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comparison sickle.xml @ 8:505f8a806d55 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit c0d7c69151c3efd66904d47757bdb6ab34c2b39b
author iuc
date Tue, 11 Feb 2025 11:01:26 +0000
parents 340de8627f41
children
comparison
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7:340de8627f41 8:505f8a806d55
1 <tool id="sickle" name="Sickle" version="1.33.2" profile="17.01"> 1 <tool id="sickle" name="Sickle" version="1.33.3" profile="23.2" license="MIT">
2 <description>windowed adaptive trimming of FASTQ data</description> 2 <description>Windowed adaptive trimming of FASTQ data</description>
3 <xrefs> 3 <xrefs>
4 <xref type="bio.tools">sickle</xref> 4 <xref type="bio.tools">sickle</xref>
5 </xrefs> 5 </xrefs>
6 <requirements> 6 <requirements>
7 <requirement type="package" version="1.33">sickle-trim</requirement> 7 <requirement type="package" version="1.33">sickle-trim</requirement>
121 #end if 121 #end if
122 122
123 #if $trunc_n: 123 #if $trunc_n:
124 -n 124 -n
125 #end if 125 #end if
126
127 #if $log_out
128 2>&1 | tee '${log}'
129 #end if
126 ]]></command> 130 ]]></command>
127 131
128 <inputs> 132 <inputs>
129 <conditional name="readtype"> 133 <conditional name="readtype">
130 <param name="single_or_paired" type="select" label="Single-end or paired-end reads?" help="Note: Sickle will infer the quality type of the file from its datatype. I.e., if the datatype is fastqsanger, then the quality type is sanger. The default is fastqsanger."> 134 <param name="single_or_paired" type="select" label="Single-end or paired-end reads?" help="Note: Sickle will infer the quality type of the file from its datatype. I.e., if the datatype is fastqsanger, then the quality type is sanger. The default is fastqsanger.">
133 <option value="pe_sep">Paired-end (two separate input files)</option> 137 <option value="pe_sep">Paired-end (two separate input files)</option>
134 <option value="pe_collection">Paired-end (as collection)</option> 138 <option value="pe_collection">Paired-end (as collection)</option>
135 </param> 139 </param>
136 140
137 <when value="se"> 141 <when value="se">
138 <param format="fastq,fastq.gz" name="input_single" type="data" label="Single-end FASTQ reads" help="(-f)" /> 142 <param format="fastq,fastq.gz" name="input_single" type="data" label="Single-end FASTQ reads" help="(-f)"/>
139 </when> 143 </when>
140 144
141 <when value="pe_combo"> 145 <when value="pe_combo">
142 <param format="fastq,fastq.gz" name="input_combo" type="data" label="Paired-end interleaved FASTQ reads" help="(-c)" /> 146 <param format="fastq,fastq.gz" name="input_combo" type="data" label="Paired-end interleaved FASTQ reads" help="(-c)"/>
143 <param name="output_n" type="boolean" label="Output only one file with all reads" help="This will output only one file with all the reads, where the reads that did not pass filter will be replaced with a single 'N', rather than discarded."/> 147 <param name="output_n" type="boolean" label="Output only one file with all reads" help="This will output only one file with all the reads, where the reads that did not pass filter will be replaced with a single 'N', rather than discarded."/>
144 </when> 148 </when>
145 149
146 <when value="pe_sep"> 150 <when value="pe_sep">
147 <param format="fastq,fastq.gz" name="input_paired1" type="data" label="Paired-end forward strand FASTQ reads" help="(-f)" /> 151 <param format="fastq,fastq.gz" name="input_paired1" type="data" label="Paired-end forward strand FASTQ reads" help="(-f)"/>
148 <param format="fastq,fastq.gz" name="input_paired2" type="data" label="Paired-end reverse strand FASTQ reads" help="(-r)" /> 152 <param format="fastq,fastq.gz" name="input_paired2" type="data" label="Paired-end reverse strand FASTQ reads" help="(-r)"/>
149 </when> 153 </when>
150 154
151 <when value="pe_collection"> 155 <when value="pe_collection">
152 <param format="fastq,fastq.gz" name="input_paired" type="data_collection" collection_type="paired" label="Paired-end FASTQ reads as paired collection" /> 156 <param format="fastq,fastq.gz" name="input_paired" type="data_collection" collection_type="paired" label="Paired-end FASTQ reads as paired collection"/>
153 </when> 157 </when>
154 </conditional> 158 </conditional>
155 159
156 <param name="qual_threshold" value="20" min="0" type="integer" optional="true" label="Quality threshold" help="Threshold for trimming based on average quality in a window (-q)" /> 160 <param name="qual_threshold" value="20" min="0" type="integer" optional="true" label="Quality threshold" help="Threshold for trimming based on average quality in a window (-q)"/>
157 161 <param name="length_threshold" value="20" min="0" type="integer" optional="true" label="Length threshold" help="Threshold to keep a read based on length after trimming (-l)"/>
158 <param name="length_threshold" value="20" min="0" type="integer" optional="true" label="Length threshold" help="Threshold to keep a read based on length after trimming (-l)" /> 162 <param name="no_five_prime" type="boolean" label="Don't do 5' trimming" help="(-x)"/>
159 163 <param name="trunc_n" type="boolean" label="Truncate sequences with Ns at first N position" help="(-n)"/>
160 <param name="no_five_prime" type="boolean" label="Don't do 5' trimming" help="(-x)" /> 164 <param name="log_out" type="boolean" label="Output log file?" truevalue="yes" falsevalue="no"/>
161 <param name="trunc_n" type="boolean" label="Truncate sequences with Ns at first N position" help="(-n)" />
162 </inputs> 165 </inputs>
163 166
164 <outputs> 167 <outputs>
165 <data name="output_single" format_source="input_single" label="Single-end output of ${tool.name} on ${on_string}"> 168 <data name="output_single" format_source="input_single" label="Single-end output of ${tool.name} on ${on_string}">
166 <filter>readtype['single_or_paired'] == 'se'</filter> 169 <filter>readtype['single_or_paired'] == 'se'</filter>
188 191
189 <collection name="output_paired_coll" type="paired" structured_like="input_paired" inherit_format="true" label="Paired-end output of ${tool.name} on ${on_string}"> 192 <collection name="output_paired_coll" type="paired" structured_like="input_paired" inherit_format="true" label="Paired-end output of ${tool.name} on ${on_string}">
190 <filter>readtype['single_or_paired'] == 'pe_collection'</filter> 193 <filter>readtype['single_or_paired'] == 'pe_collection'</filter>
191 </collection> 194 </collection>
192 195
193 <data name="output_paired_coll_single" format_source="input_paired['forward']" label="Singletons from paired-end output of ${tool.name} on ${on_string}"> 196 <data name="output_paired_coll_single" format_source="input_paired['forward']" label="Singletons from paired-end collection output of ${tool.name} on ${on_string}">
194 <filter>readtype['single_or_paired'] == 'pe_collection'</filter> 197 <filter>readtype['single_or_paired'] == 'pe_collection'</filter>
195 </data> 198 </data>
199
200 <data name="log" format="txt" label="${tool.name} on ${on_string}: Output Log">
201 <filter>log_out</filter>
202 </data>
203
196 </outputs> 204 </outputs>
197 <tests> 205 <tests>
198 <test> 206 <test expect_num_outputs="2">
199 <param name="single_or_paired" value="pe_combo" /> 207 <param name="single_or_paired" value="pe_combo"/>
200 <param name="input_combo" ftype="fastqillumina" value="test.fastq" /> 208 <param name="input_combo" ftype="fastqillumina" value="test.fastq"/>
201 <param name="qual_threshold" value="3" /> 209 <param name="qual_threshold" value="3"/>
202 <output name="output_combo" ftype="fastqillumina" file="output.c1.fastq" /> 210 <output name="output_combo" ftype="fastqillumina" file="output.c1.fastq"/>
203 <output name="output_combo_single" ftype="fastqillumina" file="output.s.fastq" /> 211 <output name="output_combo_single" ftype="fastqillumina" file="output.s.fastq"/>
204 </test> 212 </test>
205 <test> 213 <test expect_num_outputs="1">
206 <param name="single_or_paired" value="pe_combo" /> 214 <param name="single_or_paired" value="pe_combo"/>
207 <param name="input_combo" ftype="fastqillumina" value="test.fastq" /> 215 <param name="input_combo" ftype="fastqillumina" value="test.fastq"/>
208 <param name="qual_threshold" value="3" /> 216 <param name="qual_threshold" value="3"/>
209 <param name="output_n" value="true" /> 217 <param name="output_n" value="true"/>
210 <output name="output_combo" ftype="fastqillumina" file="output.c2.fastq" /> 218 <output name="output_combo" ftype="fastqillumina" file="output.c2.fastq"/>
211 </test> 219 </test>
212 <test> 220 <test expect_num_outputs="3">
213 <param name="single_or_paired" value="pe_sep" /> 221 <param name="single_or_paired" value="pe_sep"/>
214 <param name="input_paired1" ftype="fastqillumina" value="test.f.fastq" /> 222 <param name="input_paired1" ftype="fastqillumina" value="test.f.fastq"/>
215 <param name="input_paired2" ftype="fastqillumina" value="test.r.fastq" /> 223 <param name="input_paired2" ftype="fastqillumina" value="test.r.fastq"/>
216 <param name="qual_threshold" value="3" /> 224 <param name="qual_threshold" value="3"/>
217 <output name="output_paired1" ftype="fastqillumina" file="output.f.fastq" /> 225 <output name="output_paired1" ftype="fastqillumina" file="output.f.fastq"/>
218 <output name="output_paired2" ftype="fastqillumina" file="output.r.fastq" /> 226 <output name="output_paired2" ftype="fastqillumina" file="output.r.fastq"/>
219 <output name="output_paired_single" ftype="fastqillumina" file="output.s.fastq" /> 227 <output name="output_paired_single" ftype="fastqillumina" file="output.s.fastq"/>
220 </test> 228 </test>
221 <test> <!-- as above, but gzipped --> 229 <test expect_num_outputs="3"> <!-- as above, but gzipped -->
222 <param name="single_or_paired" value="pe_sep" /> 230 <param name="single_or_paired" value="pe_sep"/>
223 <param name="input_paired1" ftype="fastqillumina.gz" value="test.f.fastq.gz" /> 231 <param name="input_paired1" ftype="fastqillumina.gz" value="test.f.fastq.gz"/>
224 <param name="input_paired2" ftype="fastqillumina.gz" value="test.r.fastq.gz" /> 232 <param name="input_paired2" ftype="fastqillumina.gz" value="test.r.fastq.gz"/>
225 <param name="qual_threshold" value="3" /> 233 <param name="qual_threshold" value="3"/>
226 <output name="output_paired1" ftype="fastqillumina.gz" file="output.f.fastq.gz" /> 234 <output name="output_paired1" ftype="fastqillumina.gz" file="output.f.fastq.gz"/>
227 <output name="output_paired2" ftype="fastqillumina.gz" file="output.r.fastq.gz" /> 235 <output name="output_paired2" ftype="fastqillumina.gz" file="output.r.fastq.gz"/>
228 <output name="output_paired_single" ftype="fastqillumina.gz" file="output.s.fastq.gz" /> 236 <output name="output_paired_single" ftype="fastqillumina.gz" file="output.s.fastq.gz"/>
229 </test> 237 </test>
230 <test> 238 <test expect_num_outputs="4">
231 <param name="single_or_paired" value="pe_collection" /> 239 <param name="single_or_paired" value="pe_collection"/>
232 <param name="input_paired"> 240 <param name="input_paired">
233 <collection type="paired"> 241 <collection type="paired">
234 <element name="forward" ftype="fastqillumina" value="test.f.fastq" /> 242 <element name="forward" ftype="fastqillumina" value="test.f.fastq"/>
235 <element name="reverse" ftype="fastqillumina" value="test.r.fastq" /> 243 <element name="reverse" ftype="fastqillumina" value="test.r.fastq"/>
236 </collection> 244 </collection>
237 </param> 245 </param>
238 <param name="qual_threshold" value="3" /> 246 <param name="qual_threshold" value="3"/>
239 <output_collection name="output_paired_coll" type="paired"> 247 <output_collection name="output_paired_coll" type="paired">
240 <element name="forward" ftype="fastqillumina" file="output.f.fastq" /> 248 <element name="forward" ftype="fastqillumina" file="output.f.fastq"/>
241 <element name="reverse" ftype="fastqillumina" file="output.r.fastq" /> 249 <element name="reverse" ftype="fastqillumina" file="output.r.fastq"/>
242 </output_collection> 250 </output_collection>
243 <output name="output_paired_coll_single" ftype="fastqillumina" file="output.s.fastq" /> 251 <output name="output_paired_coll_single" ftype="fastqillumina" file="output.s.fastq"/>
244 </test> 252 </test>
245 253 <test expect_num_outputs="4"> <!-- as above, but gzipped -->
246 <test> <!-- as above, but gzipped --> 254 <param name="single_or_paired" value="pe_collection"/>
247 <param name="single_or_paired" value="pe_collection" />
248 <param name="input_paired"> 255 <param name="input_paired">
249 <collection type="paired"> 256 <collection type="paired">
250 <element name="forward" ftype="fastqillumina.gz" value="test.f.fastq.gz" /> 257 <element name="forward" ftype="fastqillumina.gz" value="test.f.fastq.gz"/>
251 <element name="reverse" ftype="fastqillumina.gz" value="test.r.fastq.gz" /> 258 <element name="reverse" ftype="fastqillumina.gz" value="test.r.fastq.gz"/>
252 </collection> 259 </collection>
253 </param> 260 </param>
254 <param name="qual_threshold" value="3" /> 261 <param name="qual_threshold" value="3"/>
255 <output_collection name="output_paired_coll" type="paired"> 262 <output_collection name="output_paired_coll" type="paired">
256 <element name="forward" ftype="fastqillumina.gz" file="output.f.fastq.gz" /> 263 <element name="forward" ftype="fastqillumina.gz" file="output.f.fastq.gz"/>
257 <element name="reverse" ftype="fastqillumina.gz" file="output.r.fastq.gz" /> 264 <element name="reverse" ftype="fastqillumina.gz" file="output.r.fastq.gz"/>
258 </output_collection> 265 </output_collection>
259 <output name="output_paired_coll_single" ftype="fastqillumina.gz" file="output.s.fastq.gz" /> 266 <output name="output_paired_coll_single" ftype="fastqillumina.gz" file="output.s.fastq.gz"/>
267 </test>
268 <test expect_num_outputs="3">
269 <param name="single_or_paired" value="pe_combo"/>
270 <param name="input_combo" ftype="fastqillumina" value="test.fastq"/>
271 <param name="qual_threshold" value="3"/>
272 <param name="log_out" value="yes"/>
273 <output name="output_combo" ftype="fastqillumina" file="output.c1.fastq"/>
274 <output name="output_combo_single" ftype="fastqillumina" file="output.s.fastq"/>
275 <output name="log" file="sickle.log" ftype="txt"/>
260 </test> 276 </test>
261 </tests> 277 </tests>
262 <help> 278 <help>
279
263 **What it does** 280 **What it does**
264 281
265 Most modern sequencing technologies produce reads that have 282 Most modern sequencing technologies produce reads that have
266 deteriorating quality towards the 3'-end and some towards the 5'-end 283 deteriorating quality towards the 3'-end and some towards the 5'-end
267 as well. Incorrectly called bases in both regions negatively impact 284 as well. Incorrectly called bases in both regions negatively impact