Mercurial > repos > iuc > hisat2
comparison hisat2.xml @ 7:5ba8e317529a draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 5c49c4049418cdca86f40df5a5d8014c2d932dde
author | iuc |
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date | Sat, 21 Jan 2017 15:42:34 -0500 |
parents | 5f4da9ec47c7 |
children | 4d0a3173cde0 |
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6:5f4da9ec47c7 | 7:5ba8e317529a |
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1 <?xml version="1.0"?> | 1 <?xml version="1.0"?> |
2 <tool id="hisat2" name="HISAT" version="2.0.3.1"> | 2 <tool id="hisat2" name="HISAT2" version="2.0.3.2"> |
3 <description>A fast and sensitive alignment program</description> | 3 <description>A fast and sensitive alignment program</description> |
4 <macros> | 4 <macros> |
5 <import>hisat2_macros.xml</import> | 5 <import>hisat2_macros.xml</import> |
6 </macros> | 6 </macros> |
7 <requirements> | 7 <requirements> |
36 #else if str($input_format.paired.paired_selector) == 'paired_collection': | 36 #else if str($input_format.paired.paired_selector) == 'paired_collection': |
37 -1 "${input_format.paired.reads.forward}" -2 "${input_format.paired.reads.reverse}" | 37 -1 "${input_format.paired.reads.forward}" -2 "${input_format.paired.reads.reverse}" |
38 @paired_end_options@ | 38 @paired_end_options@ |
39 #else: | 39 #else: |
40 -U "${input_format.paired.reads}" | 40 -U "${input_format.paired.reads}" |
41 #if str( $input_format.paired.unaligned_file ) == "true": | |
42 --un '$output_unaligned_reads_l' | |
43 #end if | |
44 #if str( $input_format.paired.aligned_file ) == "true": | |
45 --al '$output_aligned_reads_l' | |
46 #end if | |
41 #end if | 47 #end if |
42 #if $input_format.input_format_selector == 'fasta': | 48 #if $input_format.input_format_selector == 'fasta': |
43 -f | 49 -f |
44 #end if | 50 #end if |
45 #if $max_primary: | 51 #if $max_primary: |
82 #if str($paired_options.paired_options_selector) == "advanced": | 88 #if str($paired_options.paired_options_selector) == "advanced": |
83 --minins ${paired_options.minins} --maxins ${paired_options.maxins} ${paired_options.no_mixed} ${paired_options.no_discordant} | 89 --minins ${paired_options.minins} --maxins ${paired_options.maxins} ${paired_options.no_mixed} ${paired_options.no_discordant} |
84 ${paired_options.dovetail} ${paired_options.contain} ${paired_options.overlap} | 90 ${paired_options.dovetail} ${paired_options.contain} ${paired_options.overlap} |
85 #end if | 91 #end if |
86 | samtools sort - -@ \${GALAXY_SLOTS:-2} -l 6 -o hsbam > "${output_alignments}" | 92 | samtools sort - -@ \${GALAXY_SLOTS:-2} -l 6 -o hsbam > "${output_alignments}" |
93 | |
94 ## Rename any output fastq files | |
95 #if str($input_format.paired.paired_selector) == 'paired' or str($input_format.paired.paired_selector) == 'paired_collection': | |
96 #if $output_unaligned_reads_l and $output_unaligned_reads_r: | |
97 #set left = str($output_unaligned_reads_l).replace(".dat", ".1.dat") | |
98 #set right = str($output_unaligned_reads_l).replace(".dat", ".2.dat") | |
99 && mv '${left}' '${output_unaligned_reads_l}' | |
100 && mv '${right}' '${output_unaligned_reads_r}' | |
101 #end if | |
102 #if $output_aligned_reads_l and $output_aligned_reads_r: | |
103 #set left = str($output_aligned_reads_l).replace(".dat", ".1.dat") | |
104 #set right = str($output_aligned_reads_l).replace(".dat", ".2.dat") | |
105 && mv '${left}' '${output_aligned_reads_l}' | |
106 && mv '${right}' '${output_aligned_reads_r}' | |
107 #end if | |
108 #end if | |
87 ]]> | 109 ]]> |
88 </command> | 110 </command> |
89 <inputs> | 111 <inputs> |
90 <conditional name="input_format"> | 112 <conditional name="input_format"> |
91 <param label="Input data format" name="input_format_selector" type="select"> | 113 <param label="Input data format" name="input_format_selector" type="select"> |
241 </action> | 263 </action> |
242 </when> | 264 </when> |
243 </conditional> | 265 </conditional> |
244 </actions> | 266 </actions> |
245 </data> | 267 </data> |
268 <data format="fastqsanger" name="output_unaligned_reads_l" label="${tool.name} on ${on_string}: unaligned reads (L)" > | |
269 <filter>input_format['paired']['unaligned_file'] is True</filter> | |
270 <actions> | |
271 <conditional name="input_format.paired.paired_selector"> | |
272 <when value="single"> | |
273 <action type="format"> | |
274 <option type="from_param" name="input_format.paired.reads" param_attribute="ext" /> | |
275 </action> | |
276 </when> | |
277 <when value="paired"> | |
278 <action type="format"> | |
279 <option type="from_param" name="input_format.paired.reads_f" param_attribute="ext" /> | |
280 </action> | |
281 </when> | |
282 <when value="paired_collection"> | |
283 <action type="format"> | |
284 <option type="from_param" name="input_format.paired.reads" param_attribute="forward.ext" /> | |
285 </action> | |
286 </when> | |
287 </conditional> | |
288 </actions> | |
289 </data> | |
290 <data format="fastqsanger" name="output_unaligned_reads_r" label="${tool.name} on ${on_string}: unaligned reads (R)" > | |
291 <filter>input_format['paired']['unaligned_file'] is True and input_format['paired']['paired_selector'] != 'single'</filter> | |
292 <actions> | |
293 <conditional name="input_format.paired.paired_selector"> | |
294 <when value="paired"> | |
295 <action type="format"> | |
296 <option type="from_param" name="input_format.paired.reads_r" param_attribute="ext" /> | |
297 </action> | |
298 </when> | |
299 <when value="paired_collection"> | |
300 <action type="format"> | |
301 <option type="from_param" name="input_format.paired.reads" param_attribute="forward.ext" /> | |
302 </action> | |
303 </when> | |
304 </conditional> | |
305 </actions> | |
306 </data> | |
307 <data format="fastqsanger" name="output_aligned_reads_l" label="${tool.name} on ${on_string}: aligned reads${' (L)' if str($input_format.paired.paired_selector) != 'single' else ''}" > | |
308 <filter>input_format['paired']['aligned_file'] is True</filter> | |
309 <actions> | |
310 <conditional name="input_format.paired.paired_selector"> | |
311 <when value="single"> | |
312 <action type="format"> | |
313 <option type="from_param" name="input_format.paired.reads" param_attribute="ext" /> | |
314 </action> | |
315 </when> | |
316 <when value="paired"> | |
317 <action type="format"> | |
318 <option type="from_param" name="input_format.paired.reads_f" param_attribute="ext" /> | |
319 </action> | |
320 </when> | |
321 <when value="paired_collection"> | |
322 <action type="format"> | |
323 <option type="from_param" name="input_format.paired.reads" param_attribute="forward.ext" /> | |
324 </action> | |
325 </when> | |
326 </conditional> | |
327 </actions> | |
328 </data> | |
329 <data format="fastqsanger" name="output_aligned_reads_r" label="${tool.name} on ${on_string}: aligned reads (R)" > | |
330 <filter>input_format['paired']['aligned_file'] is True and input_format['paired']['paired_selector'] != 'single'</filter> | |
331 <actions> | |
332 <conditional name="input_format.paired.paired_selector"> | |
333 <when value="paired"> | |
334 <action type="format"> | |
335 <option type="from_param" name="input_format.paired.reads_r" param_attribute="ext" /> | |
336 </action> | |
337 </when> | |
338 <when value="paired_collection"> | |
339 <action type="format"> | |
340 <option type="from_param" name="input_format.paired.reads" param_attribute="forward.ext" /> | |
341 </action> | |
342 </when> | |
343 </conditional> | |
344 </actions> | |
345 </data> | |
246 </outputs> | 346 </outputs> |
247 <tests> | 347 <tests> |
248 <test> | 348 <test> |
249 <param name="input_format_selector" value="fastq" /> | 349 <param name="input_format_selector" value="fastq" /> |
250 <param name="paired_selector" value="paired" /> | 350 <param name="paired_selector" value="paired" /> |
278 <param name="reads_r" ftype="fastqsanger" value="hisat_input_2_reverse.fastq" /> | 378 <param name="reads_r" ftype="fastqsanger" value="hisat_input_2_reverse.fastq" /> |
279 <param name="paired_end_options_selector" value="advanced" /> | 379 <param name="paired_end_options_selector" value="advanced" /> |
280 <param name="no_mixed" value="True" /> | 380 <param name="no_mixed" value="True" /> |
281 <param name="no_discordant" value="True" /> | 381 <param name="no_discordant" value="True" /> |
282 <output name="output_alignments" ftype="bam" file="hisat_output_3.bam" lines_diff="2" /> | 382 <output name="output_alignments" ftype="bam" file="hisat_output_3.bam" lines_diff="2" /> |
383 </test> | |
384 <test><!-- testing unaligned output (single dataset) --> | |
385 <param name="input_format_selector" value="fasta" /> | |
386 <param name="paired_selector" value="single" /> | |
387 <param name="reference_genome_source" value="history" /> | |
388 <param name="history_item" value="phiX.fa" ftype="fasta" /> | |
389 <param name="unaligned_file" value="true" /> | |
390 <param name="aligned_file" value="true" /> | |
391 <param name="reference_genome_source" value="history" /> | |
392 <param name="history_item" value="phiX.fa" ftype="fasta" /> | |
393 <param name="reads" value="test_unaligned_reads.fasta" ftype="fasta" /> | |
394 | |
395 <output name="output_unaligned_reads_l" file="test_unaligned_reads.fasta" /> | |
396 </test> | |
397 | |
398 <test> | |
399 <param name="input_format_selector" value="fasta" /> | |
400 <param name="paired_selector" value="paired" /> | |
401 <param name="reference_genome_source" value="history" /> | |
402 <param name="history_item" value="phiX.fa" ftype="fasta" /> | |
403 <param name="unaligned_file" value="true" /> | |
404 <param name="aligned_file" value="true" /> | |
405 <param name="reference_genome_source" value="history" /> | |
406 <param name="history_item" value="phiX.fa" ftype="fasta" /> | |
407 <param name="reads_f" value="test_unaligned_reads.fasta" ftype="fasta" /> | |
408 <param name="reads_r" value="test_unaligned_reads.fasta" ftype="fasta" /> | |
409 | |
410 <output name="output_unaligned_reads_l" file="test_unaligned_reads.fasta" /> | |
411 <output name="output_unaligned_reads_r" file="test_unaligned_reads.fasta" /> | |
283 </test> | 412 </test> |
284 </tests> | 413 </tests> |
285 <help> | 414 <help> |
286 <![CDATA[ | 415 <![CDATA[ |
287 Introduction | 416 Introduction |