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comparison bcftools_roh.xml @ 25:a85677f5a2ab draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
author iuc
date Tue, 02 Dec 2025 07:53:42 +0000
parents 39cac1b56d93
children
comparison
equal deleted inserted replaced
24:39cac1b56d93 25:a85677f5a2ab
6 </macros> 6 </macros>
7 <expand macro="bio_tools" /> 7 <expand macro="bio_tools" />
8 <expand macro="requirements" /> 8 <expand macro="requirements" />
9 <expand macro="version_command" /> 9 <expand macro="version_command" />
10 <command detect_errors="aggressive"><![CDATA[ 10 <command detect_errors="aggressive"><![CDATA[
11 @PREPARE_ENV@
12 @PREPARE_INPUT_FILE@ 11 @PREPARE_INPUT_FILE@
13 #set $section = $sec_restrict 12 #set $section = $sec_restrict
14 @PREPARE_TARGETS_FILE@ 13 @PREPARE_TARGETS_FILE@
15 @PREPARE_REGIONS_FILE@ 14 @PREPARE_REGIONS_FILE@
16 ## General section 15 ## General section
76 ]]> 75 ]]>
77 </command> 76 </command>
78 <inputs> 77 <inputs>
79 <expand macro="macro_input" /> 78 <expand macro="macro_input" />
80 <section name="sec_restrict" expanded="false" title="Restrict to"> 79 <section name="sec_restrict" expanded="false" title="Restrict to">
81 <expand macro="macro_restrict" /> 80 <expand macro="macro_region_restrict" />
82 <expand macro="macro_restrict" type="target" label_type="Target" /> 81 <expand macro="macro_target_restrict" />
83 <expand macro="macro_samples" /> 82 <expand macro="macro_samples" />
84 </section> 83 </section>
85 <section name="sec_general" expanded="true" title="Roh General Options"> 84 <section name="sec_general" expanded="true" title="Roh General Options">
86 <expand macro="macro_sample" /> 85 <expand macro="macro_sample" />
87 <param name="AF_tag" type="text" value="" label="AF TAG" optional="True" 86 <param name="AF_tag" type="text" value="" label="AF TAG" optional="True"
122 <data name="output_file" format="tabular"/> 121 <data name="output_file" format="tabular"/>
123 </outputs> 122 </outputs>
124 <tests> 123 <tests>
125 <test> 124 <test>
126 <param name="input_file" ftype="vcf" value="roh.vcf" /> 125 <param name="input_file" ftype="vcf" value="roh.vcf" />
127 <param name="AF_dflt" value="0.4" /> 126 <section name="sec_general">
128 <param name="GTs_only" value="30" /> 127 <param name="AF_dflt" value="0.4" />
128 <param name="GTs_only" value="30" />
129 </section>
129 <output name="output_file"> 130 <output name="output_file">
130 <assert_contents> 131 <assert_contents>
131 <has_text_matching expression="ST\tsample\t1"/> 132 <has_text_matching expression="ST\tsample\t1"/>
132 <has_text_matching expression="RG\tsample\t1"/> 133 <has_text_matching expression="RG\tsample\t1"/>
133 </assert_contents> 134 </assert_contents>
134 </output> 135 </output>
135 </test> 136 </test>
136 <test> 137 <test>
137 <param name="input_file" ftype="vcf" value="roh.vcf" /> 138 <param name="input_file" ftype="vcf" value="roh.vcf" />
138 <param name="AF_dflt" value="0.4" /> 139 <section name="sec_general">
139 <param name="GTs_only" value="30" /> 140 <param name="AF_dflt" value="0.4" />
141 <param name="GTs_only" value="30" />
142 </section>
140 <param name="output_type" value="r" /> 143 <param name="output_type" value="r" />
141 <output name="output_file"> 144 <output name="output_file">
142 <assert_contents> 145 <assert_contents>
143 <not_has_text text="ST"/> 146 <not_has_text text="ST"/>
144 <has_text_matching expression="RG\tsample\t1"/> 147 <has_text_matching expression="RG\tsample\t1"/>
146 </output> 149 </output>
147 </test> 150 </test>
148 <!-- Test ignore homref and include noalt--> 151 <!-- Test ignore homref and include noalt-->
149 <test> 152 <test>
150 <param name="input_file" ftype="vcf" value="roh.vcf" /> 153 <param name="input_file" ftype="vcf" value="roh.vcf" />
151 <param name="AF_dflt" value="0.4" /> 154 <section name="sec_general">
152 <param name="GTs_only" value="30" /> 155 <param name="AF_dflt" value="0.4" />
156 <param name="GTs_only" value="30" />
157 <param name="ignore_homref" value="true"/>
158 <param name="include_noalt" value="true"/>
159 </section>
153 <param name="output_type" value="r" /> 160 <param name="output_type" value="r" />
154 <param name="ignore_homref" value="true"/>
155 <param name="include_noalt" value="true"/>
156 <output name="output_file"> 161 <output name="output_file">
157 <assert_contents> 162 <assert_contents>
158 <not_has_text text="ST"/> 163 <not_has_text text="ST"/>
159 <has_text_matching expression="RG\tsample\t1"/> 164 <has_text_matching expression="RG\tsample\t1"/>
160 </assert_contents> 165 </assert_contents>
170 <section name="sec_general"> 175 <section name="sec_general">
171 <param name="AF_dflt" value="0.4" /> 176 <param name="AF_dflt" value="0.4" />
172 <param name="GTs_only" value="30" /> 177 <param name="GTs_only" value="30" />
173 </section> 178 </section>
174 <section name="sec_restrict"> 179 <section name="sec_restrict">
175 <param name="regions_overlap" value="1"/> 180 <conditional name="regions">
181 <param name="regions_src" value="regions" />
182 <repeat name="region_specs">
183 <param name="chrom" value="1" />
184 </repeat>
185 </conditional>
176 </section> 186 </section>
177 <output name="output_file"> 187 <output name="output_file">
178 <assert_contents> 188 <assert_contents>
179 <has_text_matching expression="ST\tsample\t1"/> 189 <has_text_matching expression="ST\tsample\t1"/>
180 <has_text_matching expression="RG\tsample\t1"/> 190 <has_text_matching expression="RG\tsample\t1"/>
195 @REGIONS_HELP@ 205 @REGIONS_HELP@
196 @TARGETS_HELP@ 206 @TARGETS_HELP@
197 207
198 @BCFTOOLS_MANPAGE@#@EXECUTABLE@ 208 @BCFTOOLS_MANPAGE@#@EXECUTABLE@
199 209
200 @BCFTOOLS_WIKI@ 210 @BCFTOOLS_HOWTOS@
201 ]]> 211 ]]>
202 </help> 212 </help>
203 <expand macro="citations" /> 213 <expand macro="citations" />
204 </tool> 214 </tool>