Mercurial > repos > bebatut > extract_sequence_file

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planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/extract_sequence_file/ commit ffb68b2ddd94854a34a2533105f7bc08884c6e38-dirty
author bebatut
date Wed, 27 Jan 2016 02:50:51 -0500
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-1:000000000000 0:14fd6f3b0898
1 #!/bin/bash
2
3 input_data_dir="test-data/data/input/"
4 output_sequence_dir="test-data/data/output_sequence_file/"
5 output_information_dir="test-data/data/output_information_file/"
6 output_report_dir="test-data/data/output_report_file/"
7 output_qual_dir="test-data/data/output_qual_file/"
8
9 ## Fasta format
10
11 echo "Read and write fasta file"
12 test_dir="test-data/data/read_write_fasta_file/"
13 python extract_sequence_file.py \
14 --input $test_dir/"input_sequence_file.fasta" \
15 --custom_extraction_type "no" \
16 --output_sequence $test_dir/"output_sequence_file.fasta" \
17 --report $test_dir"output_report.txt" \
18 --format "fasta"
19 python test-data/src/compare_files.py \
20 --exp_file $test_dir/"input_sequence_file.fasta" \
21 --obs_file $test_dir/"output_sequence_file.fasta" \
22 --comparison "Sequence file"
23 python test-data/src/compare_files.py \
24 --exp_file $test_dir"/expected_output_report.txt" \
25 --obs_file $test_dir"output_report.txt" \
26 --comparison "Report file"
27
28 echo "Simple extraction of fasta file"
29 test_dir="test-data/data/simple_extraction_fasta_file/"
30 python extract_sequence_file.py \
31 --input $test_dir/"input_sequence_file.fasta" \
32 --custom_extraction_type "yes" \
33 --output_information $test_dir"output_information.txt" \
34 --report $test_dir"output_report.txt" \
35 --to_extract "{id,length}" \
36 --format "fasta"
37 python test-data/src/compare_files.py \
38 --exp_file $test_dir"/expected_output_report.txt" \
39 --obs_file $test_dir"output_report.txt" \
40 --comparison "Report file"
41 python test-data/src/compare_files.py \
42 --exp_file $test_dir"expected_output_information.txt" \
43 --obs_file $test_dir"output_information.txt" \
44 --comparison "Information file"
45
46 echo "Simple constraint of fasta file"
47 test_dir="test-data/data/simple_constraint_fasta_file/"
48 python extract_sequence_file.py \
49 --input $test_dir/"input_sequence_file.fasta" \
50 --custom_extraction_type "yes" \
51 --output_information $test_dir"output_information.txt" \
52 --report $test_dir"output_report.txt" \
53 --to_extract "{id,length}" \
54 --constraint "length: greater: 100" \
55 --format "fasta"
56 python test-data/src/compare_files.py \
57 --exp_file $test_dir"/expected_output_report.txt" \
58 --obs_file $test_dir"output_report.txt" \
59 --comparison "Report file"
60 python test-data/src/compare_files.py \
61 --exp_file $test_dir"expected_output_information.txt" \
62 --obs_file $test_dir"output_information.txt" \
63 --comparison "Information file"
64
65 echo "Double constraints of fasta file"
66 test_dir="test-data/data/double_constraint_fasta_file/"
67 python extract_sequence_file.py \
68 --input $test_dir/"input_sequence_file.fasta" \
69 --custom_extraction_type "yes" \
70 --output_information $test_dir"output_information.txt" \
71 --report $test_dir"output_report.txt" \
72 --to_extract "{id,length}" \
73 --constraint "length: greater: 100" \
74 --constraint "id: in: test-data/data/id_in_list.txt" \
75 --format "fasta"
76 python test-data/src/compare_files.py \
77 --exp_file $test_dir"/expected_output_report.txt" \
78 --obs_file $test_dir"output_report.txt" \
79 --comparison "Report file"
80 python test-data/src/compare_files.py \
81 --exp_file $test_dir"expected_output_information.txt" \
82 --obs_file $test_dir"output_information.txt" \
83 --comparison "Information file"
84
85 ## Fastq format
86
87 echo "Read and write fastq file"
88 test_dir="test-data/data/read_write_fastq_file/"
89 python extract_sequence_file.py \
90 --input $test_dir/"input_sequence_file.fastq" \
91 --custom_extraction_type "no" \
92 --output_sequence $test_dir/"output_sequence_file.fastq" \
93 --report $test_dir"output_report.txt" \
94 --format "fastq"
95 python test-data/src/compare_files.py \
96 --exp_file $test_dir/"input_sequence_file.fastq" \
97 --obs_file $test_dir/"output_sequence_file.fastq" \
98 --comparison "Sequence file"
99 python test-data/src/compare_files.py \
100 --exp_file $test_dir"/expected_output_report.txt" \
101 --obs_file $test_dir"output_report.txt" \
102 --comparison "Report file"
103
104 echo "Read and split fastq file"
105 test_dir="test-data/data/split_fastq_file/"
106 python extract_sequence_file.py \
107 --input $test_dir/"input_sequence_file.fastq" \
108 --custom_extraction_type "no" \
109 --split "yes" \
110 --quality_format "sanger" \
111 --output_sequence $test_dir/"output_sequence_file.fasta" \
112 --output_quality $test_dir/"output_quality.qual" \
113 --report $test_dir"output_report.txt" \
114 --format "fastq"
115 python test-data/src/compare_files.py \
116 --exp_file $test_dir/"expected_output_sequence_file.fasta" \
117 --obs_file $test_dir/"output_sequence_file.fasta" \
118 --comparison "Sequence file"
119 python test-data/src/compare_files.py \
120 --exp_file $test_dir/"output_quality.qual" \
121 --obs_file $test_dir/"expected_output_quality.qual" \
122 --comparison "Quality file"
123 python test-data/src/compare_files.py \
124 --exp_file $test_dir"/expected_output_report.txt" \
125 --obs_file $test_dir"output_report.txt" \
126 --comparison "Report file"
127
128 echo "Simple extraction of fastq file"
129 test_dir="test-data/data/simple_extraction_fastq_file/"
130 python extract_sequence_file.py \
131 --input $test_dir/"input_sequence_file.fastq" \
132 --custom_extraction_type "yes" \
133 --output_information $test_dir"output_information.txt" \
134 --report $test_dir"output_report.txt" \
135 --to_extract "{id,length}" \
136 --format "fastq"
137 python test-data/src/compare_files.py \
138 --exp_file $test_dir"/expected_output_report.txt" \
139 --obs_file $test_dir"output_report.txt" \
140 --comparison "Report file"
141 python test-data/src/compare_files.py \
142 --exp_file $test_dir"expected_output_information.txt" \
143 --obs_file $test_dir"output_information.txt" \
144 --comparison "Information file"
145
146 echo "Simple constraint of fastq file"
147 test_dir="test-data/data/simple_constraint_fastq_file/"
148 python extract_sequence_file.py \
149 --input $test_dir/"input_sequence_file.fastq" \
150 --custom_extraction_type "yes" \
151 --output_information $test_dir"output_information.txt" \
152 --report $test_dir"output_report.txt" \
153 --to_extract "{id,length}" \
154 --constraint "length: greater: 100" \
155 --format "fastq"
156 python test-data/src/compare_files.py \
157 --exp_file $test_dir"/expected_output_report.txt" \
158 --obs_file $test_dir"output_report.txt" \
159 --comparison "Report file"
160 python test-data/src/compare_files.py \
161 --exp_file $test_dir"expected_output_information.txt" \
162 --obs_file $test_dir"output_information.txt" \
163 --comparison "Information file"
164
165 echo "Double constraint of fastq file"
166 test_dir="test-data/data/double_constraint_fastq_file/"
167 python extract_sequence_file.py \
168 --input $test_dir/"input_sequence_file.fastq" \
169 --custom_extraction_type "yes" \
170 --output_information $test_dir"output_information.txt" \
171 --report $test_dir"output_report.txt" \
172 --to_extract "{id,length}" \
173 --constraint "length: greater: 100" \
174 --constraint "id: in: test-data/data/id_in_list.txt" \
175 --format "fastq"
176 python test-data/src/compare_files.py \
177 --exp_file $test_dir"/expected_output_report.txt" \
178 --obs_file $test_dir"output_report.txt" \
179 --comparison "Report file"
180 python test-data/src/compare_files.py \
181 --exp_file $test_dir"expected_output_information.txt" \
182 --obs_file $test_dir"output_information.txt" \
183 --comparison "Information file"