Mercurial > repos > iuc > samtools_fastx
comparison samtools_fastx.xml @ 4:66e23b11feae draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit cd62639660bef041ba14ecff337fb98e84e75d8a
author | iuc |
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date | Mon, 20 Nov 2023 22:15:18 +0000 |
parents | b3d99709fe1a |
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3:b3d99709fe1a | 4:66e23b11feae |
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1 <tool id="samtools_fastx" name="Samtools fastx" version="@TOOL_VERSION@+galaxy0" profile="@PROFILE@"> | 1 <tool id="samtools_fastx" name="Samtools fastx" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@"> |
2 <description>extract FASTA or FASTQ from alignment files</description> | 2 <description>extract FASTA or FASTQ from alignment files</description> |
3 <macros> | 3 <macros> |
4 <import>macros.xml</import> | 4 <import>macros.xml</import> |
5 </macros> | 5 </macros> |
6 <expand macro="requirements" /> | 6 <expand macro="requirements" /> |
158 </param> | 158 </param> |
159 <when value="no" /> | 159 <when value="no" /> |
160 <when value="yes"> | 160 <when value="yes"> |
161 <param name="write1st" argument="--i1" type="boolean" truevalue="yes" falsevalue="no" checked="true" label="write first index reads to extra data set" /> | 161 <param name="write1st" argument="--i1" type="boolean" truevalue="yes" falsevalue="no" checked="true" label="write first index reads to extra data set" /> |
162 <param name="write2nd" argument="--i2" type="boolean" truevalue="yes" falsevalue="no" checked='true' label="write second index reads to extra data set" /> | 162 <param name="write2nd" argument="--i2" type="boolean" truevalue="yes" falsevalue="no" checked='true' label="write second index reads to extra data set" /> |
163 <param name="index_format" argument="--index-format" type="text" label="Index format: How to parse barcode and quality tags"> | 163 <param argument="--index-format" type="text" label="Index format: How to parse barcode and quality tags"> |
164 <help> | 164 <help> |
165 The index-format string describes how to parse the barcode and quality tags, for example: | 165 The index-format string describes how to parse the barcode and quality tags, for example: |
166 i14i8 the first 14 characters are index 1, the next 8 characters are index 2 | 166 i14i8 the first 14 characters are index 1, the next 8 characters are index 2 |
167 n8i14 ignore the first 8 characters, and use the next 14 characters for index 1 | 167 n8i14 ignore the first 8 characters, and use the next 14 characters for index 1 |
168 If the tag contains a separator, then the numeric part can be replaced with '*' to mean | 168 If the tag contains a separator, then the numeric part can be replaced with '*' to mean |
169 'read until the separator or end of tag', for example: | 169 'read until the separator or end of tag', for example: |
170 n*i* ignore the left part of the tag until the separator, then use the second part | 170 n*i* ignore the left part of the tag until the separator, then use the second part |
171 of the tag as index 1 | 171 of the tag as index 1 |
172 </help> | 172 </help> |
173 </param> | 173 </param> |
174 <param name="barcode_tag" argument="--barcode-tag" type="text" optional="True" label="Barcode tag [default: BC]"/> | 174 <param argument="--barcode-tag" type="text" optional="True" label="Barcode tag [default: BC]"/> |
175 <param name="quality_tag" argument="--quality-tag" type="text" optional="True" label="Quality tag [default: QT]"/> | 175 <param argument="--quality-tag" type="text" optional="True" label="Quality tag [default: QT]"/> |
176 </when> | 176 </when> |
177 </conditional> | 177 </conditional> |
178 </inputs> | 178 </inputs> |
179 <outputs> | 179 <outputs> |
180 <data name="nonspecific" format="fasta" from_work_dir="nonspecific" label="${on_string} converted to ${output_fmt_cond.output_fmt_select} (nonspecific)"> | 180 <data name="nonspecific" format="fasta" from_work_dir="nonspecific" label="${on_string} converted to ${output_fmt_cond.output_fmt_select} (nonspecific)"> |
234 </actions> | 234 </actions> |
235 </data> | 235 </data> |
236 </outputs> | 236 </outputs> |
237 <tests> | 237 <tests> |
238 <!-- tests from original Galaxy tool --> | 238 <!-- tests from original Galaxy tool --> |
239 <test> | 239 <test expect_num_outputs="1"> |
240 <param name="input" value="samtools_fastx-in1.bam" ftype="bam" /> | 240 <param name="input" value="samtools_fastx-in1.bam" ftype="bam" /> |
241 <conditional name="output_fmt_cond"> | 241 <conditional name="output_fmt_cond"> |
242 <param name="output_fmt_select" value="fasta" /> | 242 <param name="output_fmt_select" value="fasta" /> |
243 </conditional> | 243 </conditional> |
244 <param name="outputs" value="other" /> | 244 <param name="outputs" value="other" /> |
245 <output name="output" file="samtools_fastx-out1.fasta" ftype="fasta" /> | 245 <output name="output" file="samtools_fastx-out1.fasta" ftype="fasta" /> |
246 </test> | 246 </test> |
247 <test> | 247 <test expect_num_outputs="3"> |
248 <param name="input" value="samtools_fastx-in2.bam" ftype="bam" /> | 248 <param name="input" value="samtools_fastx-in2.bam" ftype="bam" /> |
249 <conditional name="output_fmt_cond"> | 249 <conditional name="output_fmt_cond"> |
250 <param name="output_fmt_select" value="fastqsanger" /> | 250 <param name="output_fmt_select" value="fastqsanger" /> |
251 </conditional> | 251 </conditional> |
252 <param name="outputs" value="r0,r1,r2" /> | 252 <param name="outputs" value="r0,r1,r2" /> |
253 <output name="nonspecific" file="samtools_fastx-out2-1.fastq" ftype="fastqsanger" /> | 253 <output name="nonspecific" file="samtools_fastx-out2-1.fastq" ftype="fastqsanger" /> |
254 <output name="forward" file="samtools_fastx-out2-2.fastq" ftype="fastqsanger" /> | 254 <output name="forward" file="samtools_fastx-out2-2.fastq" ftype="fastqsanger" /> |
255 <output name="reverse" file="samtools_fastx-out2-3.fastq" ftype="fastqsanger" /> | 255 <output name="reverse" file="samtools_fastx-out2-3.fastq" ftype="fastqsanger" /> |
256 </test> | 256 </test> |
257 <test> | 257 <test expect_num_outputs="3"> |
258 <param name="input" value="samtools_fastx-in3.sam" ftype="sam" /> | 258 <param name="input" value="samtools_fastx-in3.sam" ftype="sam" /> |
259 <conditional name="output_fmt_cond"> | 259 <conditional name="output_fmt_cond"> |
260 <param name="output_fmt_select" value="fasta" /> | 260 <param name="output_fmt_select" value="fasta" /> |
261 </conditional> | 261 </conditional> |
262 <param name="outputs" value="r0,r1,r2" /> | 262 <param name="outputs" value="r0,r1,r2" /> |
265 <output name="reverse" file="samtools_fastx-out3-3.fasta" ftype="fasta" /> | 265 <output name="reverse" file="samtools_fastx-out3-3.fasta" ftype="fasta" /> |
266 </test> | 266 </test> |
267 <!-- tests from original Galaxy tool with gz output. for some reason gzip (which is used | 267 <!-- tests from original Galaxy tool with gz output. for some reason gzip (which is used |
268 for compressing stdout does not give exactly the same file contents .. the other | 268 for compressing stdout does not give exactly the same file contents .. the other |
269 compressed files seem to)--> | 269 compressed files seem to)--> |
270 <test> | 270 <test expect_num_outputs="1"> |
271 <param name="input" value="samtools_fastx-in1.bam" ftype="bam" /> | 271 <param name="input" value="samtools_fastx-in1.bam" ftype="bam" /> |
272 <conditional name="output_fmt_cond"> | 272 <conditional name="output_fmt_cond"> |
273 <param name="output_fmt_select" value="fasta.gz" /> | 273 <param name="output_fmt_select" value="fasta.gz" /> |
274 </conditional> | 274 </conditional> |
275 <param name="outputs" value="other" /> | 275 <param name="outputs" value="other" /> |
276 <output name="output" file="samtools_fastx-out1.fasta.gz" ftype="fasta.gz" decompress="true"/> | 276 <output name="output" file="samtools_fastx-out1.fasta.gz" ftype="fasta.gz" decompress="true"/> |
277 </test> | 277 </test> |
278 <test> | 278 <test expect_num_outputs="3"> |
279 <param name="input" value="samtools_fastx-in2.bam" ftype="bam" /> | 279 <param name="input" value="samtools_fastx-in2.bam" ftype="bam" /> |
280 <conditional name="output_fmt_cond"> | 280 <conditional name="output_fmt_cond"> |
281 <param name="output_fmt_select" value="fastqsanger.gz" /> | 281 <param name="output_fmt_select" value="fastqsanger.gz" /> |
282 </conditional> | 282 </conditional> |
283 <param name="outputs" value="r0,r1,r2" /> | 283 <param name="outputs" value="r0,r1,r2" /> |
284 <output name="nonspecific" file="samtools_fastx-out2-1.fastq.gz" ftype="fastqsanger.gz" decompress="true" /> | 284 <output name="nonspecific" file="samtools_fastx-out2-1.fastq.gz" ftype="fastqsanger.gz" decompress="true" /> |
285 <output name="forward" file="samtools_fastx-out2-2.fastq.gz" ftype="fastqsanger.gz" decompress="true" /> | 285 <output name="forward" file="samtools_fastx-out2-2.fastq.gz" ftype="fastqsanger.gz" decompress="true" /> |
286 <output name="reverse" file="samtools_fastx-out2-3.fastq.gz" ftype="fastqsanger.gz" decompress="true" /> | 286 <output name="reverse" file="samtools_fastx-out2-3.fastq.gz" ftype="fastqsanger.gz" decompress="true" /> |
287 </test> | 287 </test> |
288 <test> | 288 <test expect_num_outputs="3"> |
289 <param name="input" value="samtools_fastx-in3.sam" ftype="sam" /> | 289 <param name="input" value="samtools_fastx-in3.sam" ftype="sam" /> |
290 <conditional name="output_fmt_cond"> | 290 <conditional name="output_fmt_cond"> |
291 <param name="output_fmt_select" value="fasta.gz" /> | 291 <param name="output_fmt_select" value="fasta.gz" /> |
292 </conditional> | 292 </conditional> |
293 <param name="outputs" value="r0,r1,r2" /> | 293 <param name="outputs" value="r0,r1,r2" /> |
296 <output name="reverse" file="samtools_fastx-out3-3.fasta.gz" ftype="fasta.gz" decompress="true" /> | 296 <output name="reverse" file="samtools_fastx-out3-3.fasta.gz" ftype="fasta.gz" decompress="true" /> |
297 </test> | 297 </test> |
298 <!-- tests from: https://github.com/samtools/samtools/blob/6d79411685d8f0fbb34e123f52d72b63271f4dcb/test/test.pl#L2313--> | 298 <!-- tests from: https://github.com/samtools/samtools/blob/6d79411685d8f0fbb34e123f52d72b63271f4dcb/test/test.pl#L2313--> |
299 <!--# basic 2 output test without singleton tracking--> | 299 <!--# basic 2 output test without singleton tracking--> |
300 <!--test_cmd($opts, out=>'bam2fq/1.stdout.expected', out_map=>{'1.fq' => 'bam2fq/1.1.fq.expected', '2.fq' => 'bam2fq/1.2.fq.expected'},cmd=>"$$opts{bin}/samtools fastq @$threads -1 $$opts{path}/1.fq -2 $$opts{path}/2.fq $$opts{path}/dat/bam2fq.001.sam");--> | 300 <!--test_cmd($opts, out=>'bam2fq/1.stdout.expected', out_map=>{'1.fq' => 'bam2fq/1.1.fq.expected', '2.fq' => 'bam2fq/1.2.fq.expected'},cmd=>"$$opts{bin}/samtools fastq @$threads -1 $$opts{path}/1.fq -2 $$opts{path}/2.fq $$opts{path}/dat/bam2fq.001.sam");--> |
301 <test> | 301 <test expect_num_outputs="3"> |
302 <param name="input" value="bam2fq.001.sam" ftype="sam" /> | 302 <param name="input" value="bam2fq.001.sam" ftype="sam" /> |
303 <conditional name="output_fmt_cond"> | 303 <conditional name="output_fmt_cond"> |
304 <param name="output_fmt_select" value="fastqsanger" /> | 304 <param name="output_fmt_select" value="fastqsanger" /> |
305 </conditional> | 305 </conditional> |
306 <param name="outputs" value="r1,r2,other" /> | 306 <param name="outputs" value="r1,r2,other" /> |
308 <output name="reverse" file="1.2.fq.expected" ftype="fastqsanger" /> | 308 <output name="reverse" file="1.2.fq.expected" ftype="fastqsanger" /> |
309 <output name="output" file="1.stdout.expected" ftype="fastqsanger" /> | 309 <output name="output" file="1.stdout.expected" ftype="fastqsanger" /> |
310 </test> | 310 </test> |
311 <!--# basic 2 output test with singleton tracking but no singleton--> | 311 <!--# basic 2 output test with singleton tracking but no singleton--> |
312 <!--test_cmd($opts, out=>'bam2fq/2.stdout.expected', out_map=>{'1.fq' => 'bam2fq/2.1.fq.expected', '2.fq' => 'bam2fq/2.2.fq.expected', 's.fq' => 'bam2fq/2.s.fq.expected'}, cmd=>"$$opts{bin}/samtools fastq @$threads -s $$opts{path}/s.fq -1 $$opts{path}/1.fq -2 $$opts{path}/2.fq $$opts{path}/dat/bam2fq.001.sam");--> | 312 <!--test_cmd($opts, out=>'bam2fq/2.stdout.expected', out_map=>{'1.fq' => 'bam2fq/2.1.fq.expected', '2.fq' => 'bam2fq/2.2.fq.expected', 's.fq' => 'bam2fq/2.s.fq.expected'}, cmd=>"$$opts{bin}/samtools fastq @$threads -s $$opts{path}/s.fq -1 $$opts{path}/1.fq -2 $$opts{path}/2.fq $$opts{path}/dat/bam2fq.001.sam");--> |
313 <test> | 313 <test expect_num_outputs="4"> |
314 <param name="input" value="bam2fq.001.sam" ftype="sam" /> | 314 <param name="input" value="bam2fq.001.sam" ftype="sam" /> |
315 <conditional name="output_fmt_cond"> | 315 <conditional name="output_fmt_cond"> |
316 <param name="output_fmt_select" value="fastqsanger" /> | 316 <param name="output_fmt_select" value="fastqsanger" /> |
317 </conditional> | 317 </conditional> |
318 <param name="outputs" value="r1,r2,s,other" /> | 318 <param name="outputs" value="r1,r2,s,other" /> |
321 <output name="singletons" file="2.s.fq.expected" ftype="fastqsanger" /> | 321 <output name="singletons" file="2.s.fq.expected" ftype="fastqsanger" /> |
322 <output name="output" file="2.stdout.expected" ftype="fastqsanger" /> | 322 <output name="output" file="2.stdout.expected" ftype="fastqsanger" /> |
323 </test> | 323 </test> |
324 <!--# basic 2 output test with singleton tracking with a singleton in the middle--> | 324 <!--# basic 2 output test with singleton tracking with a singleton in the middle--> |
325 <!--test_cmd($opts, out=>'bam2fq/2.stdout.expected', out_map=>{'1.fq' => 'bam2fq/3.1.fq.expected', '2.fq' => 'bam2fq/3.2.fq.expected', 's.fq' => 'bam2fq/3.s.fq.expected'}, cmd=>"$$opts{bin}/samtools fastq @$threads -s $$opts{path}/s.fq -1 $$opts{path}/1.fq -2 $$opts{path}/2.fq $$opts{path}/dat/bam2fq.002.sam");--> | 325 <!--test_cmd($opts, out=>'bam2fq/2.stdout.expected', out_map=>{'1.fq' => 'bam2fq/3.1.fq.expected', '2.fq' => 'bam2fq/3.2.fq.expected', 's.fq' => 'bam2fq/3.s.fq.expected'}, cmd=>"$$opts{bin}/samtools fastq @$threads -s $$opts{path}/s.fq -1 $$opts{path}/1.fq -2 $$opts{path}/2.fq $$opts{path}/dat/bam2fq.002.sam");--> |
326 <test> | 326 <test expect_num_outputs="4"> |
327 <param name="input" value="bam2fq.002.sam" ftype="sam" /> | 327 <param name="input" value="bam2fq.002.sam" ftype="sam" /> |
328 <conditional name="output_fmt_cond"> | 328 <conditional name="output_fmt_cond"> |
329 <param name="output_fmt_select" value="fastqsanger" /> | 329 <param name="output_fmt_select" value="fastqsanger" /> |
330 </conditional> | 330 </conditional> |
331 <param name="outputs" value="r1,r2,s,other" /> | 331 <param name="outputs" value="r1,r2,s,other" /> |
334 <output name="singletons" file="3.s.fq.expected" ftype="fastqsanger" /> | 334 <output name="singletons" file="3.s.fq.expected" ftype="fastqsanger" /> |
335 <output name="output" file="3.stdout.expected" ftype="fastqsanger" /> | 335 <output name="output" file="3.stdout.expected" ftype="fastqsanger" /> |
336 </test> | 336 </test> |
337 <!--# basic 2 output test with singleton tracking with a singleton as last read--> | 337 <!--# basic 2 output test with singleton tracking with a singleton as last read--> |
338 <!--test_cmd($opts, out=>'bam2fq/2.stdout.expected', out_map=>{'1.fq' => 'bam2fq/4.1.fq.expected', '2.fq' => 'bam2fq/4.2.fq.expected', 's.fq' => 'bam2fq/4.s.fq.expected'}, cmd=>"$$opts{bin}/samtools fastq @$threads -s $$opts{path}/s.fq -1 $$opts{path}/1.fq -2 $$opts{path}/2.fq $$opts{path}/dat/bam2fq.003.sam");--> | 338 <!--test_cmd($opts, out=>'bam2fq/2.stdout.expected', out_map=>{'1.fq' => 'bam2fq/4.1.fq.expected', '2.fq' => 'bam2fq/4.2.fq.expected', 's.fq' => 'bam2fq/4.s.fq.expected'}, cmd=>"$$opts{bin}/samtools fastq @$threads -s $$opts{path}/s.fq -1 $$opts{path}/1.fq -2 $$opts{path}/2.fq $$opts{path}/dat/bam2fq.003.sam");--> |
339 <test> | 339 <test expect_num_outputs="4"> |
340 <param name="input" value="bam2fq.003.sam" ftype="sam" /> | 340 <param name="input" value="bam2fq.003.sam" ftype="sam" /> |
341 <conditional name="output_fmt_cond"> | 341 <conditional name="output_fmt_cond"> |
342 <param name="output_fmt_select" value="fastqsanger" /> | 342 <param name="output_fmt_select" value="fastqsanger" /> |
343 </conditional> | 343 </conditional> |
344 <param name="outputs" value="r1,r2,s,other" /> | 344 <param name="outputs" value="r1,r2,s,other" /> |
347 <output name="singletons" file="4.s.fq.expected" ftype="fastqsanger" /> | 347 <output name="singletons" file="4.s.fq.expected" ftype="fastqsanger" /> |
348 <output name="output" file="4.stdout.expected" ftype="fastqsanger" /> | 348 <output name="output" file="4.stdout.expected" ftype="fastqsanger" /> |
349 </test> | 349 </test> |
350 <!--# tag output test with singleton tracking with a singleton as last read--> | 350 <!--# tag output test with singleton tracking with a singleton as last read--> |
351 <!--test_cmd($opts, out=>'bam2fq/2.stdout.expected', out_map=>{'1.fq' => 'bam2fq/4.1.fq.expected', '2.fq' => 'bam2fq/4.2.fq.expected', 's.fq' => 'bam2fq/4.s.fq.expected', 'bc.fq' => 'bam2fq/bc.fq.expected'}, cmd=>"$$opts{bin}/samtools fastq @$threads \-\-barcode-tag BC \-\-index-format 'n2i2' \-\-i1 $$opts{path}/bc.fq -s $$opts{path}/s.fq -1 $$opts{path}/1.fq -2 $$opts{path}/2.fq $$opts{path}/dat/bam2fq.004.sam");--> | 351 <!--test_cmd($opts, out=>'bam2fq/2.stdout.expected', out_map=>{'1.fq' => 'bam2fq/4.1.fq.expected', '2.fq' => 'bam2fq/4.2.fq.expected', 's.fq' => 'bam2fq/4.s.fq.expected', 'bc.fq' => 'bam2fq/bc.fq.expected'}, cmd=>"$$opts{bin}/samtools fastq @$threads \-\-barcode-tag BC \-\-index-format 'n2i2' \-\-i1 $$opts{path}/bc.fq -s $$opts{path}/s.fq -1 $$opts{path}/1.fq -2 $$opts{path}/2.fq $$opts{path}/dat/bam2fq.004.sam");--> |
352 <test> | 352 <test expect_num_outputs="5"> |
353 <param name="input" value="bam2fq.004.sam" ftype="sam" /> | 353 <param name="input" value="bam2fq.004.sam" ftype="sam" /> |
354 <conditional name="output_fmt_cond"> | 354 <conditional name="output_fmt_cond"> |
355 <param name="output_fmt_select" value="fastqsanger" /> | 355 <param name="output_fmt_select" value="fastqsanger" /> |
356 </conditional> | 356 </conditional> |
357 <param name="outputs" value="r1,r2,s,other" /> | 357 <param name="outputs" value="r1,r2,s,other" /> |
358 <conditional name="idxout_cond"> | 358 <conditional name="idxout_cond"> |
359 <param name="idxout_select" value="yes"/> | 359 <param name="idxout_select" value="yes"/> |
360 <param name="write1st" value="yes"/> | 360 <param name="write1st" value="true"/> |
361 <param name="write2nd" value="false"/> | |
361 <param name="barcode_tag" value="BC"/> | 362 <param name="barcode_tag" value="BC"/> |
362 <param name="index_format" value="n2i2"/> | 363 <param name="index_format" value="n2i2"/> |
363 </conditional> | 364 </conditional> |
364 <output name="forward" file="4.1.fq.expected" ftype="fastqsanger" /> | 365 <output name="forward" file="4.1.fq.expected" ftype="fastqsanger" /> |
365 <output name="reverse" file="4.2.fq.expected" ftype="fastqsanger" /> | 366 <output name="reverse" file="4.2.fq.expected" ftype="fastqsanger" /> |
367 <output name="output" file="4.stdout.expected" ftype="fastqsanger" /> | 368 <output name="output" file="4.stdout.expected" ftype="fastqsanger" /> |
368 <output name="i1" file="bc.fq.expected" ftype="fastqsanger" /> | 369 <output name="i1" file="bc.fq.expected" ftype="fastqsanger" /> |
369 </test> | 370 </test> |
370 <!--# test -O flag with no OQ tags--> | 371 <!--# test -O flag with no OQ tags--> |
371 <!--test_cmd($opts, out=>'bam2fq/2.stdout.expected', out_map=>{'1.fq' => 'bam2fq/4.1.fq.expected', '2.fq' => 'bam2fq/4.2.fq.expected', 's.fq' => 'bam2fq/4.s.fq.expected', 'bc.fq' => 'bam2fq/bc.fq.expected'}, cmd=>"$$opts{bin}/samtools fastq @$threads \-\-barcode-tag BC -O \-\-index-format 'n2i2' \-\-i1 $$opts{path}/bc.fq -s $$opts{path}/s.fq -1 $$opts{path}/1.fq -2 $$opts{path}/2.fq $$opts{path}/dat/bam2fq.004.sam");--> | 372 <!--test_cmd($opts, out=>'bam2fq/2.stdout.expected', out_map=>{'1.fq' => 'bam2fq/4.1.fq.expected', '2.fq' => 'bam2fq/4.2.fq.expected', 's.fq' => 'bam2fq/4.s.fq.expected', 'bc.fq' => 'bam2fq/bc.fq.expected'}, cmd=>"$$opts{bin}/samtools fastq @$threads \-\-barcode-tag BC -O \-\-index-format 'n2i2' \-\-i1 $$opts{path}/bc.fq -s $$opts{path}/s.fq -1 $$opts{path}/1.fq -2 $$opts{path}/2.fq $$opts{path}/dat/bam2fq.004.sam");--> |
372 <test> | 373 <test expect_num_outputs="5"> |
373 <param name="input" value="bam2fq.010.sam" ftype="sam" /> | 374 <param name="input" value="bam2fq.010.sam" ftype="sam" /> |
374 <conditional name="output_fmt_cond"> | 375 <conditional name="output_fmt_cond"> |
375 <param name="output_fmt_select" value="fastqsanger" /> | 376 <param name="output_fmt_select" value="fastqsanger" /> |
376 <param name="output_quality" value="-O" /> | 377 <param name="output_quality" value="-O" /> |
377 </conditional> | 378 </conditional> |
378 <param name="outputs" value="r1,r2,s,other" /> | 379 <param name="outputs" value="r1,r2,s,other" /> |
379 <conditional name="idxout_cond"> | 380 <conditional name="idxout_cond"> |
380 <param name="idxout_select" value="yes"/> | 381 <param name="idxout_select" value="yes"/> |
381 <param name="write1st" value="yes"/> | 382 <param name="write1st" value="true"/> |
383 <param name="write2nd" value="false"/> | |
382 <param name="barcode_tag" value="BC"/> | 384 <param name="barcode_tag" value="BC"/> |
383 <param name="index_format" value="n2i2"/> | 385 <param name="index_format" value="n2i2"/> |
384 </conditional> | 386 </conditional> |
385 <output name="forward" file="10.1.fq.expected" ftype="fastqsanger" /> | 387 <output name="forward" file="10.1.fq.expected" ftype="fastqsanger" /> |
386 <output name="reverse" file="10.2.fq.expected" ftype="fastqsanger" /> | 388 <output name="reverse" file="10.2.fq.expected" ftype="fastqsanger" /> |
388 <output name="output" file="2.stdout.expected" ftype="fastqsanger" /> | 390 <output name="output" file="2.stdout.expected" ftype="fastqsanger" /> |
389 <output name="i1" file="bc10.fq.expected" ftype="fastqsanger" /> | 391 <output name="i1" file="bc10.fq.expected" ftype="fastqsanger" /> |
390 </test> | 392 </test> |
391 <!--# test -O flag with OQ tags--> | 393 <!--# test -O flag with OQ tags--> |
392 <!--test_cmd($opts, out=>'bam2fq/2.stdout.expected', out_map=>{'1.fq' => 'bam2fq/10.1.fq.expected', '2.fq' => 'bam2fq/10.2.fq.expected', 's.fq' => 'bam2fq/10.s.fq.expected', 'bc.fq' => 'bam2fq/bc10.fq.expected'}, cmd=>"$$opts{bin}/samtools fastq @$threads \-\-barcode-tag BC -O \-\-index-format 'n2i2' \-\-i1 $$opts{path}/bc.fq -s $$opts{path}/s.fq -1 $$opts{path}/1.fq -2 $$opts{path}/2.fq $$opts{path}/dat/bam2fq.010.sam");--> | 394 <!--test_cmd($opts, out=>'bam2fq/2.stdout.expected', out_map=>{'1.fq' => 'bam2fq/10.1.fq.expected', '2.fq' => 'bam2fq/10.2.fq.expected', 's.fq' => 'bam2fq/10.s.fq.expected', 'bc.fq' => 'bam2fq/bc10.fq.expected'}, cmd=>"$$opts{bin}/samtools fastq @$threads \-\-barcode-tag BC -O \-\-index-format 'n2i2' \-\-i1 $$opts{path}/bc.fq -s $$opts{path}/s.fq -1 $$opts{path}/1.fq -2 $$opts{path}/2.fq $$opts{path}/dat/bam2fq.010.sam");--> |
393 <test> | 395 <test expect_num_outputs="5"> |
394 <param name="input" value="bam2fq.010.sam" ftype="sam" /> | 396 <param name="input" value="bam2fq.010.sam" ftype="sam" /> |
395 <conditional name="output_fmt_cond"> | 397 <conditional name="output_fmt_cond"> |
396 <param name="output_fmt_select" value="fastqsanger" /> | 398 <param name="output_fmt_select" value="fastqsanger" /> |
397 <param name="output_quality" value="-O" /> | 399 <param name="output_quality" value="-O" /> |
398 </conditional> | 400 </conditional> |
399 <param name="outputs" value="r1,r2,s,other" /> | 401 <param name="outputs" value="r1,r2,s,other" /> |
400 <conditional name="idxout_cond"> | 402 <conditional name="idxout_cond"> |
401 <param name="idxout_select" value="yes"/> | 403 <param name="idxout_select" value="yes"/> |
402 <param name="write1st" value="yes"/> | 404 <param name="write1st" value="true"/> |
405 <param name="write2nd" value="false"/> | |
403 <param name="barcode_tag" value="BC"/> | 406 <param name="barcode_tag" value="BC"/> |
404 <param name="index_format" value="n2i2"/> | 407 <param name="index_format" value="n2i2"/> |
405 </conditional> | 408 </conditional> |
406 <output name="forward" file="10.1.fq.expected" ftype="fastqsanger" /> | 409 <output name="forward" file="10.1.fq.expected" ftype="fastqsanger" /> |
407 <output name="reverse" file="10.2.fq.expected" ftype="fastqsanger" /> | 410 <output name="reverse" file="10.2.fq.expected" ftype="fastqsanger" /> |
409 <output name="output" file="2.stdout.expected" ftype="fastqsanger" /> | 412 <output name="output" file="2.stdout.expected" ftype="fastqsanger" /> |
410 <output name="i1" file="bc10.fq.expected" ftype="fastqsanger" /> | 413 <output name="i1" file="bc10.fq.expected" ftype="fastqsanger" /> |
411 </test> | 414 </test> |
412 <!--# tag output test with separators and -N flag--> | 415 <!--# tag output test with separators and -N flag--> |
413 <!--test_cmd($opts, out=>'bam2fq/2.stdout.expected', out_map=>{'1.fq' => 'bam2fq/5.1.fq.expected', '2.fq' => 'bam2fq/5.2.fq.expected', 's.fq' => 'bam2fq/5.s.fq.expected', 'bc_split.fq' => 'bam2fq/bc_split.fq.expected'}, cmd=>"$$opts{bin}/samtools fastq @$threads \-\-barcode-tag BC -N \-\-index-format 'n*i*' \-\-i1 $$opts{path}/bc_split.fq -s $$opts{path}/s.fq -1 $$opts{path}/1.fq -2 $$opts{path}/2.fq $$opts{path}/dat/bam2fq.005.sam");--> | 416 <!--test_cmd($opts, out=>'bam2fq/2.stdout.expected', out_map=>{'1.fq' => 'bam2fq/5.1.fq.expected', '2.fq' => 'bam2fq/5.2.fq.expected', 's.fq' => 'bam2fq/5.s.fq.expected', 'bc_split.fq' => 'bam2fq/bc_split.fq.expected'}, cmd=>"$$opts{bin}/samtools fastq @$threads \-\-barcode-tag BC -N \-\-index-format 'n*i*' \-\-i1 $$opts{path}/bc_split.fq -s $$opts{path}/s.fq -1 $$opts{path}/1.fq -2 $$opts{path}/2.fq $$opts{path}/dat/bam2fq.005.sam");--> |
414 <test> | 417 <test expect_num_outputs="5"> |
415 <param name="input" value="bam2fq.005.sam" ftype="sam" /> | 418 <param name="input" value="bam2fq.005.sam" ftype="sam" /> |
416 <conditional name="output_fmt_cond"> | 419 <conditional name="output_fmt_cond"> |
417 <param name="output_fmt_select" value="fastqsanger" /> | 420 <param name="output_fmt_select" value="fastqsanger" /> |
418 </conditional> | 421 </conditional> |
419 <param name="outputs" value="r1,r2,s,other" /> | 422 <param name="outputs" value="r1,r2,s,other" /> |
420 <param name="read_numbering" value="-N"/> | 423 <param name="read_numbering" value="-N"/> |
421 <conditional name="idxout_cond"> | 424 <conditional name="idxout_cond"> |
422 <param name="idxout_select" value="yes"/> | 425 <param name="idxout_select" value="yes"/> |
423 <param name="write1st" value="yes"/> | 426 <param name="write1st" value="true"/> |
427 <param name="write2nd" value="false"/> | |
424 <param name="barcode_tag" value="BC"/> | 428 <param name="barcode_tag" value="BC"/> |
425 <param name="index_format" value="n*i*"/> | 429 <param name="index_format" value="n*i*"/> |
426 </conditional> | 430 </conditional> |
427 <output name="forward" file="5.1.fq.expected" ftype="fastqsanger" /> | 431 <output name="forward" file="5.1.fq.expected" ftype="fastqsanger" /> |
428 <output name="reverse" file="5.2.fq.expected" ftype="fastqsanger" /> | 432 <output name="reverse" file="5.2.fq.expected" ftype="fastqsanger" /> |
430 <output name="output" file="2.stdout.expected" ftype="fastqsanger" /> | 434 <output name="output" file="2.stdout.expected" ftype="fastqsanger" /> |
431 <output name="i1" file="bc_split.fq.expected" ftype="fastqsanger" /> | 435 <output name="i1" file="bc_split.fq.expected" ftype="fastqsanger" /> |
432 </test> | 436 </test> |
433 <!--# -t flag--> | 437 <!--# -t flag--> |
434 <!--test_cmd($opts, out=>'bam2fq/2.stdout.expected', out_map=>{'1.fq' => 'bam2fq/6.1.fq.expected', '2.fq' => 'bam2fq/6.2.fq.expected', 's.fq' => 'bam2fq/6.s.fq.expected'}, cmd=>"$$opts{bin}/samtools fastq @$threads -N -t -s $$opts{path}/s.fq -1 $$opts{path}/1.fq -2 $$opts{path}/2.fq $$opts{path}/dat/bam2fq.005.sam");--> | 438 <!--test_cmd($opts, out=>'bam2fq/2.stdout.expected', out_map=>{'1.fq' => 'bam2fq/6.1.fq.expected', '2.fq' => 'bam2fq/6.2.fq.expected', 's.fq' => 'bam2fq/6.s.fq.expected'}, cmd=>"$$opts{bin}/samtools fastq @$threads -N -t -s $$opts{path}/s.fq -1 $$opts{path}/1.fq -2 $$opts{path}/2.fq $$opts{path}/dat/bam2fq.005.sam");--> |
435 <test> | 439 <test expect_num_outputs="4"> |
436 <param name="input" value="bam2fq.005.sam" ftype="sam" /> | 440 <param name="input" value="bam2fq.005.sam" ftype="sam" /> |
437 <conditional name="output_fmt_cond"> | 441 <conditional name="output_fmt_cond"> |
438 <param name="output_fmt_select" value="fastqsanger" /> | 442 <param name="output_fmt_select" value="fastqsanger" /> |
439 </conditional> | 443 </conditional> |
440 <param name="outputs" value="r1,r2,s,other" /> | 444 <param name="outputs" value="r1,r2,s,other" /> |
445 <output name="singletons" file="6.s.fq.expected" ftype="fastqsanger" /> | 449 <output name="singletons" file="6.s.fq.expected" ftype="fastqsanger" /> |
446 <output name="output" file="2.stdout.expected" ftype="fastqsanger" /> | 450 <output name="output" file="2.stdout.expected" ftype="fastqsanger" /> |
447 </test> | 451 </test> |
448 <!--# -T flag--> | 452 <!--# -T flag--> |
449 <!--test_cmd($opts, out=>'bam2fq/2.stdout.expected', out_map=>{'1.fq' => 'bam2fq/7.1.fq.expected', '2.fq' => 'bam2fq/7.2.fq.expected', 's.fq' => 'bam2fq/7.s.fq.expected'}, cmd=>"$$opts{bin}/samtools fastq @$threads -N -t -T MD,ia -s $$opts{path}/s.fq -1 $$opts{path}/1.fq -2 $$opts{path}/2.fq $$opts{path}/dat/bam2fq.005.sam");--> | 453 <!--test_cmd($opts, out=>'bam2fq/2.stdout.expected', out_map=>{'1.fq' => 'bam2fq/7.1.fq.expected', '2.fq' => 'bam2fq/7.2.fq.expected', 's.fq' => 'bam2fq/7.s.fq.expected'}, cmd=>"$$opts{bin}/samtools fastq @$threads -N -t -T MD,ia -s $$opts{path}/s.fq -1 $$opts{path}/1.fq -2 $$opts{path}/2.fq $$opts{path}/dat/bam2fq.005.sam");--> |
450 <test> | 454 <test expect_num_outputs="4"> |
451 <param name="input" value="bam2fq.005.sam" ftype="sam" /> | 455 <param name="input" value="bam2fq.005.sam" ftype="sam" /> |
452 <conditional name="output_fmt_cond"> | 456 <conditional name="output_fmt_cond"> |
453 <param name="output_fmt_select" value="fastqsanger" /> | 457 <param name="output_fmt_select" value="fastqsanger" /> |
454 </conditional> | 458 </conditional> |
455 <param name="outputs" value="r1,r2,s,other" /> | 459 <param name="outputs" value="r1,r2,s,other" /> |
461 <output name="singletons" file="7.s.fq.expected" ftype="fastqsanger" /> | 465 <output name="singletons" file="7.s.fq.expected" ftype="fastqsanger" /> |
462 <output name="output" file="2.stdout.expected" ftype="fastqsanger" /> | 466 <output name="output" file="2.stdout.expected" ftype="fastqsanger" /> |
463 </test> | 467 </test> |
464 <!--# -i flag with no index--> | 468 <!--# -i flag with no index--> |
465 <!--test_cmd($opts, out=>'bam2fq/2.stdout.expected', out_map=>{'1.fq' => 'bam2fq/7.1.fq.expected', '2.fq' => 'bam2fq/7.2.fq.expected', 's.fq' => 'bam2fq/7.s.fq.expected'}, cmd=>"$$opts{bin}/samtools fastq @$threads -N -t -i -T MD,ia -s $$opts{path}/s.fq -1 $$opts{path}/1.fq -2 $$opts{path}/2.fq $$opts{path}/dat/bam2fq.005.sam");--> | 469 <!--test_cmd($opts, out=>'bam2fq/2.stdout.expected', out_map=>{'1.fq' => 'bam2fq/7.1.fq.expected', '2.fq' => 'bam2fq/7.2.fq.expected', 's.fq' => 'bam2fq/7.s.fq.expected'}, cmd=>"$$opts{bin}/samtools fastq @$threads -N -t -i -T MD,ia -s $$opts{path}/s.fq -1 $$opts{path}/1.fq -2 $$opts{path}/2.fq $$opts{path}/dat/bam2fq.005.sam");--> |
466 <test> | 470 <test expect_num_outputs="6"> |
467 <param name="input" value="bam2fq.005.sam" ftype="sam" /> | 471 <param name="input" value="bam2fq.005.sam" ftype="sam" /> |
468 <conditional name="output_fmt_cond"> | 472 <conditional name="output_fmt_cond"> |
469 <param name="output_fmt_select" value="fastqsanger" /> | 473 <param name="output_fmt_select" value="fastqsanger" /> |
470 <param name="ilumina_casava" value="-i" /> | 474 <param name="ilumina_casava" value="-i" /> |
471 </conditional> | 475 </conditional> |
479 <param name="read_numbering" value="-N"/> | 483 <param name="read_numbering" value="-N"/> |
480 <output name="forward" file="11.1.fq.expected" ftype="fastqsanger" /> | 484 <output name="forward" file="11.1.fq.expected" ftype="fastqsanger" /> |
481 <output name="reverse" file="11.2.fq.expected" ftype="fastqsanger" /> | 485 <output name="reverse" file="11.2.fq.expected" ftype="fastqsanger" /> |
482 <output name="singletons" file="11.s.fq.expected" ftype="fastqsanger" /> | 486 <output name="singletons" file="11.s.fq.expected" ftype="fastqsanger" /> |
483 <output name="output" file="2.stdout.expected" ftype="fastqsanger" /> | 487 <output name="output" file="2.stdout.expected" ftype="fastqsanger" /> |
488 <output name="i1" file="11.i.fq.expected" ftype="fastqsanger" /> | |
489 <output name="i2" file="11.i2.fq.expected" ftype="fastqsanger" /> | |
484 </test> | 490 </test> |
485 <!--# -i flag with index--> | 491 <!--# -i flag with index--> |
486 <!--test_cmd($opts, out=>'bam2fq/2.stdout.expected', out_map=>{'1.fq' => 'bam2fq/8.1.fq.expected', '2.fq' => 'bam2fq/8.2.fq.expected', 's.fq' => 'bam2fq/8.s.fq.expected', 'i.fq' => 'bam2fq/8.i.fq.expected'}, cmd=>"$$opts{bin}/samtools fastq @$threads \-\-barcode-tag BC -i \-\-index-format 'n2i2' \-\-i1 $$opts{path}/i.fq -s $$opts{path}/s.fq -1 $$opts{path}/1.fq -2 $$opts{path}/2.fq $$opts{path}/dat/bam2fq.004.sam");--> | 492 <!--test_cmd($opts, out=>'bam2fq/2.stdout.expected', out_map=>{'1.fq' => 'bam2fq/8.1.fq.expected', '2.fq' => 'bam2fq/8.2.fq.expected', 's.fq' => 'bam2fq/8.s.fq.expected', 'i.fq' => 'bam2fq/8.i.fq.expected'}, cmd=>"$$opts{bin}/samtools fastq @$threads \-\-barcode-tag BC -i \-\-index-format 'n2i2' \-\-i1 $$opts{path}/i.fq -s $$opts{path}/s.fq -1 $$opts{path}/1.fq -2 $$opts{path}/2.fq $$opts{path}/dat/bam2fq.004.sam");--> |
487 <test> | 493 <test expect_num_outputs="6"> |
488 <param name="input" value="bam2fq.004.sam" ftype="sam" /> | 494 <param name="input" value="bam2fq.004.sam" ftype="sam" /> |
489 <conditional name="output_fmt_cond"> | 495 <conditional name="output_fmt_cond"> |
490 <param name="output_fmt_select" value="fastqsanger" /> | 496 <param name="output_fmt_select" value="fastqsanger" /> |
491 <param name="ilumina_casava" value="-i" /> | 497 <param name="ilumina_casava" value="-i" /> |
492 </conditional> | 498 </conditional> |
493 <param name="outputs" value="r1,r2,s,other" /> | 499 <param name="outputs" value="r1,r2,s,other" /> |
494 <conditional name="idxout_cond"> | 500 <conditional name="idxout_cond"> |
495 <param name="idxout_select" value="yes"/> | 501 <param name="idxout_select" value="yes"/> |
496 <param name="write1st" value="yes"/> | 502 <param name="write1st" value="true"/> |
497 <param name="barcode_tag" value="BC"/> | 503 <param name="barcode_tag" value="BC"/> |
498 <param name="index_format" value="n2i2"/> | 504 <param name="index_format" value="n2i2"/> |
499 </conditional> | 505 </conditional> |
500 <output name="forward" file="8.1.fq.expected" ftype="fastqsanger" /> | 506 <output name="forward" file="8.1.fq.expected" ftype="fastqsanger" /> |
501 <output name="reverse" file="8.2.fq.expected" ftype="fastqsanger" /> | 507 <output name="reverse" file="8.2.fq.expected" ftype="fastqsanger" /> |
502 <output name="singletons" file="8.s.fq.expected" ftype="fastqsanger" /> | 508 <output name="singletons" file="8.s.fq.expected" ftype="fastqsanger" /> |
503 <output name="output" file="2.stdout.expected" ftype="fastqsanger" /> | 509 <output name="output" file="2.stdout.expected" ftype="fastqsanger" /> |
504 <output name="i1" file="8.i.fq.expected" ftype="fastqsanger" /> | 510 <output name="i1" file="8.i.fq.expected" ftype="fastqsanger" /> |
511 <output name="i2" file="8.i2.fq.expected" ftype="fastqsanger" /> | |
505 </test> | 512 </test> |
506 </tests> | 513 </tests> |
507 <help><![CDATA[ | 514 <help><![CDATA[ |
508 This tool uses `Samtools <http://www.htslib.org/>`_ to extract sequences from a | 515 This tool uses `Samtools <http://www.htslib.org/>`_ to extract sequences from a |
509 SAM or BAM file in FASTA or FASTQ format. | 516 SAM or BAM file in FASTA or FASTQ format. |