annotate tools/fastq/fastq_groomer.xml @ 0:9071e359b9a3

Uploaded
author xuebing
date Fri, 09 Mar 2012 19:37:19 -0500
parents
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
1 <tool id="fastq_groomer" name="FASTQ Groomer" version="1.0.4">
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
2 <description>convert between various FASTQ quality formats</description>
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
3 <command interpreter="python">fastq_groomer.py '$input_file' '$input_type' '$output_file'
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
4 #if str( $options_type['options_type_selector'] ) == 'basic':
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
5 #if str( $input_type ) == 'cssanger':
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
6 'cssanger'
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
7 #else:
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
8 'sanger'
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
9 #end if
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
10 'ascii' 'summarize_input'
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
11 #else:
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
12 '${options_type.output_type}' '${options_type.force_quality_encoding}' '${options_type.summarize_input}'
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
13 #end if
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
14 </command>
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
15 <inputs>
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
16 <param name="input_file" type="data" format="fastq" label="File to groom" />
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
17 <param name="input_type" type="select" label="Input FASTQ quality scores type">
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
18 <option value="solexa">Solexa</option>
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
19 <option value="illumina">Illumina 1.3+</option>
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
20 <option value="sanger" selected="True">Sanger</option>
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
21 <option value="cssanger">Color Space Sanger</option>
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
22 </param>
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
23 <conditional name="options_type">
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
24 <param name="options_type_selector" type="select" label="Advanced Options">
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
25 <option value="basic" selected="True">Hide Advanced Options</option>
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
26 <option value="advanced">Show Advanced Options</option>
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
27 </param>
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
28 <when value="basic">
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
29 <!-- no options -->
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
30 </when>
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
31 <when value="advanced">
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
32 <param name="output_type" type="select" label="Output FASTQ quality scores type" help="Galaxy tools are designed to work with the Sanger Quality score format.">
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
33 <option value="solexa">Solexa</option>
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
34 <option value="illumina">Illumina 1.3+</option>
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
35 <option value="sanger" selected="True">Sanger (recommended)</option>
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
36 <option value="cssanger">Color Space Sanger</option>
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
37 </param>
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
38 <param name="force_quality_encoding" type="select" label="Force Quality Score encoding">
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
39 <option value="None">Use Source Encoding</option>
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
40 <option value="ascii" selected="True">ASCII</option>
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
41 <option value="decimal">Decimal</option>
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
42 </param>
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
43 <param name="summarize_input" type="select" label="Summarize input data">
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
44 <option value="summarize_input" selected="True">Summarize Input</option>
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
45 <option value="dont_summarize_input">Do not Summarize Input (faster)</option>
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
46 </param>
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
47 </when>
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
48 </conditional>
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
49 </inputs>
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
50 <outputs>
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
51 <data name="output_file" format="fastqsanger">
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
52 <change_format>
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
53 <when input="input_type" value="cssanger" format="fastqcssanger" />
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
54 <when input="options_type.output_type" value="solexa" format="fastqsolexa" />
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
55 <when input="options_type.output_type" value="illumina" format="fastqillumina" />
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
56 <when input="options_type.output_type" value="sanger" format="fastqsanger" />
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
57 <when input="options_type.output_type" value="cssanger" format="fastqcssanger" />
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
58 </change_format>
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
59 </data>
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
60 </outputs>
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
61 <tests>
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
62 <!-- These tests include test files adapted from supplemental material in Cock PJ, Fields CJ, Goto N, Heuer ML, Rice PM. The Sanger FASTQ file format for sequences with quality scores, and the Solexa/Illumina FASTQ variants. Nucleic Acids Res. 2009 Dec 16. -->
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
63 <!-- Unfortunately, cannot test for expected failures -->
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
64 <!-- Test basic options -->
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
65 <test>
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
66 <param name="input_file" value="sanger_full_range_original_sanger.fastqsanger" ftype="fastq" />
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
67 <param name="input_type" value="sanger" />
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
68 <param name="options_type_selector" value="basic" />
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
69 <output name="output_file" file="sanger_full_range_original_sanger.fastqsanger" />
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
70 </test>
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
71 <test>
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
72 <param name="input_file" value="sanger_full_range_as_cssanger.fastqcssanger" ftype="fastq" />
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
73 <param name="input_type" value="cssanger" />
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
74 <param name="options_type_selector" value="basic" />
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
75 <output name="output_file" file="sanger_full_range_as_cssanger.fastqcssanger" />
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
76 </test>
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
77 <test>
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
78 <param name="input_file" value="illumina_full_range_original_illumina.fastqillumina" ftype="fastq" />
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
79 <param name="input_type" value="illumina" />
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
80 <param name="options_type_selector" value="basic" />
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
81 <output name="output_file" file="illumina_full_range_as_sanger.fastqsanger" />
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
82 </test>
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
83 <test>
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
84 <param name="input_file" value="solexa_full_range_original_solexa.fastqsolexa" ftype="fastq" />
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
85 <param name="input_type" value="solexa" />
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
86 <param name="options_type_selector" value="basic" />
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
87 <output name="output_file" file="solexa_full_range_as_sanger.fastqsanger" />
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
88 </test>
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
89 <test>
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
90 <param name="input_file" value="sanger_full_range_as_illumina.fastqillumina" ftype="fastq" />
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
91 <param name="input_type" value="sanger" />
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
92 <param name="options_type_selector" value="basic" />
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
93 <output name="output_file" file="sanger_full_range_as_illumina.fastqillumina" />
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
94 </test>
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
95 <!-- Test grooming from illumina -->
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
96 <test>
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
97 <param name="input_file" value="illumina_full_range_original_illumina.fastqillumina" ftype="fastq" />
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
98 <param name="input_type" value="illumina" />
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
99 <param name="options_type_selector" value="advanced" />
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
100 <param name="output_type" value="illumina" />
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
101 <param name="force_quality_encoding" value="None" />
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
102 <param name="summarize_input" value="summarize_input" />
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
103 <output name="output_file" file="illumina_full_range_original_illumina.fastqillumina" />
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
104 </test>
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
105 <test>
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
106 <param name="input_file" value="illumina_full_range_original_illumina.fastqillumina" ftype="fastq" />
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
107 <param name="input_type" value="illumina" />
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
108 <param name="options_type_selector" value="advanced" />
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
109 <param name="output_type" value="sanger" />
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
110 <param name="force_quality_encoding" value="None" />
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
111 <param name="summarize_input" value="summarize_input" />
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
112 <output name="output_file" file="illumina_full_range_as_sanger.fastqsanger" />
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
113 </test>
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
114 <test>
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
115 <param name="input_file" value="illumina_full_range_original_illumina.fastqillumina" ftype="fastq" />
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
116 <param name="input_type" value="illumina" />
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
117 <param name="options_type_selector" value="advanced" />
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
118 <param name="output_type" value="solexa" />
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
119 <param name="force_quality_encoding" value="None" />
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
120 <param name="summarize_input" value="summarize_input" />
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
121 <output name="output_file" file="illumina_full_range_as_solexa.fastqsolexa" />
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
122 </test>
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
123 <test>
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
124 <param name="input_file" value="illumina_full_range_original_illumina.fastqillumina" ftype="fastq" />
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
125 <param name="input_type" value="illumina" />
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
126 <param name="options_type_selector" value="advanced" />
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
127 <param name="output_type" value="cssanger" />
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
128 <param name="force_quality_encoding" value="None" />
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
129 <param name="summarize_input" value="summarize_input" />
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
130 <output name="output_file" file="illumina_full_range_as_cssanger.fastqcssanger" />
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
131 </test>
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
132 <!-- Test grooming from sanger -->
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
133 <test>
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
134 <param name="input_file" value="sanger_full_range_original_sanger.fastqsanger" ftype="fastq" />
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
135 <param name="input_type" value="sanger" />
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
136 <param name="options_type_selector" value="advanced" />
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
137 <param name="output_type" value="sanger" />
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
138 <param name="force_quality_encoding" value="None" />
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
139 <param name="summarize_input" value="summarize_input" />
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
140 <output name="output_file" file="sanger_full_range_original_sanger.fastqsanger" />
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
141 </test>
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
142 <test>
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
143 <param name="input_file" value="sanger_full_range_original_sanger.fastqsanger" ftype="fastq" />
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
144 <param name="input_type" value="sanger" />
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
145 <param name="options_type_selector" value="advanced" />
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
146 <param name="output_type" value="illumina" />
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
147 <param name="force_quality_encoding" value="None" />
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
148 <param name="summarize_input" value="summarize_input" />
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
149 <output name="output_file" file="sanger_full_range_as_illumina.fastqillumina" />
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
150 </test>
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
151 <test>
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
152 <param name="input_file" value="sanger_full_range_original_sanger.fastqsanger" ftype="fastq" />
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
153 <param name="input_type" value="sanger" />
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
154 <param name="options_type_selector" value="advanced" />
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
155 <param name="output_type" value="solexa" />
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
156 <param name="force_quality_encoding" value="None" />
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
157 <param name="summarize_input" value="summarize_input" />
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
158 <output name="output_file" file="sanger_full_range_as_solexa.fastqsolexa" />
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
159 </test>
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
160 <test>
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
161 <param name="input_file" value="sanger_full_range_original_sanger.fastqsanger" ftype="fastq" />
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
162 <param name="input_type" value="sanger" />
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
163 <param name="options_type_selector" value="advanced" />
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
164 <param name="output_type" value="cssanger" />
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
165 <param name="force_quality_encoding" value="None" />
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
166 <param name="summarize_input" value="summarize_input" />
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
167 <output name="output_file" file="sanger_full_range_as_cssanger.fastqcssanger" />
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
168 </test>
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
169 <!-- Test grooming from solexa -->
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
170 <test>
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
171 <param name="input_file" value="solexa_full_range_original_solexa.fastqsolexa" ftype="fastq" />
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
172 <param name="input_type" value="solexa" />
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
173 <param name="options_type_selector" value="advanced" />
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
174 <param name="output_type" value="solexa" />
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
175 <param name="force_quality_encoding" value="None" />
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
176 <param name="summarize_input" value="summarize_input" />
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
177 <output name="output_file" file="solexa_full_range_original_solexa.fastqsolexa" />
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
178 </test>
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
179 <test>
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
180 <param name="input_file" value="solexa_full_range_original_solexa.fastqsolexa" ftype="fastq" />
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
181 <param name="input_type" value="solexa" />
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
182 <param name="options_type_selector" value="advanced" />
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
183 <param name="output_type" value="illumina" />
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
184 <param name="force_quality_encoding" value="None" />
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
185 <param name="summarize_input" value="summarize_input" />
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
186 <output name="output_file" file="solexa_full_range_as_illumina.fastqillumina" />
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
187 </test>
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
188 <test>
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
189 <param name="input_file" value="solexa_full_range_original_solexa.fastqsolexa" ftype="fastq" />
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
190 <param name="input_type" value="solexa" />
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
191 <param name="options_type_selector" value="advanced" />
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
192 <param name="output_type" value="sanger" />
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
193 <param name="force_quality_encoding" value="None" />
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
194 <param name="summarize_input" value="summarize_input" />
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
195 <output name="output_file" file="solexa_full_range_as_sanger.fastqsanger" />
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
196 </test>
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
197 <test>
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
198 <param name="input_file" value="solexa_full_range_original_solexa.fastqsolexa" ftype="fastq" />
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
199 <param name="input_type" value="solexa" />
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
200 <param name="options_type_selector" value="advanced" />
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
201 <param name="output_type" value="cssanger" />
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
202 <param name="force_quality_encoding" value="None" />
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
203 <param name="summarize_input" value="summarize_input" />
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
204 <output name="output_file" file="solexa_full_range_as_cssanger.fastqcssanger" />
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
205 </test>
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
206 <!-- Test grooming from cssanger -->
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
207 <test>
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
208 <param name="input_file" value="sanger_full_range_as_cssanger.fastqcssanger" ftype="fastq" />
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
209 <param name="input_type" value="cssanger" />
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
210 <param name="options_type_selector" value="advanced" />
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
211 <param name="output_type" value="cssanger" />
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
212 <param name="force_quality_encoding" value="None" />
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
213 <param name="summarize_input" value="summarize_input" />
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
214 <output name="output_file" file="sanger_full_range_as_cssanger.fastqcssanger" />
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
215 </test>
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
216 <test>
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
217 <param name="input_file" value="sanger_full_range_as_cssanger.fastqcssanger" ftype="fastq" />
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
218 <param name="input_type" value="cssanger" />
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
219 <param name="options_type_selector" value="advanced" />
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
220 <param name="output_type" value="sanger" />
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
221 <param name="force_quality_encoding" value="None" />
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
222 <param name="summarize_input" value="summarize_input" />
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
223 <output name="output_file" file="sanger_full_range_original_sanger.fastqsanger" />
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
224 </test>
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
225 <test>
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
226 <param name="input_file" value="sanger_full_range_as_cssanger.fastqcssanger" ftype="fastq" />
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
227 <param name="input_type" value="cssanger" />
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
228 <param name="options_type_selector" value="advanced" />
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
229 <param name="output_type" value="illumina" />
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
230 <param name="force_quality_encoding" value="None" />
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
231 <param name="summarize_input" value="summarize_input" />
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
232 <output name="output_file" file="sanger_full_range_as_illumina.fastqillumina" />
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
233 </test>
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
234 <test>
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
235 <param name="input_file" value="sanger_full_range_as_cssanger.fastqcssanger" ftype="fastq" />
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
236 <param name="input_type" value="cssanger" />
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
237 <param name="options_type_selector" value="advanced" />
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
238 <param name="output_type" value="solexa" />
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
239 <param name="force_quality_encoding" value="None" />
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
240 <param name="summarize_input" value="summarize_input" />
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
241 <output name="output_file" file="sanger_full_range_as_solexa.fastqsolexa" />
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
242 </test>
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
243 <test>
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
244 <param name="input_file" value="sanger_full_range_as_cssanger_adapter_base_with_quality_score.fastqcssanger_fake_score" ftype="fastq" />
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
245 <param name="input_type" value="cssanger" />
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
246 <param name="options_type_selector" value="advanced" />
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
247 <param name="output_type" value="cssanger" />
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
248 <param name="force_quality_encoding" value="None" />
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
249 <param name="summarize_input" value="summarize_input" />
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
250 <output name="output_file" file="sanger_full_range_as_cssanger.fastqcssanger" />
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
251 </test>
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
252 <!-- Test fastq with line wrapping -->
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
253 <test>
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
254 <param name="input_file" value="wrapping_original_sanger.fastqsanger" ftype="fastq" />
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
255 <param name="input_type" value="sanger" />
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
256 <param name="options_type_selector" value="advanced" />
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
257 <param name="output_type" value="sanger" />
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
258 <param name="force_quality_encoding" value="None" />
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
259 <param name="summarize_input" value="summarize_input" />
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
260 <output name="output_file" file="wrapping_as_sanger.fastqsanger" />
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
261 </test>
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
262 <test>
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
263 <param name="input_file" value="wrapping_original_sanger.fastqsanger" ftype="fastq" />
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
264 <param name="input_type" value="sanger" />
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
265 <param name="options_type_selector" value="advanced" />
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
266 <param name="output_type" value="illumina" />
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
267 <param name="force_quality_encoding" value="None" />
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
268 <param name="summarize_input" value="summarize_input" />
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
269 <output name="output_file" file="wrapping_as_illumina.fastqillumina" />
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
270 </test>
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
271 <test>
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
272 <param name="input_file" value="wrapping_original_sanger.fastqsanger" ftype="fastq" />
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
273 <param name="input_type" value="sanger" />
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
274 <param name="options_type_selector" value="advanced" />
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
275 <param name="output_type" value="solexa" />
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
276 <param name="force_quality_encoding" value="None" />
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
277 <param name="summarize_input" value="summarize_input" />
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
278 <output name="output_file" file="wrapping_as_solexa.fastqsolexa" />
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
279 </test>
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
280 <!-- Test forcing quality score encoding -->
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
281 <!-- Sanger, range 0 - 93 -->
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
282 <test>
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
283 <param name="input_file" value="sanger_full_range_as_decimal_sanger.fastqsanger" ftype="fastq" />
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
284 <param name="input_type" value="sanger" />
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
285 <param name="options_type_selector" value="advanced" />
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
286 <param name="output_type" value="sanger" />
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
287 <param name="force_quality_encoding" value="ascii" />
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
288 <param name="summarize_input" value="summarize_input" />
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
289 <output name="output_file" file="sanger_full_range_original_sanger.fastqsanger" />
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
290 </test>
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
291 <test>
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
292 <param name="input_file" value="sanger_full_range_original_sanger.fastqsanger" ftype="fastq" />
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
293 <param name="input_type" value="sanger" />
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
294 <param name="options_type_selector" value="advanced" />
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
295 <param name="output_type" value="sanger" />
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
296 <param name="force_quality_encoding" value="decimal" />
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
297 <param name="summarize_input" value="summarize_input" />
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
298 <output name="output_file" file="sanger_full_range_as_decimal_sanger.fastqsanger" />
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
299 </test>
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
300 <test>
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
301 <param name="input_file" value="sanger_full_range_as_tab_decimal_sanger.fastqsanger" ftype="fastq" />
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
302 <param name="input_type" value="sanger" />
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
303 <param name="options_type_selector" value="advanced" />
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
304 <param name="output_type" value="sanger" />
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
305 <param name="force_quality_encoding" value="ascii" />
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
306 <param name="summarize_input" value="summarize_input" />
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
307 <output name="output_file" file="sanger_full_range_original_sanger.fastqsanger" />
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
308 </test>
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
309 <!-- Solexa, range -5 - 62 -->
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
310 <test>
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
311 <param name="input_file" value="solexa_full_range_as_decimal_solexa.fastqsolexa" ftype="fastq" />
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
312 <param name="input_type" value="solexa" />
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
313 <param name="options_type_selector" value="advanced" />
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
314 <param name="output_type" value="solexa" />
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
315 <param name="force_quality_encoding" value="ascii" />
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
316 <param name="summarize_input" value="summarize_input" />
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
317 <output name="output_file" file="solexa_full_range_original_solexa.fastqsolexa" />
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
318 </test>
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
319 <test>
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
320 <param name="input_file" value="solexa_full_range_original_solexa.fastqsolexa" ftype="fastq" />
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
321 <param name="input_type" value="solexa" />
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
322 <param name="options_type_selector" value="advanced" />
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
323 <param name="output_type" value="solexa" />
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
324 <param name="force_quality_encoding" value="decimal" />
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
325 <param name="summarize_input" value="summarize_input" />
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
326 <output name="output_file" file="solexa_full_range_as_decimal_solexa.fastqsolexa" />
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
327 </test>
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
328 </tests>
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
329 <help>
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
330 **What it does**
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
331
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
332 This tool offers several conversions options relating to the FASTQ format.
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
333
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
334 When using *Basic* options, the output will be *sanger* formatted or *cssanger* formatted (when the input is Color Space Sanger).
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
335
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
336 When converting, if a quality score falls outside of the target score range, it will be coerced to the closest available value (i.e. the minimum or maximum).
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
337
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
338 When converting between Solexa and the other formats, quality scores are mapped between Solexa and PHRED scales using the equations found in `Cock PJ, Fields CJ, Goto N, Heuer ML, Rice PM. The Sanger FASTQ file format for sequences with quality scores, and the Solexa/Illumina FASTQ variants. Nucleic Acids Res. 2009 Dec 16.`_
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
339
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
340 When converting between color space (csSanger) and base/sequence space (Sanger, Illumina, Solexa) formats, adapter bases are lost or gained; if gained, the base 'G' is used as the adapter. You cannot convert a color space read to base space if there is no adapter present in the color space sequence. Any masked or ambiguous nucleotides in base space will be converted to 'N's when determining color space encoding.
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
341
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
342 -----
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
343
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
344 **Quality Score Comparison**
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
345
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
346 ::
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
347
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
348 SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
349 ...............................IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
350 ..........................XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
351 !"#$%&amp;'()*+,-./0123456789:;&lt;=&gt;?@ABCDEFGHIJKLMNOPQRSTUVWXYZ[\]^_`abcdefghijklmnopqrstuvwxyz{|}~
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
352 | | | | | |
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
353 33 59 64 73 104 126
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
354
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
355 S - Sanger Phred+33, 93 values (0, 93) (0 to 60 expected in raw reads)
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
356 I - Illumina 1.3 Phred+64, 62 values (0, 62) (0 to 40 expected in raw reads)
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
357 X - Solexa Solexa+64, 67 values (-5, 62) (-5 to 40 expected in raw reads)
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
358
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
359 Diagram adapted from http://en.wikipedia.org/wiki/FASTQ_format
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
360
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
361 ------
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
362
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
363 **Citation**
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
364
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
365 If you use this tool, please cite `Blankenberg D, Gordon A, Von Kuster G, Coraor N, Taylor J, Nekrutenko A; Galaxy Team. Manipulation of FASTQ data with Galaxy. Bioinformatics. 2010 Jul 15;26(14):1783-5. &lt;http://www.ncbi.nlm.nih.gov/pubmed/20562416&gt;`_
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
366
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
367
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
368 .. _Cock PJ, Fields CJ, Goto N, Heuer ML, Rice PM. The Sanger FASTQ file format for sequences with quality scores, and the Solexa/Illumina FASTQ variants. Nucleic Acids Res. 2009 Dec 16.: http://www.ncbi.nlm.nih.gov/pubmed/20015970
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
369
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
370 </help>
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
371 </tool>