Mercurial > repos > jjohnson > pileup_to_vcf

comparison pileup_to_vcf.xml @ 5:8688e29ba96f

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Fix test 2
author Jim Johnson <jj@umn.edu>
date Tue, 19 Mar 2013 15:05:20 -0500
parents fafa105e5f58
children c0a6e8f595ec
comparison
equal deleted inserted replaced
4:fafa105e5f58 5:8688e29ba96f
90 </output> 90 </output>
91 </test> 91 </test>
92 <test> 92 <test>
93 <param name="input_file" ftype="pileup" value="test.pileup" /> 93 <param name="input_file" ftype="pileup" value="test.pileup" />
94 <param name="select_order" value="no"/> 94 <param name="select_order" value="no"/>
95 <param name="min_base_qual" value="20"/> 95 <param name="min_base_qual" value="5"/>
96 <param name="min_cvrg" value="5"/> 96 <param name="min_cvrg" value="5"/>
97 <param name="min_var_pct" value=".1"/> 97 <param name="min_var_pct" value=".1"/>
98 <param name="allow_multiples" value="True"/> 98 <param name="allow_multiples" value="True"/>
99 <param name="snps_only" value="False"/> 99 <param name="snps_only" value="False"/>
100 <param name="depth_as" value="ref"/> 100 <param name="depth_as" value="ref"/>
101 <output name="output_file"> 101 <output name="output_file">
102 <assert_contents> 102 <assert_contents>
103 <has_text_matching expression="seq2\t156\t.\tA\tG,AAG\t.\tPASS\t.*" /> 103 <has_text_matching expression="seq2\t156\t.\tA\tG,AAG\t.\tPASS\t.*" />
104 <has_text_matching expression="chr1\t158571283\t.\tA\tC\t.\tPASS\t.*" /> 104 <has_text_matching expression="chr1\t158571283\t.\tA\tT\t.\tPASS\t.*" />
105 <not_has_text text="125070485" />
105 </assert_contents> 106 </assert_contents>
106 </output> 107 </output>
107 </test> 108 </test>
108 109
109 </tests> 110 </tests>