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comparison extract_sequence_file.xml @ 0:14fd6f3b0898 draft

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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 <tool id="extract_sequence_file" name="Extract" version="0.1.0">
2
3 <description>from sequence file</description>
4
5 <macros>
6 <xml name="fasta_option">
7 <option value="id">Identifiant</option>
8 <option value="length">Length</option>
9 <option value="description">Description</option>
10 </xml>
11 <xml name="fastq_option">
12 <option value="id">Identifiant</option>
13 <option value="length">Length</option>
14 <option value="description">Description</option>
15 </xml>
16 <xml name="test_constrain_extraction">
17 <param name='constrained_extraction' type='boolean' checked="false"
18 truevalue='true' falsevalue='false' label="Constrain extraction?" help=""/>
19 </xml>
20 <xml name="constrain_string">
21 <conditional name="constraint_type">
22 <param name="type" type="select" display="radio" label="Type of
23 constraint" help="">
24 <option value="equal">Equal a value</option>
25 <option value="in">In a list</option>
26 <option value="not_in">Not in a list</option>
27 </param>
28 <when value="equal">
29 <param name="value" type="text" size="200" label="Equal to"
30 help=""/>
31 <validator type="empty_field" message="Give a value"/>
32 </when>
33 <when value="in">
34 <param format="txt" name="value" type="data" label="List of
35 constraint" help="Text file with a value per line and
36 nothing else"/>
37 <validator type="unspecified_build" message="Select a file"/>
38 </when>
39 <when value="not_in">
40 <param format="txt" name="value" type="data" label="List of
41 constraint" help="Text file with a value per line and
42 nothing else"/>
43 <validator type="unspecified_build" message="Select a file"/>
44 </when>
45 </conditional>
46 </xml>
47 <xml name="constrain_number">
48 <param name="type" type="select" label="Type of constraint" help="">
49 <option value="equal">Equal to </option>
50 <option value="lower">Lower than </option>
51 <option value="strictly_lower">Strictly lower than </option>
52 <option value="greater">Greater than </option>
53 <option value="strictly_greater">Strictly greater than </option>
54 </param>
55 </xml>
56 <xml name="constraint_definitions">
57 <conditional name="constraints">
58 <expand macro="test_constrain_extraction" />
59 <when value="true">
60 <repeat name="constraint_definition" title="Constraints on
61 sequences" min="1">
62 <conditional name="constrained_information">
63 <param name="info_to_constrain" type="select"
64 label="Information to constrain" help="">
65 <option value="id">Identifiant</option>
66 <option value="length">Length</option>
67 </param>
68 <when value="id">
69 <expand macro="constrain_string" />
70 </when>
71 <when value="length">
72 <repeat name="constraint_definition" title="Constraint
73 on sequence length" min="1">
74 <expand macro="constrain_number" />
75 <param name="value" type="integer" min="0"
76 max="3000" value="100" label="Value" help=""/>
77 </repeat>
78 </when>
79 </conditional>
80 </repeat>
81 </when>
82 <when value="false" />
83 </conditional>
84 </xml>
85 </macros>
86
87 <requirements>
88 </requirements>
89
90 <stdio>
91 </stdio>
92
93 <version_command><![CDATA[python -version]]></version_command>
94
95 <!--<command>-->
96 <command><![CDATA[
97 python $__tool_directory__/extract_sequence_file.py
98 --input=$sequence_file_format.sequence_file
99
100 --custom_extraction_type=$sequence_file_format.extraction.specific_extraction
101 #if $sequence_file_format.extraction.specific_extraction :
102 --to_extract="{$sequence_file_format.extraction.to_extract}"
103 --output_information=$information_file
104 #else if $sequence_file_format.format=="fastq":
105 --split=$sequence_file_format.extraction.split.split_test
106 #if $sequence_file_format.extraction.split.split_test :
107 --quality_format=$sequence_file_format.extraction.split.quality_format
108 --output_sequence=$fasta_sequence_file_from_fastq
109 --output_quality=$quality_file
110 #else:
111 --output_sequence=$fastq_sequence_file
112 #end if
113 #else:
114 --output_sequence=$fasta_sequence_file
115 #end if
116
117 #if $constraints.constrained_extraction :
118 #for $i, $constrain in enumerate( $constraints.constraint_definition )
119 #set info_to_constrain=$constrain.constrained_information['info_to_constrain']
120 #if $info_to_constrain in ("id"):
121 --constraint="$info_to_constrain:
122 ${constrain.constrained_information.constraint_type.type}:
123 ${constrain.constrained_information.constraint_type.value}"
124 #else:
125 #for $j, $sub_constrain in enumerate( $constrain.constrained_information.constraint_definition )
126 --constraint="$info_to_constrain:
127 ${sub_constrain.type}:
128 ${sub_constrain.value}"
129 #end for
130 #end if
131 #end for
132 #end if
133
134 --report $report_filepath
135 --format=$sequence_file_format.format
136 ]]>
137 </command>
138
139 <inputs>
140 <conditional name="sequence_file_format">
141 <param name="format" type="select" display="radio"
142 label="Format of the sequence file" help="">
143 <option value="fasta">Fasta</option>
144 <option value="fastq">FastQ</option>
145 </param>
146 <when value="fastq">
147 <param name="sequence_file" type="data" format="fastq"
148 label="Sequence file" help=""/>
149 <conditional name="extraction">
150 <param name='specific_extraction' type='boolean'
151 checked="false" truevalue='true' falsevalue='false'
152 label="Extract specific information?"
153 help="If no is selected, a sequence file is generated.
154 If yes, a text file containing the wanted information is
155 generated"/>
156 <when value="true">
157 <param name="to_extract" type="select" display="checkboxes"
158 multiple="true" label="Information to extract" help="">
159 <expand macro="fasta_option" />
160 <validator type="no_options" message="Select at least
161 one information to extract"/>
162 </param>
163 </when>
164 <when value="false">
165 <conditional name="split">
166 <param name='split_test' type='boolean' checked="false"
167 truevalue='true' falsevalue='false' label="Split
168 file into sequence and quality files?" help="If
169 yes is selected, a fasta and a quality file are
170 generated. If no, a fastq file is generated"/>
171 <when value="true">
172 <param name="quality_format" type="select"
173 display="radio" label="Coding of quality
174 scores?" help="">
175 <option value="sanger" selected="true">Sanger (Phred+33)</option>
176 <option value="solexa">Solexa (Solexa+64) </option>
177 <option value="illumina_1_3">Illumina 1.3+ (Phred+64) </option>
178 <option value="illumina_1_5">Illumina 1.5+ (Phred+64) </option>
179 <option value="illumina_1_8">Illumina 1.8+ (Phred+33) </option>
180 </param>
181 </when>
182 <when value="false" />
183 </conditional>
184 </when>
185 </conditional>
186 </when>
187 <when value="fasta">
188 <param name="sequence_file" type="data" format="fasta"
189 label="Sequence file" help=""/>
190 <conditional name="extraction">
191 <param name='specific_extraction' type='boolean' checked="false"
192 truevalue='true' falsevalue='false' label="Extract specific
193 information?" help="If no is selected, a sequence file is
194 generated. If yes, a text file containing the wanted
195 information is generated"/>
196 <when value="true">
197 <param name="to_extract" type="select" display="checkboxes"
198 multiple="true" label="Information to extract" help="">
199 <expand macro="fasta_option" />
200 <validator type="no_options" message="Select at least
201 one information to extract"/>
202 </param>
203 </when>
204 <when value="false" />
205 </conditional>
206 </when>
207 </conditional>
208
209 <expand macro="constraint_definitions" />
210 </inputs>
211
212 <outputs>
213 <data format="txt" name="information_file"
214 label="${tool.name} on ${on_string}: Information">
215 <filter>((sequence_file_format['extraction']['specific_extraction']))</filter>
216 </data>
217
218 <data format="fasta" name="fasta_sequence_file"
219 label="${tool.name} on ${on_string}: Extracted sequences" >
220 <filter>((sequence_file_format['format'] == 'fasta' and
221 not sequence_file_format['extraction']['specific_extraction']))</filter>
222 </data>
223
224 <data format="fastq" name="fastq_sequence_file"
225 label="${tool.name} on ${on_string}: Extracted sequences">
226 <filter>((sequence_file_format['format'] == 'fastq' and
227 not sequence_file_format['extraction']['specific_extraction'] and
228 not sequence_file_format['extraction']['split']['split_test']))</filter>
229 </data>
230
231 <data format="qual" name="quality_file"
232 label="${tool.name} on ${on_string}: Extracted quality">
233 <filter>((sequence_file_format['format'] == 'fastq' and
234 not sequence_file_format['extraction']['specific_extraction'] and
235 sequence_file_format['extraction']['split']['split_test']))</filter>
236 </data>
237
238 <data format="fasta" name="fasta_sequence_file_from_fastq"
239 label="${tool.name} on ${on_string}: Extracted sequences">
240 <filter>((sequence_file_format['format'] == 'fastq' and
241 not sequence_file_format['extraction']['specific_extraction'] and
242 sequence_file_format['extraction']['split']['split_test']))</filter>
243 </data>
244
245 <data format="txt" name="report_filepath"
246 label="${tool.name} on ${on_string}: Report"/>
247 </outputs>
248
249 <tests>
250 <test>
251 <param name="sequence_file_format.sequence_file"
252 value="read_write_fasta_file/input_sequence_file.fasta"/>
253 <param name="sequence_file_format.extraction.specific_extraction"
254 value="false"/>
255 <param name="$sequence_file_format.format" value="fasta" />
256 <output name="fasta_sequence_file"
257 file="read_write_fasta_file/input_sequence_file.fasta"/>
258 <output name="report_filepath"
259 file="read_write_fasta_file/expected_output_report.txt"/>
260 </test>
261 </tests>
262
263 <help><![CDATA[
264
265 **What it does**
266
267 This tool extracts information from sequence files.
268
269 Some constraints could be added to extraction. For example, you choose
270 to extract only sequences for which the length is greater than 30 bp.
271
272 More information on `ASaiM documentation <http://asaim.readthedocs.org/>`_...
273
274 -----
275
276 **Input**
277
278 The input is one file in fasta or fastq.
279
280 -----
281
282 **Outputs**
283
284 The tool generates different outputs given the choosen parameters:
285
286 - a sequence file
287 - a text file
288 - a sequence file and a quality file
289
290 ]]>
291 </help>
292
293 <citations>
294 </citations>
295 </tool>
296