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comparison samtools_fastx.xml @ 5:344c3c1177a9 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 9c5a35ce695c3d134e41d8695487edd5f71ea33c
author iuc
date Sun, 08 Sep 2024 03:22:32 +0000
parents 1c46e3315853
children
comparison
equal deleted inserted replaced
4:1c46e3315853 5:344c3c1177a9
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.