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comparison bcftools_filter.xml @ 7:cdb7b4927742 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 2684e1443f03bfe2ae20c31d23817415ec8f7e69
author iuc
date Thu, 21 Feb 2019 16:02:58 -0500
parents cfd95c205d55
children c01a175420f5
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6:963a3635b2e1 7:cdb7b4927742
1 <?xml version='1.0' encoding='utf-8'?> 1 <?xml version='1.0' encoding='utf-8'?>
2 <tool name="bcftools @EXECUTABLE@" id="bcftools_@EXECUTABLE@" version="@VERSION@"> 2 <tool name="bcftools @EXECUTABLE@" id="bcftools_@EXECUTABLE@" version="@TOOL_VERSION@">
3 <description>Apply fixed-threshold filters</description> 3 <description>Apply fixed-threshold filters</description>
4 <macros> 4 <macros>
5 <token name="@EXECUTABLE@">filter</token> 5 <token name="@EXECUTABLE@">filter</token>
6 <import>macros.xml</import> 6 <import>macros.xml</import>
7 </macros> 7 </macros>
112 </assert_contents> 112 </assert_contents>
113 </output> 113 </output>
114 </test> 114 </test>
115 <test> 115 <test>
116 <param name="input_file" ftype="vcf" value="filter.3.vcf" /> 116 <param name="input_file" ftype="vcf" value="filter.3.vcf" />
117 <param name="exclude" value="DP=19" /> 117 <param name="exclude" value="INFO/DP=19" />
118 <param name="output_type" value="v" /> 118 <param name="output_type" value="v" />
119 <output name="output_file"> 119 <output name="output_file">
120 <assert_contents> 120 <assert_contents>
121 <not_has_text text="3162006" /> 121 <not_has_text text="3162006" />
122 <has_text text="3162007" /> 122 <has_text text="3162007" />
124 </output> 124 </output>
125 </test> 125 </test>
126 126
127 <test> 127 <test>
128 <param name="input_file" ftype="vcf" value="filter.3.vcf" /> 128 <param name="input_file" ftype="vcf" value="filter.3.vcf" />
129 <param name="exclude" value="DP=19" /> 129 <param name="exclude" value="INFO/DP=19" />
130 <param name="soft_filter" value="XX" /> 130 <param name="soft_filter" value="XX" />
131 <param name="output_type" value="v" /> 131 <param name="output_type" value="v" />
132 <output name="output_file"> 132 <output name="output_file">
133 <assert_contents> 133 <assert_contents>
134 <has_text_matching expression="\tXX\tDP=19" /> 134 <has_text_matching expression="\tXX\tDP=19" />
136 </assert_contents> 136 </assert_contents>
137 </output> 137 </output>
138 </test> 138 </test>
139 <test> 139 <test>
140 <param name="input_file" ftype="vcf" value="filter.3.vcf" /> 140 <param name="input_file" ftype="vcf" value="filter.3.vcf" />
141 <param name="exclude" value="DP=19" /> 141 <param name="exclude" value="INFO/DP=19" />
142 <param name="soft_filter" value="XX" /> 142 <param name="soft_filter" value="XX" />
143 <param name="mode" value="+" /> 143 <param name="mode" value="+" />
144 <param name="output_type" value="v" /> 144 <param name="output_type" value="v" />
145 <output name="output_file"> 145 <output name="output_file">
146 <assert_contents> 146 <assert_contents>
149 </assert_contents> 149 </assert_contents>
150 </output> 150 </output>
151 </test> 151 </test>
152 <test> 152 <test>
153 <param name="input_file" ftype="vcf" value="filter.3.vcf" /> 153 <param name="input_file" ftype="vcf" value="filter.3.vcf" />
154 <param name="exclude" value="DP=19" /> 154 <param name="exclude" value="INFO/DP=19" />
155 <param name="soft_filter" value="XX" /> 155 <param name="soft_filter" value="XX" />
156 <param name="mode" value="x" /> 156 <param name="mode" value="x" />
157 <param name="output_type" value="v" /> 157 <param name="output_type" value="v" />
158 <output name="output_file"> 158 <output name="output_file">
159 <assert_contents> 159 <assert_contents>
162 </assert_contents> 162 </assert_contents>
163 </output> 163 </output>
164 </test> 164 </test>
165 <test> 165 <test>
166 <param name="input_file" ftype="vcf" value="filter.3.vcf" /> 166 <param name="input_file" ftype="vcf" value="filter.3.vcf" />
167 <param name="exclude" value="DP=19" /> 167 <param name="exclude" value="INFO/DP=19" />
168 <param name="soft_filter" value="XX" /> 168 <param name="soft_filter" value="XX" />
169 <param name="mode" value="+,x" /> 169 <param name="mode" value="+,x" />
170 <param name="output_type" value="v" /> 170 <param name="output_type" value="v" />
171 <output name="output_file"> 171 <output name="output_file">
172 <assert_contents> 172 <assert_contents>