6e38-dirty
bebatut
parents:
diff changeset
135 --to_extract "{id,length}" \
14fd6f3b0898 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/extract_sequence_file/ commit ffb68b2ddd94854a34a2533105f7bc08884c6e38-dirty
bebatut
parents:
diff changeset
136 --format "fastq"
14fd6f3b0898 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/extract_sequence_file/ commit ffb68b2ddd94854a34a2533105f7bc08884c6e38-dirty
bebatut
parents:
diff changeset
137 python test-data/src/compare_files.py \
14fd6f3b0898 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/extract_sequence_file/ commit ffb68b2ddd94854a34a2533105f7bc08884c6e38-dirty
bebatut
parents:
diff changeset
138 --exp_file $test_dir"/expected_output_report.txt" \
14fd6f3b0898 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/extract_sequence_file/ commit ffb68b2ddd94854a34a2533105f7bc08884c6e38-dirty
bebatut
parents:
diff changeset
139 --obs_file $test_dir"output_report.txt" \
14fd6f3b0898 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/extract_sequence_file/ commit ffb68b2ddd94854a34a2533105f7bc08884c6e38-dirty
bebatut
parents:
diff changeset
140 --comparison "Report file"
14fd6f3b0898 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/extract_sequence_file/ commit ffb68b2ddd94854a34a2533105f7bc08884c6e38-dirty
bebatut
parents:
diff changeset
141 python test-data/src/compare_files.py \
14fd6f3b0898 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/extract_sequence_file/ commit ffb68b2ddd94854a34a2533105f7bc08884c6e38-dirty
bebatut
parents:
diff changeset
142 --exp_file $test_dir"expected_output_information.txt" \
14fd6f3b0898 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/extract_sequence_file/ commit ffb68b2ddd94854a34a2533105f7bc08884c6e38-dirty
bebatut
parents:
diff changeset
143 --obs_file $test_dir"output_information.txt" \
14fd6f3b0898 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/extract_sequence_file/ commit ffb68b2ddd94854a34a2533105f7bc08884c6e38-dirty
bebatut
parents:
diff changeset
144 --comparison "Information file"
14fd6f3b0898 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/extract_sequence_file/ commit ffb68b2ddd94854a34a2533105f7bc08884c6e38-dirty
bebatut
parents:
diff changeset
145
14fd6f3b0898 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/extract_sequence_file/ commit ffb68b2ddd94854a34a2533105f7bc08884c6e38-dirty
bebatut
parents:
diff changeset
146 echo "Simple constraint of fastq file"
14fd6f3b0898 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/extract_sequence_file/ commit ffb68b2ddd94854a34a2533105f7bc08884c6e38-dirty
bebatut
parents:
diff changeset
147 test_dir="test-data/data/simple_constraint_fastq_file/"
14fd6f3b0898 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/extract_sequence_file/ commit ffb68b2ddd94854a34a2533105f7bc08884c6e38-dirty
bebatut
parents:
diff changeset
148 python extract_sequence_file.py \
14fd6f3b0898 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/extract_sequence_file/ commit ffb68b2ddd94854a34a2533105f7bc08884c6e38-dirty
bebatut
parents:
diff changeset
149 --input $test_dir/"input_sequence_file.fastq" \
14fd6f3b0898 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/extract_sequence_file/ commit ffb68b2ddd94854a34a2533105f7bc08884c6e38-dirty
bebatut
parents:
diff changeset
150 --custom_extraction_type "yes" \
14fd6f3b0898 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/extract_sequence_file/ commit ffb68b2ddd94854a34a2533105f7bc08884c6e38-dirty
bebatut
parents:
diff changeset
151 --output_information $test_dir"output_information.txt" \
14fd6f3b0898 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/extract_sequence_file/ commit ffb68b2ddd94854a34a2533105f7bc08884c6e38-dirty
bebatut
parents:
diff changeset
152 --report $test_dir"output_report.txt" \
14fd6f3b0898 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/extract_sequence_file/ commit ffb68b2ddd94854a34a2533105f7bc08884c6e38-dirty
bebatut
parents:
diff changeset
153 --to_extract "{id,length}" \
14fd6f3b0898 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/extract_sequence_file/ commit ffb68b2ddd94854a34a2533105f7bc08884c6e38-dirty
bebatut
parents:
diff changeset
154 --constraint "length: greater: 100" \
14fd6f3b0898 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/extract_sequence_file/ commit ffb68b2ddd94854a34a2533105f7bc08884c6e38-dirty
bebatut
parents:
diff changeset
155 --format "fastq"
14fd6f3b0898 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/extract_sequence_file/ commit ffb68b2ddd94854a34a2533105f7bc08884c6e38-dirty
bebatut
parents:
diff changeset
156 python test-data/src/compare_files.py \
14fd6f3b0898 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/extract_sequence_file/ commit ffb68b2ddd94854a34a2533105f7bc08884c6e38-dirty
bebatut
parents:
diff changeset
157 --exp_file $test_dir"/expected_output_report.txt" \
14fd6f3b0898 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/extract_sequence_file/ commit ffb68b2ddd94854a34a2533105f7bc08884c6e38-dirty
bebatut
parents:
diff changeset
158 --obs_file $test_dir"output_report.txt" \
14fd6f3b0898 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/extract_sequence_file/ commit ffb68b2ddd94854a34a2533105f7bc08884c6e38-dirty
bebatut
parents:
diff changeset
159 --comparison "Report file"
14fd6f3b0898 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/extract_sequence_file/ commit ffb68b2ddd94854a34a2533105f7bc08884c6e38-dirty
bebatut
parents:
diff changeset
160 python test-data/src/compare_files.py \
14fd6f3b0898 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/extract_sequence_file/ commit ffb68b2ddd94854a34a2533105f7bc08884c6e38-dirty
bebatut
parents:
diff changeset
161 --exp_file $test_dir"expected_output_information.txt" \
14fd6f3b0898 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/extract_sequence_file/ commit ffb68b2ddd94854a34a2533105f7bc08884c6e38-dirty
bebatut
parents:
diff changeset
162 --obs_file $test_dir"output_information.txt" \
14fd6f3b0898 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/extract_sequence_file/ commit ffb68b2ddd94854a34a2533105f7bc08884c6e38-dirty
bebatut
parents:
diff changeset
163 --comparison "Information file"
14fd6f3b0898 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/extract_sequence_file/ commit ffb68b2ddd94854a34a2533105f7bc08884c6e38-dirty
bebatut
parents:
diff changeset
164
14fd6f3b0898 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/extract_sequence_file/ commit ffb68b2ddd94854a34a2533105f7bc08884c6e38-dirty
bebatut
parents:
diff changeset
165 echo "Double constraint of fastq file"
14fd6f3b0898 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/extract_sequence_file/ commit ffb68b2ddd94854a34a2533105f7bc08884c6e38-dirty
bebatut
parents:
diff changeset
166 test_dir="test-data/data/double_constraint_fastq_file/"
14fd6f3b0898 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/extract_sequence_file/ commit ffb68b2ddd94854a34a2533105f7bc08884c6e38-dirty
bebatut
parents:
diff changeset
167 python extract_sequence_file.py \
14fd6f3b0898 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/extract_sequence_file/ commit ffb68b2ddd94854a34a2533105f7bc08884c6e38-dirty
bebatut
parents:
diff changeset
168 --input $test_dir/"input_sequence_file.fastq" \
14fd6f3b0898 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/extract_sequence_file/ commit ffb68b2ddd94854a34a2533105f7bc08884c6e38-dirty
bebatut
parents:
diff changeset
169 --custom_extraction_type "yes" \
14fd6f3b0898 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/extract_sequence_file/ commit ffb68b2ddd94854a34a2533105f7bc08884c6e38-dirty
bebatut
parents:
diff changeset
170 --output_information $test_dir"output_information.txt" \
14fd6f3b0898 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/extract_sequence_file/ commit ffb68b2ddd94854a34a2533105f7bc08884c6e38-dirty
bebatut
parents:
diff changeset
171 --report $test_dir"output_report.txt" \
14fd6f3b0898 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/extract_sequence_file/ commit ffb68b2ddd94854a34a2533105f7bc08884c6e38-dirty
bebatut
parents:
diff changeset
172 --to_extract "{id,length}" \
14fd6f3b0898 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/extract_sequence_file/ commit ffb68b2ddd94854a34a2533105f7bc08884c6e38-dirty
bebatut
parents:
diff changeset
173 --constraint "length: greater: 100" \
14fd6f3b0898 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/extract_sequence_file/ commit ffb68b2ddd94854a34a2533105f7bc08884c6e38-dirty
bebatut
parents:
diff changeset
174 --constraint "id: in: test-data/data/id_in_list.txt" \
14fd6f3b0898 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/extract_sequence_file/ commit ffb68b2ddd94854a34a2533105f7bc08884c6e38-dirty
bebatut
parents:
diff changeset
175 --format "fastq"
14fd6f3b0898 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/extract_sequence_file/ commit ffb68b2ddd94854a34a2533105f7bc08884c6e38-dirty
bebatut
parents:
diff changeset
176 python test-data/src/compare_files.py \
14fd6f3b0898 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/extract_sequence_file/ commit ffb68b2ddd94854a34a2533105f7bc08884c6e38-dirty
bebatut
parents:
diff changeset
177 --exp_file $test_dir"/expected_output_report.txt" \
14fd6f3b0898 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/extract_sequence_file/ commit ffb68b2ddd94854a34a2533105f7bc08884c6e38-dirty
bebatut
parents:
diff changeset
178 --obs_file $test_dir"output_report.txt" \
14fd6f3b0898 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/extract_sequence_file/ commit ffb68b2ddd94854a34a2533105f7bc08884c6e38-dirty
bebatut
parents:
diff changeset
179 --comparison "Report file"
14fd6f3b0898 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/extract_sequence_file/ commit ffb68b2ddd94854a34a2533105f7bc08884c6e38-dirty
bebatut
parents:
diff changeset
180 python test-data/src/compare_files.py \
14fd6f3b0898 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/extract_sequence_file/ commit ffb68b2ddd94854a34a2533105f7bc08884c6e38-dirty
bebatut
parents:
diff changeset
181 --exp_file $test_dir"expected_output_information.txt" \
14fd6f3b0898 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/extract_sequence_file/ commit ffb68b2ddd94854a34a2533105f7bc08884c6e38-dirty
bebatut
parents:
diff changeset
182 --obs_file $test_dir"output_information.txt" \
14fd6f3b0898 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/extract_sequence_file/ commit ffb68b2ddd94854a34a2533105f7bc08884c6e38-dirty
bebatut
parents:
diff changeset
183 --comparison "Information file"