Mercurial > repos > iuc > varscan_somatic
comparison varscan_somatic.xml @ 8:b79bb8b09822 draft
planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit bd1034af3217cd9fc654d7187bf674a89465755b
| author | iuc |
|---|---|
| date | Thu, 28 Mar 2019 18:19:00 -0400 |
| parents | 2c66c4025db2 |
| children | 4e97191a1ff7 |
comparison
equal
deleted
inserted
replaced
| 7:2657ab48e16a | 8:b79bb8b09822 |
|---|---|
| 1 <tool id="varscan_somatic" name="VarScan somatic" version="@VERSION@.3"> | 1 <tool id="varscan_somatic" name="VarScan somatic" version="@VERSION@.4"> |
| 2 <description>Call germline/somatic and LOH variants from tumor-normal sample pairs</description> | 2 <description>Call germline/somatic and LOH variants from tumor-normal sample pairs</description> |
| 3 <macros> | 3 <macros> |
| 4 <import>macros.xml</import> | 4 <import>macros.xml</import> |
| 5 <macro name="test_mentions_contig"> | 5 <macro name="test_mentions_contig"> |
| 6 <assert_contents> | 6 <assert_contents> |
| 451 <output name="output"> | 451 <output name="output"> |
| 452 <expand macro="test_mentions_contig" /> | 452 <expand macro="test_mentions_contig" /> |
| 453 <expand macro="test_mentions_filters" /> | 453 <expand macro="test_mentions_filters" /> |
| 454 </output> | 454 </output> |
| 455 </test> | 455 </test> |
| 456 <test expect_num_outputs="1"> | |
| 457 <!-- Test with an input bam with extremely high coverage at a | |
| 458 variant site (high enough to trigger an AssertionError from | |
| 459 pysam.libcalignedsegment.get_query_sequences) to see if the | |
| 460 tool can handle this. | |
| 461 Also test that the tool doesn't report SNVs against Ns in | |
| 462 the reference genome (this would lead to more than one variant | |
| 463 getting called). --> | |
| 464 <conditional name="reference"> | |
| 465 <param name="source" value="history" /> | |
| 466 <param name="genome" value="hg19_chrM.fa" /> | |
| 467 </conditional> | |
| 468 <param name="normal_bam" value="high_cov_chrM.bam" /> | |
| 469 <param name="tumor_bam" value="high_cov_chrM.bam" /> | |
| 470 <param name="split_output" value="false" /> | |
| 471 <conditional name="call_params"> | |
| 472 <param name="settings" value="varscan_defaults" /> | |
| 473 </conditional> | |
| 474 <conditional name="filter_params"> | |
| 475 <param name="settings" value="varscan_defaults" /> | |
| 476 </conditional> | |
| 477 <output name="output"> | |
| 478 <expand macro="test_mentions_contig" /> | |
| 479 <expand macro="test_mentions_filters" /> | |
| 480 <metadata name="data_lines" value="1" /> | |
| 481 </output> | |
| 482 </test> | |
| 456 </tests> | 483 </tests> |
| 457 | 484 |
| 458 <help> | 485 <help> |
| 459 @HELP_HEADER@ | 486 @HELP_HEADER@ |
| 460 | 487 |