Mercurial > repos > iuc > varscan_somatic
diff 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 |
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--- a/varscan_somatic.xml Mon Jan 21 12:05:00 2019 -0500 +++ b/varscan_somatic.xml Thu Mar 28 18:19:00 2019 -0400 @@ -1,4 +1,4 @@ -<tool id="varscan_somatic" name="VarScan somatic" version="@VERSION@.3"> +<tool id="varscan_somatic" name="VarScan somatic" version="@VERSION@.4"> <description>Call germline/somatic and LOH variants from tumor-normal sample pairs</description> <macros> <import>macros.xml</import> @@ -453,6 +453,33 @@ <expand macro="test_mentions_filters" /> </output> </test> + <test expect_num_outputs="1"> + <!-- Test with an input bam with extremely high coverage at a + variant site (high enough to trigger an AssertionError from + pysam.libcalignedsegment.get_query_sequences) to see if the + tool can handle this. + Also test that the tool doesn't report SNVs against Ns in + the reference genome (this would lead to more than one variant + getting called). --> + <conditional name="reference"> + <param name="source" value="history" /> + <param name="genome" value="hg19_chrM.fa" /> + </conditional> + <param name="normal_bam" value="high_cov_chrM.bam" /> + <param name="tumor_bam" value="high_cov_chrM.bam" /> + <param name="split_output" value="false" /> + <conditional name="call_params"> + <param name="settings" value="varscan_defaults" /> + </conditional> + <conditional name="filter_params"> + <param name="settings" value="varscan_defaults" /> + </conditional> + <output name="output"> + <expand macro="test_mentions_contig" /> + <expand macro="test_mentions_filters" /> + <metadata name="data_lines" value="1" /> + </output> + </test> </tests> <help>