Mercurial > repos > bgruening > trim_galore

comparison trim_galore.xml @ 14:949f01671246 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 6aa3014c2c6f9ef9ee71b20cfffec461b3a102a5
author bgruening
date Thu, 01 Jun 2017 12:15:10 -0400
parents b6c00b82f623
children 084bbd8ba7b8
comparison
equal deleted inserted replaced
13:b6c00b82f623 14:949f01671246
336 <test> 336 <test>
337 <param name="input_singles" value="sanger_full_range_original_sanger.fastq.gz" ftype="fastqsanger.gz" /> 337 <param name="input_singles" value="sanger_full_range_original_sanger.fastq.gz" ftype="fastqsanger.gz" />
338 <param name="sPaired" value="single" /> 338 <param name="sPaired" value="single" />
339 <param name="settingsType" value="custom" /> 339 <param name="settingsType" value="custom" />
340 <param name="report" value="true" /> 340 <param name="report" value="true" />
341 <output name="trimmed_reads_single" file="sanger_full_range_results1.fastq.gz" ftype="fastqsanger.gz" compare="sim_size" delta="0"/> 341 <output name="trimmed_reads_single" file="sanger_full_range_results1.fastq.gz" ftype="fastqsanger.gz" decompress="true" />
342 <output name="report_file" file="sanger_full_range_report_results1gz.txt" ftype="txt" lines_diff="9" /> 342 <output name="report_file" file="sanger_full_range_report_results1gz.txt" ftype="txt" lines_diff="9" />
343 </test> 343 </test>
344 344
345 <test> 345 <test>
346 <param name="input_singles" value="sanger_full_range_original_sanger.fastqsanger" ftype="fastqsanger" /> 346 <param name="input_singles" value="sanger_full_range_original_sanger.fastqsanger" ftype="fastqsanger" />
350 </test> 350 </test>
351 <test> 351 <test>
352 <param name="input_singles" value="sanger_full_range_original_sanger.fastq.gz" ftype="fastqsanger.gz" /> 352 <param name="input_singles" value="sanger_full_range_original_sanger.fastq.gz" ftype="fastqsanger.gz" />
353 <param name="sPaired" value="single" /> 353 <param name="sPaired" value="single" />
354 <param name="trimming_select" value="--illumina" /> 354 <param name="trimming_select" value="--illumina" />
355 <output name="trimmed_reads_single" file="sanger_full_range_results2.fastq.gz" ftype="fastqsanger.gz" compare="sim_size" delta="0"/> 355 <output name="trimmed_reads_single" file="sanger_full_range_results2.fastq.gz" ftype="fastqsanger.gz" decompress="true" />
356 </test> 356 </test>
357 357
358 <test> 358 <test>
359 <param name="input_singles" value="sanger_full_range_original_sanger.fastqsanger" ftype="fastqsanger" /> 359 <param name="input_singles" value="sanger_full_range_original_sanger.fastqsanger" ftype="fastqsanger" />
360 <param name="sPaired" value="single" /> 360 <param name="sPaired" value="single" />
363 </test> 363 </test>
364 <test> 364 <test>
365 <param name="input_singles" value="sanger_full_range_original_sanger.fastq.gz" ftype="fastqsanger.gz" /> 365 <param name="input_singles" value="sanger_full_range_original_sanger.fastq.gz" ftype="fastqsanger.gz" />
366 <param name="sPaired" value="single" /> 366 <param name="sPaired" value="single" />
367 <param name="adapter" value="AAAGAGC" /> 367 <param name="adapter" value="AAAGAGC" />
368 <output name="trimmed_reads_single" file="sanger_full_range_results3.fastq.gz" ftype="fastqsanger.gz" compare="sim_size" delta="0"/> 368 <output name="trimmed_reads_single" file="sanger_full_range_results3.fastq.gz" ftype="fastqsanger.gz" decompress="true" />
369 </test> 369 </test>
370 370
371 <test> 371 <test>
372 <param name="input_mate1" value="bwa-mem-fastq1.fq" ftype="fastqsanger" /> 372 <param name="input_mate1" value="bwa-mem-fastq1.fq" ftype="fastqsanger" />
373 <param name="input_mate2" value="bwa-mem-fastq2.fq" ftype="fastqsanger" /> 373 <param name="input_mate2" value="bwa-mem-fastq2.fq" ftype="fastqsanger" />
382 <param name="input_mate1" value="bwa-mem-fastq1.fq.gz" ftype="fastqsanger.gz" /> 382 <param name="input_mate1" value="bwa-mem-fastq1.fq.gz" ftype="fastqsanger.gz" />
383 <param name="input_mate2" value="bwa-mem-fastq2.fq.gz" ftype="fastqsanger.gz" /> 383 <param name="input_mate2" value="bwa-mem-fastq2.fq.gz" ftype="fastqsanger.gz" />
384 <param name="sPaired" value="paired" /> 384 <param name="sPaired" value="paired" />
385 <param name="settingsType" value="custom" /> 385 <param name="settingsType" value="custom" />
386 <param name="report" value="true" /> 386 <param name="report" value="true" />
387 <output name="trimmed_reads_pair1" file="paired_example_pair1_results2.fastq.gz" ftype="fastqsanger.gz" compare="sim_size" delta="30"/> 387 <output name="trimmed_reads_pair1" file="paired_example_pair1_results2.fastq.gz" ftype="fastqsanger.gz" decompress="true" />
388 <output name="trimmed_reads_pair2" file="paired_example_pair2_results2.fastq.gz" ftype="fastqsanger.gz" compare="sim_size" delta="30"/> 388 <output name="trimmed_reads_pair2" file="paired_example_pair2_results2.fastq.gz" ftype="fastqsanger.gz" decompress="true" />
389 <output name="report_file" file="paired_example_results2gz.txt" ftype="txt" lines_diff="24" /> 389 <output name="report_file" file="paired_example_results2gz.txt" ftype="txt" lines_diff="24" />
390 </test> 390 </test>
391 391
392 <test> 392 <test>
393 <param name="input_mate_pairs"> 393 <param name="input_mate_pairs">
428 <param name="retain_unpaired_select" value="retain_unpaired_output" /> 428 <param name="retain_unpaired_select" value="retain_unpaired_output" />
429 429
430 <output name="report_file" file="paired_collection_example_results3gz.txt" ftype="txt" lines_diff="25" /> 430 <output name="report_file" file="paired_collection_example_results3gz.txt" ftype="txt" lines_diff="25" />
431 431
432 <output_collection name="trimmed_reads_paired_collection" type="paired"> 432 <output_collection name="trimmed_reads_paired_collection" type="paired">
433 <element name="forward" file="paired_collection_example_pair1_results3.fastq.gz" ftype="fastqsanger.gz" compare="sim_size" delta="30"/> 433 <element name="forward" file="paired_collection_example_pair1_results3.fastq.gz" ftype="fastqsanger.gz" decompress="true" />
434 <element name="reverse" file="paired_collection_example_pair2_results3.fastq.gz" ftype="fastqsanger.gz" compare="sim_size" delta="30"/> 434 <element name="reverse" file="paired_collection_example_pair2_results3.fastq.gz" ftype="fastqsanger.gz" decompress="true" />
435 </output_collection> 435 </output_collection>
436 436
437 <output_collection name="trimmed_reads_unpaired_collection" type="paired"> 437 <output_collection name="trimmed_reads_unpaired_collection" type="paired">
438 <element name="forward" file="paired_collection_example_unpair1_results3.fastq.gz" ftype="fastqsanger.gz" compare="sim_size" delta="30"/> 438 <element name="forward" file="paired_collection_example_unpair1_results3.fastq.gz" ftype="fastqsanger.gz" decompress="true" />
439 <element name="reverse" file="paired_collection_example_unpair2_results3.fastq.gz" ftype="fastqsanger.gz" compare="sim_size" delta="30"/> 439 <element name="reverse" file="paired_collection_example_unpair2_results3.fastq.gz" ftype="fastqsanger.gz" decompress="true" />
440 </output_collection> 440 </output_collection>
441 </test> 441 </test>
442 </tests> 442 </tests>
443 <help><![CDATA[ 443 <help><![CDATA[
444 **What it does** 444 **What it does**