Mercurial > repos > iuc > varscan_somatic

comparison varscan_somatic.xml @ 10:a57606054bd7 draft

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"planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 46018cbdd8b4ca124d5c6230862012b9081d56e4"
author iuc
date Sat, 18 Jan 2020 03:19:29 -0500
parents 4e97191a1ff7
children
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9:4e97191a1ff7 10:a57606054bd7
1 <tool id="varscan_somatic" name="VarScan somatic" version="@VERSION@.5"> 1 <tool id="varscan_somatic" name="VarScan somatic" version="@VERSION@.6">
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>
408 <conditional name="filter_params"> 408 <conditional name="filter_params">
409 <param name="settings" value="varscan_defaults" /> 409 <param name="settings" value="varscan_defaults" />
410 </conditional> 410 </conditional>
411 <assert_stderr> 411 <assert_stderr>
412 <has_line_matching 412 <has_line_matching
413 expression=" Min coverage:&#09;2x for Normal, 2x for Tumor" /> 413 expression=" *Min coverage:&#09;2x for Normal, 2x for Tumor" />
414 <has_line_matching 414 <has_line_matching
415 expression="Min reads2:&#09;1" /> 415 expression="Min reads2:&#09;1" />
416 <has_line_matching 416 <has_line_matching
417 expression="Min var freq:&#09;0.01" /> 417 expression="Min var freq:&#09;0.01" />
418 <has_line_matching 418 <has_line_matching