Mercurial > repos > iuc > read_it_and_keep
comparison read-it-and-keep.xml @ 1:1563b58905f4 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/read-it-and-keep commit 5fcc308928ab2417b7e40227b27a3955f227649d"
author | iuc |
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date | Thu, 17 Mar 2022 11:12:09 +0000 |
parents | 554aa2a63f04 |
children | fa7086274673 |
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0:554aa2a63f04 | 1:1563b58905f4 |
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1 <tool id="read_it_and_keep" name="Read It and Keep" version="@TOOL_VERSION@+galaxy0" profile="20.09"> | 1 <tool id="read_it_and_keep" name="Read It and Keep" version="@TOOL_VERSION@+galaxy0" profile="20.09"> |
2 <macros> | 2 <macros> |
3 <token name="@FASTQ_FORMATS@">fastq,fastq.gz,fastqsanger,fastqsanger.gz</token> | 3 <token name="@INPUT_FORMATS@">fasta,fastq,fasta.gz,fastq.gz</token> |
4 <token name="@TOOL_VERSION@">0.1.0</token> | 4 <token name="@TOOL_VERSION@">0.2.2</token> |
5 </macros> | 5 </macros> |
6 <requirements> | 6 <requirements> |
7 <requirement type="package" version="@TOOL_VERSION@">read-it-and-keep</requirement> | 7 <requirement type="package" version="@TOOL_VERSION@">read-it-and-keep</requirement> |
8 <requirement type="package">python</requirement> | 8 <requirement type="package" version="3.10">python</requirement> |
9 </requirements> | 9 </requirements> |
10 <version_command><![CDATA[readItAndKeep -V]]></version_command> | |
10 <command detect_errors="exit_code"><![CDATA[ | 11 <command detect_errors="exit_code"><![CDATA[ |
11 #if $ref_source.source == "history" | 12 #if $ref_source.source == "history" |
12 ln -s '$ref_source.ref_fasta' ref${trim_reference}.fasta && | 13 ln -s '$ref_source.ref_fasta' ref${trim_reference}.fasta && |
13 #elif $ref_source.source == "builtin" | 14 #elif $ref_source.source == "builtin" |
14 ln -s '$ref_source.ref_fasta_builtin.path' ref${trim_reference}.fasta && | 15 ln -s '$ref_source.ref_fasta_builtin.path' ref${trim_reference}.fasta && |
15 #end if | 16 #end if |
16 #if $trim_reference | 17 #if $trim_reference |
17 python '$__tool_directory__/trim_reference.py' ref${trim_reference}.fasta ref.fasta && | 18 python '$__tool_directory__/trim_reference.py' ref${trim_reference}.fasta ref.fasta && |
18 #end if | 19 #end if |
19 #if $reads.read_type == "paired" | 20 #if $reads.read_type == "paired" |
20 ln -s '$reads.read1' read1.fastq && | 21 #set $ext_out1 = 'fasta' if $reads.read1.ext in ['fasta', 'fasta.gz'] else 'fastq' |
21 ln -s '$reads.read2' read2.fastq && | 22 #set $ext_out2 = 'fasta' if $reads.read1.ext in ['fasta', 'fasta.gz'] else 'fastq' |
23 ln -s '$reads.read1' read1 && | |
24 ln -s '$reads.read2' read2 && | |
22 #elif $reads.read_type == 'paired_collection' | 25 #elif $reads.read_type == 'paired_collection' |
23 ln -s '$reads.paired_reads.forward' read1.fastq && | 26 #set $ext_out1 = 'fasta' if $reads.paired_reads.forward.ext in ['fasta', 'fasta.gz'] else 'fastq' |
24 ln -s '$reads.paired_reads.reverse' read2.fastq && | 27 #set $ext_out2 = 'fasta' if $reads.paired_reads.reverse.ext in ['fasta', 'fasta.gz'] else 'fastq' |
28 ln -s '$reads.paired_reads.forward' read1 && | |
29 ln -s '$reads.paired_reads.reverse' read2 && | |
25 #elif $reads.read_type == 'single' | 30 #elif $reads.read_type == 'single' |
26 ln -s '$reads.single_read1' read1.fastq && | 31 #set $ext_out1 = 'fasta' if $reads.read1.ext in ['fasta', 'fasta.gz'] else 'fastq' |
32 ln -s '$reads.read1' read1 && | |
27 #end if | 33 #end if |
28 readItAndKeep | 34 readItAndKeep |
29 --tech $sequencing_tech | 35 --tech $sequencing_tech |
30 --ref_fasta ref.fasta | 36 --ref_fasta ref.fasta |
31 --min_map_length $adv.min_map_length | 37 --min_map_length $adv.min_map_length |
32 --min_map_length_pc $adv.min_map_length_pc | 38 --min_map_length_pc $adv.min_map_length_pc |
33 --reads1 read1.fastq | 39 $adv.enumerate_names |
40 --reads1 read1 | |
34 #if $reads.read_type != "single" | 41 #if $reads.read_type != "single" |
35 --reads2 read2.fastq | 42 --reads2 read2 |
36 #end if | 43 #end if |
37 -o output | 44 -o output |
38 #if $reads.read_type == 'single' | 45 #if $reads.read_type == 'single': |
39 && mv output.reads.fastq.gz output.reads_1.fastq.gz | 46 && mv output.reads.${ext_out1}.gz output.reads_1.${ext_out1}.gz |
47 #end if | |
48 #if $reads.read_type == 'paired_collection': | |
49 #if not $reads.paired_reads.forward.ext.endswith('.gz'): | |
50 && gunzip ./output.reads_1.${ext_out1}.gz | |
51 && gunzip ./output.reads_2.${ext_out2}.gz | |
52 #end if | |
53 #elif not $reads.read1.ext.endswith('.gz'): | |
54 && gunzip ./output.reads_1.${ext_out1}.gz | |
55 #if $reads.read_type != 'single' and not $reads.read2.ext.endswith('.gz'): | |
56 && gunzip ./output.reads_2.${ext_out2}.gz | |
57 #end if | |
40 #end if | 58 #end if |
41 ]]></command> | 59 ]]></command> |
42 <inputs> | 60 <inputs> |
43 <conditional name="reads"> | 61 <conditional name="reads"> |
44 <param type="select" label="Read type" name="read_type"> | 62 <param type="select" label="Read type" name="read_type"> |
45 <option value="paired" selected="true">Paired end</option> | 63 <option value="paired" selected="true">Paired end</option> |
46 <option value="paired_collection">Paired collection</option> | 64 <option value="paired_collection">Paired collection</option> |
47 <option value="single">Single ended</option> | 65 <option value="single">Single ended</option> |
48 </param> | 66 </param> |
49 <when value="paired"> | 67 <when value="paired"> |
50 <param type="data" format="@FASTQ_FORMATS@" name="read1" label="Read1" /> | 68 <param type="data" format="@INPUT_FORMATS@" name="read1" label="Read1" /> |
51 <param type="data" format="@FASTQ_FORMATS@" name="read2" label="Read2" /> | 69 <param type="data" format="@INPUT_FORMATS@" name="read2" label="Read2" /> |
52 </when> | 70 </when> |
53 <when value="paired_collection"> | 71 <when value="paired_collection"> |
54 <param type="data_collection" collection_type="paired" format="@FASTQ_FORMATS@" name="paired_reads" label="Reads" /> | 72 <param type="data_collection" collection_type="paired" format="@INPUT_FORMATS@" name="paired_reads" label="Reads" /> |
55 </when> | 73 </when> |
56 <when value="single"> | 74 <when value="single"> |
57 <param type="data" format="@FASTQ_FORMATS@" name="single_read1" label="Read1" /> | 75 <param type="data" format="@INPUT_FORMATS@" name="read1" label="Read1" /> |
58 </when> | 76 </when> |
59 </conditional> | 77 </conditional> |
60 <conditional name="ref_source"> | 78 <conditional name="ref_source"> |
61 <param type="select" label="Reference genome source" name="source"> | 79 <param type="select" label="Reference genome source" name="source"> |
62 <option value="history" selected="true">History</option> | 80 <option value="history" selected="true">History</option> |
77 <option value="ont">Oxford Nanopore</option> | 95 <option value="ont">Oxford Nanopore</option> |
78 </param> | 96 </param> |
79 <section name="adv" title="Advanced options"> | 97 <section name="adv" title="Advanced options"> |
80 <param argument="--min_map_length" type="integer" min="0" value="50" label="Shortest match required to keep a read (in bp)" /> | 98 <param argument="--min_map_length" type="integer" min="0" value="50" label="Shortest match required to keep a read (in bp)" /> |
81 <param argument="--min_map_length_pc" type="float" min="0.0" max="100.0" value="50.0" label="Minimum length of match required to keep a read (as percentage of read length" /> | 99 <param argument="--min_map_length_pc" type="float" min="0.0" max="100.0" value="50.0" label="Minimum length of match required to keep a read (as percentage of read length" /> |
100 <param name="enumerate_names" type="boolean" truevalue="--enumerate_names" falsevalue="" label="Rename the reads 1,2,3,... (for paired reads, will also add /1 or /2 to the end of names)" /> | |
82 </section> | 101 </section> |
83 </inputs> | 102 </inputs> |
84 <outputs> | 103 <outputs> |
85 <data name="output_reads1" format="fastqsanger.gz" label="Filtered reads ${on_string} - reads1" from_work_dir="output.reads_1.fastq.gz"> | 104 <data name="output_reads1" format_source="read1" label="Filtered reads ${on_string} - reads1" from_work_dir="output.reads_1.fast*"> |
86 <filter>reads["read_type"] == "single" or reads["read_type"] == "paired"</filter> | 105 <filter>reads["read_type"] == "single" or reads["read_type"] == "paired"</filter> |
87 </data> | 106 </data> |
88 <data name="output_reads2" format="fastqsanger.gz" label="Filtered reads ${on_string} - reads2" from_work_dir="output.reads_2.fastq.gz"> | 107 <data name="output_reads2" format_source="read2" label="Filtered reads ${on_string} - reads2" from_work_dir="output.reads_2.fast*"> |
89 <filter>reads["read_type"] == "paired"</filter> | 108 <filter>reads["read_type"] == "paired"</filter> |
90 </data> | 109 </data> |
91 <collection type="paired" format="fastqsanger.gz" name="output_collection" label="Filtered reads ${on_string}"> | 110 <collection type="paired" name="output_collection" format_source="paired_reads" label="Filtered reads ${on_string}"> |
92 <filter>reads["read_type"] == "paired_collection"</filter> | 111 <filter>reads["read_type"] == "paired_collection"</filter> |
93 <data name="forward" format="fastqsanger.gz" from_work_dir="output.reads_1.fastq.gz" /> | 112 <data name="forward" from_work_dir="output.reads_1.fast*" /> |
94 <data name="reverse" format="fastqsanger.gz" from_work_dir="output.reads_2.fastq.gz" /> | 113 <data name="reverse" from_work_dir="output.reads_2.fast*" /> |
95 </collection> | 114 </collection> |
96 </outputs> | 115 </outputs> |
97 <tests> | 116 <tests> |
117 <!--Testing uncompressed fastq input--> | |
118 <test expect_num_outputs="2"> | |
119 <conditional name="reads"> | |
120 <param name="read_type" value="paired" /> | |
121 <param name="read1" value="test1.fastq.gz" ftype="fastqsanger" /> | |
122 <param name="read2" value="test2.fastq.gz" ftype="fastqsanger" /> | |
123 </conditional> | |
124 <conditional name="ref_source"> | |
125 <param name="source" value="history" /> | |
126 <param name="ref_fasta" value="reference.fasta" ftype="fasta" /> | |
127 </conditional> | |
128 <param name="sequencing_tech" value="illumina" /> | |
129 <output name="output_reads1" file="output.test1.reads_1.fastq" ftype="fastqsanger"/> | |
130 <output name="output_reads2" file="output.test1.reads_2.fastq" ftype="fastqsanger"/> | |
131 </test> | |
132 <test expect_num_outputs="3"> | |
133 <conditional name="reads"> | |
134 <param name="read_type" value="paired_collection" /> | |
135 <param name="paired_reads"> | |
136 <collection type="paired"> | |
137 <element name="forward" value="test1.fastq.gz" ftype="fastqsanger" /> | |
138 <element name="reverse" value="test2.fastq.gz" ftype="fastqsanger" /> | |
139 </collection> | |
140 </param> | |
141 </conditional> | |
142 <conditional name="ref_source"> | |
143 <param name="source" value="history" /> | |
144 <param name="ref_fasta" value="reference.fasta" ftype="fasta" /> | |
145 </conditional> | |
146 <param name="sequencing_tech" value="illumina" /> | |
147 <output_collection name="output_collection" type="paired"> | |
148 <element name="forward" file="output.test1.reads_1.fastq" ftype="fastqsanger"/> | |
149 <element name="reverse" file="output.test1.reads_2.fastq" ftype="fastqsanger"/> | |
150 </output_collection> | |
151 </test> | |
152 <test expect_num_outputs="1"> | |
153 <conditional name="reads"> | |
154 <param name="read_type" value="single" /> | |
155 <param name="read1" value="test3.fastq.gz" ftype="fastqsanger"/> | |
156 </conditional> | |
157 <conditional name="ref_source"> | |
158 <param name="source" value="history" /> | |
159 <param name="ref_fasta" value="reference.fasta" ftype="fasta" /> | |
160 </conditional> | |
161 <param name="sequencing_tech" value="ont" /> | |
162 <param name="enumerate_names" value="True" /> | |
163 <output name="output_reads1" file="output.test3.reads_1.fastq" ftype="fastqsanger"/> | |
164 </test> | |
165 <!--Testing uncompressed fasta input--> | |
166 <test expect_num_outputs="2"> | |
167 <conditional name="reads"> | |
168 <param name="read_type" value="paired" /> | |
169 <param name="read1" value="test1.fasta.gz" ftype="fasta" /> | |
170 <param name="read2" value="test2.fasta.gz" ftype="fasta" /> | |
171 </conditional> | |
172 <conditional name="ref_source"> | |
173 <param name="source" value="history" /> | |
174 <param name="ref_fasta" value="reference.fasta" ftype="fasta" /> | |
175 </conditional> | |
176 <param name="sequencing_tech" value="illumina" /> | |
177 <output name="output_reads1" file="output.test1.reads_1.fasta" ftype="fasta"/> | |
178 <output name="output_reads2" file="output.test1.reads_2.fasta" ftype="fasta"/> | |
179 </test> | |
180 <test expect_num_outputs="3"> | |
181 <conditional name="reads"> | |
182 <param name="read_type" value="paired_collection" /> | |
183 <param name="paired_reads"> | |
184 <collection type="paired"> | |
185 <element name="forward" value="test1.fasta.gz" ftype="fasta" /> | |
186 <element name="reverse" value="test2.fasta.gz" ftype="fasta" /> | |
187 </collection> | |
188 </param> | |
189 </conditional> | |
190 <conditional name="ref_source"> | |
191 <param name="source" value="history" /> | |
192 <param name="ref_fasta" value="reference.fasta" ftype="fasta" /> | |
193 </conditional> | |
194 <param name="sequencing_tech" value="illumina" /> | |
195 <output_collection name="output_collection" type="paired"> | |
196 <element name="forward" file="output.test1.reads_1.fasta" ftype="fasta"/> | |
197 <element name="reverse" file="output.test1.reads_2.fasta" ftype="fasta"/> | |
198 </output_collection> | |
199 </test> | |
200 <test expect_num_outputs="1"> | |
201 <conditional name="reads"> | |
202 <param name="read_type" value="single" /> | |
203 <param name="read1" value="test3.fasta.gz" ftype="fasta"/> | |
204 </conditional> | |
205 <conditional name="ref_source"> | |
206 <param name="source" value="history" /> | |
207 <param name="ref_fasta" value="reference.fasta" ftype="fasta" /> | |
208 </conditional> | |
209 <param name="sequencing_tech" value="ont" /> | |
210 <param name="enumerate_names" value="True" /> | |
211 <output name="output_reads1" file="output.test3.reads_1.fasta" ftype="fasta"/> | |
212 </test> | |
213 <!--Testing compressed fasta input--> | |
214 <test expect_num_outputs="2"> | |
215 <conditional name="reads"> | |
216 <param name="read_type" value="paired" /> | |
217 <param name="read1" value="test1.fasta.gz" ftype="fasta.gz" /> | |
218 <param name="read2" value="test2.fasta.gz" ftype="fasta.gz" /> | |
219 </conditional> | |
220 <conditional name="ref_source"> | |
221 <param name="source" value="history" /> | |
222 <param name="ref_fasta" value="reference.fasta" ftype="fasta" /> | |
223 </conditional> | |
224 <param name="sequencing_tech" value="illumina" /> | |
225 <output name="output_reads1" decompress="true" file="output.test1.reads_1.fasta" ftype="fasta.gz"/> | |
226 <output name="output_reads2" decompress="true" file="output.test1.reads_2.fasta" ftype="fasta.gz"/> | |
227 </test> | |
228 <test expect_num_outputs="3"> | |
229 <conditional name="reads"> | |
230 <param name="read_type" value="paired_collection" /> | |
231 <param name="paired_reads"> | |
232 <collection type="paired"> | |
233 <element name="forward" value="test1.fasta.gz" ftype="fasta.gz" /> | |
234 <element name="reverse" value="test2.fasta.gz" ftype="fasta.gz" /> | |
235 </collection> | |
236 </param> | |
237 </conditional> | |
238 <conditional name="ref_source"> | |
239 <param name="source" value="history" /> | |
240 <param name="ref_fasta" value="reference.fasta" ftype="fasta" /> | |
241 </conditional> | |
242 <param name="sequencing_tech" value="illumina" /> | |
243 <output_collection name="output_collection" type="paired"> | |
244 <element name="forward" ftype="fasta.gz"> | |
245 <assert_contents> | |
246 <has_size value="680" delta="50" /> | |
247 </assert_contents> | |
248 </element> | |
249 <element name="reverse" ftype="fasta.gz"> | |
250 <assert_contents> | |
251 <has_size value="670" delta="50" /> | |
252 </assert_contents> | |
253 </element> | |
254 </output_collection> | |
255 </test> | |
256 <test expect_num_outputs="1"> | |
257 <conditional name="reads"> | |
258 <param name="read_type" value="single" /> | |
259 <param name="read1" value="test3.fasta.gz" ftype="fasta.gz"/> | |
260 </conditional> | |
261 <conditional name="ref_source"> | |
262 <param name="source" value="history" /> | |
263 <param name="ref_fasta" value="reference.fasta" ftype="fasta" /> | |
264 </conditional> | |
265 <param name="sequencing_tech" value="ont" /> | |
266 <param name="enumerate_names" value="True" /> | |
267 <output name="output_reads1" decompress="true" file="output.test3.reads_1.fasta" ftype="fasta.gz"/> | |
268 </test> | |
269 <!--Testing compressed fastq input--> | |
98 <test expect_num_outputs="2"> | 270 <test expect_num_outputs="2"> |
99 <conditional name="reads"> | 271 <conditional name="reads"> |
100 <param name="read_type" value="paired" /> | 272 <param name="read_type" value="paired" /> |
101 <param name="read1" value="test1.fastq.gz" ftype="fastqsanger.gz" /> | 273 <param name="read1" value="test1.fastq.gz" ftype="fastqsanger.gz" /> |
102 <param name="read2" value="test2.fastq.gz" ftype="fastqsanger.gz" /> | 274 <param name="read2" value="test2.fastq.gz" ftype="fastqsanger.gz" /> |
104 <conditional name="ref_source"> | 276 <conditional name="ref_source"> |
105 <param name="source" value="history" /> | 277 <param name="source" value="history" /> |
106 <param name="ref_fasta" value="reference.fasta" ftype="fasta" /> | 278 <param name="ref_fasta" value="reference.fasta" ftype="fasta" /> |
107 </conditional> | 279 </conditional> |
108 <param name="sequencing_tech" value="illumina" /> | 280 <param name="sequencing_tech" value="illumina" /> |
109 <output name="output_reads1" value="output_test1.fastq.gz" /> | 281 <output name="output_reads1" decompress="true" file="output.test1.reads_1.fastq" ftype="fastqsanger.gz"/> |
110 <output name="output_reads2" value="output_test2.fastq.gz" /> | 282 <output name="output_reads2" decompress="true" file="output.test1.reads_2.fastq" ftype="fastqsanger.gz"/> |
111 </test> | 283 </test> |
112 <test expect_num_outputs="3"> | 284 <test expect_num_outputs="3"> |
113 <conditional name="reads"> | 285 <conditional name="reads"> |
114 <param name="read_type" value="paired_collection" /> | 286 <param name="read_type" value="paired_collection" /> |
115 <param name="paired_reads"> | 287 <param name="paired_reads"> |
116 <collection type="paired"> | 288 <collection type="paired"> |
117 <element name="forward" value="test1.fastq.gz" ftype="fastqsanger.gz" /> | 289 <element name="forward" value="test1.fastq.gz" ftype="fastqsanger.gz" /> |
118 <element name="reverse" value="test2.fastq.gz" ftype="fastqsanger.gz" /> | 290 <element name="reverse" value="test2.fastq.gz" ftype="fastqsanger.gz" /> |
119 </collection> | 291 </collection> |
120 </param> | 292 </param> |
121 </conditional> | 293 </conditional> |
122 <conditional name="ref_source"> | 294 <conditional name="ref_source"> |
123 <param name="source" value="history" /> | 295 <param name="source" value="history" /> |
124 <param name="ref_fasta" value="reference.fasta" ftype="fasta" /> | 296 <param name="ref_fasta" value="reference.fasta" ftype="fasta" /> |
125 </conditional> | 297 </conditional> |
126 <param name="sequencing_tech" value="illumina" /> | 298 <param name="sequencing_tech" value="illumina" /> |
127 <output_collection name="output_collection"> | 299 <output_collection name="output_collection" type="paired"> |
128 <element name="forward" value="output_test1.fastq.gz" /> | 300 <element name="forward" ftype="fastqsanger.gz"> |
129 <element name="reverse" value="output_test2.fastq.gz" /> | 301 <assert_contents> |
302 <has_size value="995" delta="50" /> | |
303 </assert_contents> | |
304 </element> | |
305 <element name="reverse" ftype="fastqsanger.gz"> | |
306 <assert_contents> | |
307 <has_size value="960" delta="50" /> | |
308 </assert_contents> | |
309 </element> | |
130 </output_collection> | 310 </output_collection> |
131 </test> | 311 </test> |
132 <test expect_num_outputs="1"> | 312 <test expect_num_outputs="1"> |
133 <conditional name="reads"> | 313 <conditional name="reads"> |
134 <param name="read_type" value="single" /> | 314 <param name="read_type" value="single" /> |
135 <param name="single_read1" value="test3.fastq.gz" ftype="fastqsanger.gz"/> | 315 <param name="read1" value="test3.fastq.gz" ftype="fastqsanger.gz"/> |
136 </conditional> | 316 </conditional> |
137 <conditional name="ref_source"> | 317 <conditional name="ref_source"> |
138 <param name="source" value="history" /> | 318 <param name="source" value="history" /> |
139 <param name="ref_fasta" value="reference.fasta" ftype="fasta" /> | 319 <param name="ref_fasta" value="reference.fasta" ftype="fasta" /> |
140 </conditional> | 320 </conditional> |
141 <param name="sequencing_tech" value="ont" /> | 321 <param name="sequencing_tech" value="ont" /> |
142 <output name="output_reads1" value="output_test3.fastq.gz" /> | 322 <param name="enumerate_names" value="True" /> |
323 <output name="output_reads1" decompress="true" file="output.test3.reads_1.fastq" ftype="fastqsanger.gz"/> | |
143 </test> | 324 </test> |
144 </tests> | 325 </tests> |
145 <help><![CDATA[ | 326 <help><![CDATA[ |
146 ReadItAndKeep | 327 ReadItAndKeep |
147 ------------- | 328 ------------- |