Mercurial > repos > iuc > bcftools_concat

comparison bcftools_concat.xml @ 26:11c2dc7762b8 draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
author iuc
date Tue, 02 Dec 2025 07:50:00 +0000
parents c16fe9d71fe1
children
comparison
equal deleted inserted replaced
25:1234ce354b19 26:11c2dc7762b8
1 <?xml version='1.0' encoding='utf-8'?>
2 <tool name="bcftools @EXECUTABLE@" id="bcftools_@EXECUTABLE@" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@"> 1 <tool name="bcftools @EXECUTABLE@" id="bcftools_@EXECUTABLE@" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
3 <description>Concatenate or combine VCF/BCF files</description> 2 <description>Concatenate or combine VCF/BCF files</description>
4 <macros> 3 <macros>
5 <token name="@EXECUTABLE@">concat</token> 4 <token name="@EXECUTABLE@">concat</token>
6 <import>macros.xml</import> 5 <import>macros.xml</import>
7 </macros> 6 </macros>
8 <expand macro="bio_tools" /> 7 <expand macro="bio_tools"/>
9 <expand macro="requirements" /> 8 <expand macro="requirements"/>
10 <expand macro="version_command" /> 9 <expand macro="version_command"/>
11 <command detect_errors="aggressive"><![CDATA[ 10 <command detect_errors="aggressive"><![CDATA[
12 @PREPARE_ENV@
13 @PREPARE_INPUT_FILES@ 11 @PREPARE_INPUT_FILES@
14 #set $section = $sec_restrict 12 #set $section = $sec_restrict
15 @PREPARE_REGIONS_FILE@ 13 @PREPARE_REGIONS_FILE@
16 14
17 bcftools @EXECUTABLE@ 15 bcftools @EXECUTABLE@
51 #else: 49 #else:
52 > '$output_file' 50 > '$output_file'
53 #end if 51 #end if
54 ]]></command> 52 ]]></command>
55 <inputs> 53 <inputs>
56 <expand macro="macro_inputs" /> 54 <expand macro="macro_inputs"/>
57 <section name="sec_restrict" expanded="false" title="Restrict to"> 55 <section name="sec_restrict" expanded="false" title="Restrict to">
58 <expand macro="macro_restrict" /> 56 <expand macro="macro_region_restrict"/>
59 </section> 57 </section>
60 <section name="sec_default" expanded="true" title="Concat Options"> 58 <section name="sec_default" expanded="true" title="Concat Options">
61 <conditional name="mode"> 59 <conditional name="mode">
62 <param argument="--naive" type="select" label="Naive concat"> 60 <param argument="--naive" type="select" label="Naive concat">
63 <help><![CDATA[ 61 <help><![CDATA[
89 <option value="none">none - output multiple records instead</option> 87 <option value="none">none - output multiple records instead</option>
90 </param> 88 </param>
91 </when> 89 </when>
92 <when value="no"/> 90 <when value="no"/>
93 </conditional> 91 </conditional>
94 <param name="ligate" type="boolean" truevalue="--ligate" falsevalue="" label="Ligate" 92 <param name="ligate" type="boolean" truevalue="--ligate" falsevalue="" label="Ligate" help="Ligate phased VCFs by matching phase at overlapping haplotypes"/>
95 help="Ligate phased VCFs by matching phase at overlapping haplotypes" />
96 <param name="ligate_mode" type="select" optional="true" label="Ligate mode" help="It allows finer control of --ligate behavior"> 93 <param name="ligate_mode" type="select" optional="true" label="Ligate mode" help="It allows finer control of --ligate behavior">
97 <option value="--ligate-warn">Ligate warn: Drop sites that are present in one chunk but absent in the other (--ligate-warn)</option> 94 <option value="--ligate-warn">Ligate warn: Drop sites that are present in one chunk but absent in the other (--ligate-warn)</option>
98 <option value="--ligate-force">Ligate force: Kepp sites that are present only in one chunk (--ligate-force)</option> 95 <option value="--ligate-force">Ligate force: Kepp sites that are present only in one chunk (--ligate-force)</option>
99 </param> 96 </param>
100 </when> 97 </when>
101 </conditional> 98 </conditional>
102 <param name="compact_PS" type="boolean" truevalue="--compact-PS" falsevalue="" label="Compact Ps" 99 <param name="compact_PS" type="boolean" truevalue="--compact-PS" falsevalue="" label="Compact Ps" help="Do not output PS tag at each site, only at the start of a new phase set block."/>
103 help="Do not output PS tag at each site, only at the start of a new phase set block." /> 100 <param name="min_PQ" type="integer" label="Min Pq" value="30" optional="true" help="Break phase set if phasing quality is lower than &lt;int&gt;"/>
104 <param name="min_PQ" type="integer" label="Min Pq" value="30" optional="true"
105 help="Break phase set if phasing quality is lower than &lt;int&gt;" />
106 </section> 101 </section>
107 <expand macro="macro_select_output_type" /> 102 <expand macro="macro_select_output_type"/>
108 </inputs> 103 </inputs>
109 <outputs> 104 <outputs>
110 <expand macro="macro_vcf_output"/> 105 <expand macro="macro_vcf_output"/>
111 </outputs> 106 </outputs>
112 <tests> 107 <tests>
113 <test> 108 <test>
114 <param name="input_files" ftype="vcf" value="concat.1.b.vcf,concat.1.a.vcf" /> 109 <param name="input_files" ftype="vcf" value="concat.1.b.vcf,concat.1.a.vcf"/>
115 <param name="output_type" value="v" /> 110 <param name="output_type" value="v"/>
116 <output name="output_file"> 111 <output name="output_file">
117 <assert_contents> 112 <assert_contents>
118 <has_text_matching expression="1\t100"/> 113 <has_text_matching expression="1\t100"/>
119 <has_text_matching expression="3\t192"/> 114 <has_text_matching expression="3\t192"/>
120 </assert_contents> 115 </assert_contents>
121 </output> 116 </output>
122 </test> 117 </test>
123 <test> 118 <test>
124 <param name="input_files" ftype="vcf" value="concat.1.b.vcf,concat.1.a.vcf" /> 119 <param name="input_files" ftype="vcf" value="concat.1.b.vcf,concat.1.a.vcf"/>
125 <param name="naive" value="no" /> 120 <section name="sec_default">
126 <param name="output_type" value="v" /> 121 <conditional name="mode">
127 <output name="output_file"> 122 <param name="naive" value="no"/>
128 <assert_contents> 123 </conditional>
129 <has_text_matching expression="1\t100"/> 124 </section>
130 <has_text_matching expression="3\t192"/> 125 <param name="output_type" value="v"/>
131 </assert_contents> 126 <output name="output_file">
132 </output> 127 <assert_contents>
133 </test> 128 <has_text_matching expression="1\t100"/>
134 <test> 129 <has_text_matching expression="3\t192"/>
135 <param name="input_files" ftype="vcf" value="concat.2.b.vcf,concat.2.a.vcf" /> 130 </assert_contents>
136 <param name="allow_overlaps" value="yes" /> 131 </output>
137 <param name="output_type" value="v" /> 132 </test>
133 <test>
134 <param name="input_files" ftype="vcf" value="concat.2.b.vcf,concat.2.a.vcf"/>
135 <section name="sec_default">
136 <conditional name="mode">
137 <param name="naive" value="no"/>
138 <conditional name="overlaps">
139 <param name="allow_overlaps" value="yes"/>
140 </conditional>
141 </conditional>
142 </section>
143 <param name="output_type" value="v"/>
138 <output name="output_file"> 144 <output name="output_file">
139 <assert_contents> 145 <assert_contents>
140 <has_text_matching expression="2\t140\t.\tA\tG"/> 146 <has_text_matching expression="2\t140\t.\tA\tG"/>
141 <has_text_matching expression="2\t140\t.\tGT\tG"/> 147 <has_text_matching expression="2\t140\t.\tGT\tG"/>
142 </assert_contents> 148 </assert_contents>
143 </output> 149 </output>
144 </test> 150 </test>
145 <test> 151 <test>
146 <param name="input_files" ftype="vcf" value="concat.2.b.vcf,concat.2.a.vcf" /> 152 <param name="input_files" ftype="vcf" value="concat.2.b.vcf,concat.2.a.vcf"/>
147 <param name="allow_overlaps" value="yes" /> 153 <section name="sec_default">
148 <param name="rm_dups" value="none" /> 154 <conditional name="mode">
149 <param name="output_type" value="v" /> 155 <param name="naive" value="no"/>
156 <conditional name="overlaps">
157 <param name="allow_overlaps" value="yes"/>
158 <param name="rm_dups" value="none"/>
159 </conditional>
160 </conditional>
161 </section>
162 <param name="output_type" value="v"/>
150 <output name="output_file"> 163 <output name="output_file">
151 <assert_contents> 164 <assert_contents>
152 <has_text_matching expression="2\t160\t.\tTAAAA"/> 165 <has_text_matching expression="2\t160\t.\tTAAAA"/>
153 </assert_contents> 166 </assert_contents>
154 </output> 167 </output>
155 </test> 168 </test>
156 <!-- Test region overlap--> 169 <!-- Test region overlap-->
157 <test> 170 <test>
158 <param name="input_files" ftype="vcf" value="concat.1.b.vcf,concat.1.a.vcf" /> 171 <param name="input_files" ftype="vcf" value="concat.1.b.vcf,concat.1.a.vcf"/>
159 <param name="output_type" value="v" /> 172 <param name="output_type" value="v"/>
160 <section name="sec_restrict"> 173 <section name="sec_restrict">
161 <param name="regions_overlap" value="1"/> 174 <conditional name="regions">
175 <param name="regions_src" value="regions" />
176 <repeat name="region_specs">
177 <param name="chrom" value="1" />
178 </repeat>
179 <repeat name="region_specs">
180 <param name="chrom" value="3" />
181 </repeat>
182 </conditional>
162 </section> 183 </section>
163 <output name="output_file"> 184 <output name="output_file">
164 <assert_contents> 185 <assert_contents>
165 <has_text_matching expression="1\t100"/> 186 <has_text_matching expression="1\t100"/>
166 <has_text_matching expression="3\t192"/> 187 <has_text_matching expression="3\t192"/>
167 </assert_contents> 188 </assert_contents>
168 </output> 189 </output>
169 <assert_command> 190 <assert_command>
170 <has_text text="--regions-overlap" /> 191 <has_text text="--regions-overlap"/>
171 </assert_command> 192 </assert_command>
172 </test> 193 </test>
173 <!-- Test ligate options --> 194 <!-- Test ligate options -->
174 <test> 195 <test>
175 <param name="input_files" ftype="vcf" value="concat.1.b.vcf,concat.1.a.vcf" /> 196 <param name="input_files" ftype="vcf" value="concat.1.b.vcf,concat.1.a.vcf"/>
176 <param name="output_type" value="v" /> 197 <param name="output_type" value="v"/>
177 <section name="sec_default"> 198 <section name="sec_default">
178 <conditional name="mode"> 199 <conditional name="mode">
179 <conditional name="overlaps"> 200 <conditional name="overlaps">
180 <param name="allow_overlaps" value="no"/> 201 <param name="allow_overlaps" value="no"/>
181 </conditional> 202 </conditional>
188 <has_text_matching expression="1\t100"/> 209 <has_text_matching expression="1\t100"/>
189 <has_text_matching expression="3\t192"/> 210 <has_text_matching expression="3\t192"/>
190 </assert_contents> 211 </assert_contents>
191 </output> 212 </output>
192 <assert_command> 213 <assert_command>
193 <has_text text="--ligate-warn" /> 214 <has_text text="--ligate-warn"/>
194 </assert_command> 215 </assert_command>
195 </test> 216 </test>
196 </tests> 217 </tests>
197 <help><![CDATA[ 218 <help><![CDATA[
198 ===================================== 219 =====================================
209 230
210 @REGIONS_HELP@ 231 @REGIONS_HELP@
211 232
212 @BCFTOOLS_MANPAGE@#@EXECUTABLE@ 233 @BCFTOOLS_MANPAGE@#@EXECUTABLE@
213 234
214 @BCFTOOLS_WIKI@ 235 @BCFTOOLS_HOWTOS@
215 ]]></help> 236 ]]></help>
216 <expand macro="citations" /> 237 <expand macro="citations"/>
217 </tool> 238 </tool>