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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 07:49:22 +0000
parents 10da4a86ee5c
children
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19:10da4a86ee5c 20:0ab4bbd0f9b5
2 <description>Haplotype aware consequence predictor</description> 2 <description>Haplotype aware consequence predictor</description>
3 <macros> 3 <macros>
4 <token name="@EXECUTABLE@">csq</token> 4 <token name="@EXECUTABLE@">csq</token>
5 <import>macros.xml</import> 5 <import>macros.xml</import>
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="samtools_requirement"/> 9 <expand macro="samtools_requirement"/>
10 </expand> 10 </expand>
11 <expand macro="version_command" /> 11 <expand macro="version_command"/>
12 <command detect_errors="aggressive"><![CDATA[ 12 <command detect_errors="aggressive"><![CDATA[
13 @PREPARE_ENV@
14 @PREPARE_INPUT_FILE@ 13 @PREPARE_INPUT_FILE@
15 #set $section = $sec_required.reference_source 14 #set $section = $sec_required.reference_source
16 @PREPARE_FASTA_REF@ 15 @PREPARE_FASTA_REF@
17 16
18 #set $section = $sec_restrict 17 #set $section = $sec_restrict
37 #if str($sec_csq_opts.custom_tag): 36 #if str($sec_csq_opts.custom_tag):
38 --custom-tag '$sec_csq_opts.custom_tag' 37 --custom-tag '$sec_csq_opts.custom_tag'
39 #end if 38 #end if
40 #if str($sec_csq_opts.trim_protein_seq) 39 #if str($sec_csq_opts.trim_protein_seq)
41 --trim-protein-seq $sec_csq_opts.trim_protein_seq 40 --trim-protein-seq $sec_csq_opts.trim_protein_seq
41 #end if
42 #if $sec_csq_opts.genetic_code
43 --genetic-code '$sec_csq_opts.genetic_code'
42 #end if 44 #end if
43 45
44 ## Subset section 46 ## Subset section
45 #set $section = $sec_subset 47 #set $section = $sec_subset
46 @SAMPLES@ 48 @SAMPLES@
59 > '$output_file' 61 > '$output_file'
60 62
61 ]]> 63 ]]>
62 </command> 64 </command>
63 <inputs> 65 <inputs>
64 <expand macro="macro_input" /> 66 <expand macro="macro_input"/>
65 <section name="sec_required" expanded="true" title="Required References"> 67 <section name="sec_required" expanded="true" title="Required References">
66 <expand macro="macro_fasta_ref" /> 68 <expand macro="macro_fasta_ref"/>
67 <param name="gff_annot" type="data" format="gff3" label="GFF3 annotation file" 69 <param name="gff_annot" type="data" format="gff3" label="GFF3 annotation file" help="From Ensembl: ftp://ftp.ensembl.org/pub/current_gff3/"/>
68 help="From Ensembl: ftp://ftp.ensembl.org/pub/current_gff3/"/>
69 </section> 70 </section>
70 <section name="sec_csq_opts" expanded="true" title="CSQ Options"> 71 <section name="sec_csq_opts" expanded="true" title="CSQ Options">
71 <param name="ncsq" type="integer" value="16" min="1" max="50" label="maximum number of consequences to consider per site" 72 <param name="ncsq" type="integer" value="16" min="1" max="50" label="maximum number of consequences to consider per site" help="-ncsq 16"/>
72 help="-ncsq 16"/> 73 <param name="local_csq" type="boolean" truevalue="--local-csq" falsevalue="" checked="false" label="run localized predictions considering only one VCF record at a time" help="--local-csq switch off haplotype-aware calling, run localized predictions considering only one VCF record at a time"/>
73 <param name="local_csq" type="boolean" truevalue="--local-csq" falsevalue="" checked="false" label="run localized predictions considering only one VCF record at a time" 74 <param name="phase" type="select" optional="true" label="phase" help="how to construct haplotypes and how to deal with unphased data">
74 help="--local-csq switch off haplotype-aware calling, run localized predictions considering only one VCF record at a time"/> 75 <option value="a">take GTs as is, create haplotypes regardless of phase (0/1 -&gt; 0|1)</option>
75 <param name="phase" type="select" optional="true" label="phase" 76 <option value="m">merge *all* GTs into a single haplotype (0/1 -&gt; 1, 1/2 -&gt; 1)</option>
76 help="how to construct haplotypes and how to deal with unphased data">
77 <option value="a">take GTs as is, create haplotypes regardless of phase (0/1 -> 0|1)</option>
78 <option value="m">merge *all* GTs into a single haplotype (0/1 -> 1, 1/2 -> 1)</option>
79 <option value="r">require phased GTs, throw an error on unphased het GTs</option> 77 <option value="r">require phased GTs, throw an error on unphased het GTs</option>
80 <option value="R">create non-reference haplotypes if possible (0/1 -> 1|1, 1/2 -> 1|2)</option> 78 <option value="R">create non-reference haplotypes if possible (0/1 -&gt; 1|1, 1/2 -&gt; 1|2)</option>
81 <option value="s">skip unphased GTs</option> 79 <option value="s">skip unphased GTs</option>
82 </param> 80 </param>
83 <param name="custom_tag" type="text" value="" optional="true" 81 <param name="custom_tag" type="text" value="" optional="true" label="use this custom tag to store consequences rather than the default BCSQ tag">
84 label="use this custom tag to store consequences rather than the default BCSQ tag"> 82 <validator type="regex" message="">^(\w+)?$</validator>
85 <validator type="regex" message="">^(\w+)?$</validator>
86 </param> 83 </param>
87 <param argument="--trim-protein-seq" type="integer" min="0" value="" optional="true" label="Abbreviate protein-changing predictions" 84 <param argument="--trim-protein-seq" type="integer" min="0" value="" optional="true" label="Abbreviate protein-changing predictions" help="Abbreviate protein-changing predictions to max INT aminoacids"/>
88 help="Abbreviate protein-changing predictions to max INT aminoacids" /> 85 <param argument="--genetic-code" type="select" optional="true" label="Genetic code table" help="Choose a predefined genetic code table used to translate coding sequences. Leave unset for the default bcftools behaviour.">
89 </section> 86 <option value="0">0: Standard simplified</option>
90 87 <option value="1">1: Standard</option>
88 <option value="2">2: Vertebrate mitochondrial</option>
89 <option value="3">3: Yeast mitochondrial</option>
90 <option value="4">4: Mold, Protozoan, Coelenterate mitochondrial; Mycoplasma; Spiroplasma</option>
91 <option value="5">5: Invertebrate mitochondrial</option>
92 <option value="6">6: Ciliate, Dasycladacean and Hexamita nuclear</option>
93 <option value="9">9: Echinoderm and Flatworm mitochondrial</option>
94 <option value="10">10: Euplotid nuclear</option>
95 <option value="11">11: Bacterial, Archaeal and Plant plastid</option>
96 <option value="12">12: Alternative yeast nuclear</option>
97 <option value="13">13: Ascidian mitochondrial</option>
98 <option value="14">14: Alternative flatworm mitochondrial</option>
99 <option value="15">15: Blepharisma nuclear</option>
100 <option value="16">16: Chlorophycean mitochondrial</option>
101 <option value="21">21: Trematode mitochondrial</option>
102 <option value="22">22: Scenedesmus obliquus mitochondrial</option>
103 <option value="23">23: Thraustochytrium mitochondrial</option>
104 <option value="24">24: Pterobranchia mitochondrial</option>
105 <option value="25">25: Candidate Division SR1 and Gracilibacteria</option>
106 <option value="26">26: Pachysolen tannophilus nuclear</option>
107 <option value="27">27: Karyorelict nuclear</option>
108 <option value="28">28: Condylostoma nuclear</option>
109 <option value="29">29: Mesodinium nuclear</option>
110 <option value="30">30: Peritrich nuclear</option>
111 <option value="31">31: Blastocrithidia nuclear</option>
112 <option value="33">33: Cephalodiscidae mitochondrial UAA-Tyr</option>
113 </param>
114 </section>
91 <section name="sec_restrict" expanded="false" title="Restrict to"> 115 <section name="sec_restrict" expanded="false" title="Restrict to">
92 <expand macro="macro_restrict" /> 116 <expand macro="macro_region_restrict"/>
93 <expand macro="macro_restrict" type="target" label_type="Target" /> 117 <expand macro="macro_target_restrict"/>
94 <expand macro="macro_include" /> 118 <expand macro="macro_include"/>
95 <expand macro="macro_exclude" /> 119 <expand macro="macro_exclude"/>
96 </section> 120 </section>
97 <section name="sec_subset" expanded="false" title="Subset Options"> 121 <section name="sec_subset" expanded="false" title="Subset Options">
98 <expand macro="macro_samples" /> 122 <expand macro="macro_samples"/>
99 </section> 123 </section>
100 <expand macro="macro_select_output_type" /> 124 <expand macro="macro_select_output_type"/>
101 </inputs> 125 </inputs>
102 <outputs> 126 <outputs>
103 <expand macro="macro_vcf_output" /> 127 <expand macro="macro_vcf_output"/>
104 </outputs> 128 </outputs>
105 <tests> 129 <tests>
106 <test> 130 <test>
107 <param name="input_file" ftype="vcf" value="csq.vcf" /> 131 <param name="input_file" ftype="vcf" value="csq.vcf"/>
108 <expand macro="test_using_reference" ref="csq.fa" /> 132 <section name="sec_required">
109 <param name="gff_annot" ftype="gff3" value="csq.gff3" /> 133 <expand macro="test_using_reference" ref="csq.fa"/>
110 <param name="output_type" value="v" /> 134 </section>
111 <output name="output_file"> 135 <section name="sec_required">
112 <assert_contents> 136 <param name="gff_annot" ftype="gff3" value="csq.gff3"/>
113 <has_text text="BCSQ" /> 137 </section>
114 </assert_contents> 138 <param name="output_type" value="v"/>
115 </output> 139 <output name="output_file">
116 </test> 140 <assert_contents>
117 <test> 141 <has_text text="BCSQ"/>
118 <param name="input_file" ftype="vcf" value="csq.vcf" /> 142 </assert_contents>
119 <expand macro="test_using_reference" select_from="cached" ref="csq" /> 143 </output>
120 <param name="gff_annot" ftype="gff3" value="csq.gff3" /> 144 </test>
121 <param name="output_type" value="v" /> 145 <test>
122 <output name="output_file"> 146 <param name="input_file" ftype="vcf" value="csq.vcf"/>
123 <assert_contents> 147 <section name="sec_required">
124 <has_text text="BCSQ" /> 148 <expand macro="test_using_reference" select_from="cached" ref="csq"/>
149 </section>
150 <section name="sec_required">
151 <param name="gff_annot" ftype="gff3" value="csq.gff3"/>
152 </section>
153 <param name="output_type" value="v"/>
154 <output name="output_file">
155 <assert_contents>
156 <has_text text="BCSQ"/>
125 </assert_contents> 157 </assert_contents>
126 </output> 158 </output>
127 </test> 159 </test>
128 <!-- Test protein seq prediction--> 160 <!-- Test protein seq prediction-->
129 <test> 161 <test>
130 <param name="input_file" ftype="vcf" value="csq.vcf" /> 162 <param name="input_file" ftype="vcf" value="csq.vcf"/>
131 <expand macro="test_using_reference" select_from="cached" ref="csq" /> 163 <section name="sec_required">
132 <param name="gff_annot" ftype="gff3" value="csq.gff3" /> 164 <expand macro="test_using_reference" select_from="cached" ref="csq"/>
133 <param name="output_type" value="v" /> 165 </section>
166 <section name="sec_required">
167 <param name="gff_annot" ftype="gff3" value="csq.gff3"/>
168 </section>
169 <param name="output_type" value="v"/>
134 <section name="sec_csq_opts"> 170 <section name="sec_csq_opts">
135 <param name="trim_protein_seq" value="10"/> 171 <param name="trim_protein_seq" value="10"/>
136 </section> 172 <param name="genetic_code" value="1"/>
137 <output name="output_file"> 173 </section>
138 <assert_contents> 174 <output name="output_file">
139 <has_text text="BCSQ" /> 175 <assert_contents>
176 <has_text text="BCSQ"/>
140 </assert_contents> 177 </assert_contents>
141 </output> 178 </output>
142 <assert_command> 179 <assert_command>
143 <has_text text="--trim-protein-seq" /> 180 <has_text text="--trim-protein-seq"/>
181 <has_text text="--genetic-code '1'"/>
144 </assert_command> 182 </assert_command>
145 </test> 183 </test>
146 <!-- Test region overlap--> 184 <!-- Test region overlap-->
147 <test> 185 <test>
148 <param name="input_file" ftype="vcf" value="csq.vcf" /> 186 <param name="input_file" ftype="vcf" value="csq.vcf"/>
149 <expand macro="test_using_reference" select_from="cached" ref="csq" /> 187 <section name="sec_required">
150 <param name="gff_annot" ftype="gff3" value="csq.gff3" /> 188 <expand macro="test_using_reference" select_from="cached" ref="csq"/>
151 <param name="output_type" value="v" /> 189 </section>
190 <section name="sec_required">
191 <param name="gff_annot" ftype="gff3" value="csq.gff3"/>
192 </section>
193 <param name="output_type" value="v"/>
152 <section name="sec_restrict"> 194 <section name="sec_restrict">
153 <param name="regions_overlap" value="1"/> 195 <conditional name="regions">
154 </section> 196 <param name="regions_src" value="regions" />
155 <output name="output_file"> 197 <repeat name="region_specs">
156 <assert_contents> 198 <param name="chrom" value="1" />
157 <has_text text="BCSQ" /> 199 </repeat>
200 </conditional>
201 </section>
202 <output name="output_file">
203 <assert_contents>
204 <has_text text="BCSQ"/>
158 </assert_contents> 205 </assert_contents>
159 </output> 206 </output>
160 <assert_command> 207 <assert_command>
161 <has_text text="--regions-overlap" /> 208 <has_text text="--regions-overlap"/>
162 </assert_command> 209 </assert_command>
163 </test> 210 </test>
164 </tests> 211 </tests>
165 <help><![CDATA[ 212 <help><![CDATA[
166 ===================================== 213 =====================================
195 @REGIONS_HELP@ 242 @REGIONS_HELP@
196 @TARGETS_HELP@ 243 @TARGETS_HELP@
197 244
198 @BCFTOOLS_MANPAGE@#@EXECUTABLE@ 245 @BCFTOOLS_MANPAGE@#@EXECUTABLE@
199 246
200 @BCFTOOLS_WIKI@ 247 @BCFTOOLS_HOWTOS@
201 ]]> 248 ]]>
202 </help> 249 </help>
203 <expand macro="citations" /> 250 <expand macro="citations"/>
204 </tool> 251 </tool>