Mercurial > repos > iuc > bcftools_filter
comparison bcftools_filter.xml @ 16:e7452697afd9 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit db275932cbb485cb44ae91e0b421d6f57698db49
author | iuc |
---|---|
date | Tue, 20 Sep 2022 13:17:14 +0000 |
parents | e4988fd4d503 |
children | 46fcafba49ec |
comparison
equal
deleted
inserted
replaced
15:33bd9301568c | 16:e7452697afd9 |
---|---|
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="@TOOL_VERSION@"> | 2 <tool name="bcftools @EXECUTABLE@" id="bcftools_@EXECUTABLE@" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@"> |
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> |
27 #end if | 27 #end if |
28 #if $section.mode: | 28 #if $section.mode: |
29 #set $mode = str($section.mode).replace(',','') | 29 #set $mode = str($section.mode).replace(',','') |
30 --mode '$mode' | 30 --mode '$mode' |
31 #end if | 31 #end if |
32 #if $section.soft_filter: | 32 #if $section.conditional_soft_filter.selector == 'enabled': |
33 --soft-filter "${section.soft_filter}" | 33 --soft-filter '${section.conditional_soft_filter.soft_filter}' |
34 @MASK@ | |
34 #end if | 35 #end if |
35 #if $section.select_set_GTs: | 36 #if $section.select_set_GTs: |
36 --set-GTs "${section.select_set_GTs}" | 37 --set-GTs "${section.select_set_GTs}" |
37 #end if | 38 #end if |
38 | 39 |
68 and setting to "PASS" when the FILTER string is absent. | 69 and setting to "PASS" when the FILTER string is absent. |
69 </help> | 70 </help> |
70 <option value="+">(+) append new FILTER strings of failed sites instead of replacing them</option> | 71 <option value="+">(+) append new FILTER strings of failed sites instead of replacing them</option> |
71 <option value="x">(x) resets filters of sites which pass to "PASS"</option> | 72 <option value="x">(x) resets filters of sites which pass to "PASS"</option> |
72 </param> | 73 </param> |
73 <param name="soft_filter" type="text" value="" label="Soft Filter" optional="true"> | 74 <conditional name="conditional_soft_filter"> |
74 <help><![CDATA[ (-s) | 75 <param name="selector" type="select" label="Perform soft filtering"> |
75 Annotate FILTER column with STRING or, with +, a unique filter name generated by the program ("Filter%d"). | 76 <option value="disabled">Disabled</option> |
76 ]]></help> | 77 <option value="enabled">Enabled</option> |
77 </param> | 78 </param> |
79 <when value="disabled"/> | |
80 <when value="enabled"> | |
81 <param argument="--soft-filter" type="text" value="" label="Soft Filter" optional="true"> | |
82 <help><![CDATA[ (-s) | |
83 Annotate FILTER column with STRING or, with +, a unique filter name generated by the program ("Filter%d"). | |
84 ]]></help> | |
85 </param> | |
86 <expand macro="macro_restrict" type="mask" label_type="Mask"/> | |
87 </when> | |
88 </conditional> | |
89 | |
78 <param name="select_set_GTs" type="select" label="Set genotypes of failed samples" optional="true" help="(-S)"> | 90 <param name="select_set_GTs" type="select" label="Set genotypes of failed samples" optional="true" help="(-S)"> |
79 <option value=".">to missing (.)</option> | 91 <option value=".">to missing (.)</option> |
80 <option value="0">to REF (0)</option> | 92 <option value="0">to REF (0)</option> |
81 </param> | 93 </param> |
82 </section> | 94 </section> |
105 <param name="soft_filter" value="Modified" /> | 117 <param name="soft_filter" value="Modified" /> |
106 <param name="select_set_GTs" value="." /> | 118 <param name="select_set_GTs" value="." /> |
107 <param name="output_type" value="v" /> | 119 <param name="output_type" value="v" /> |
108 <output name="output_file"> | 120 <output name="output_file"> |
109 <assert_contents> | 121 <assert_contents> |
110 <has_text text="Modified" /> | 122 <has_text text="genotypes" /> |
111 <has_text text="AN=2;AC=1" /> | 123 <has_text text="AN=2;AC=1" /> |
112 <has_text_matching expression="TAAAA\tTA,T\t61.5\tModified" /> | 124 <has_text_matching expression="TAAAA\tTA,T\t61.5\tPASS" /> |
113 </assert_contents> | 125 </assert_contents> |
114 </output> | 126 </output> |
115 </test> | 127 </test> |
116 <test> | 128 <test> |
117 <param name="input_file" ftype="vcf" value="filter.3.vcf" /> | 129 <param name="input_file" ftype="vcf" value="filter.3.vcf" /> |
126 </test> | 138 </test> |
127 | 139 |
128 <test> | 140 <test> |
129 <param name="input_file" ftype="vcf" value="filter.3.vcf" /> | 141 <param name="input_file" ftype="vcf" value="filter.3.vcf" /> |
130 <param name="exclude" value="INFO/DP=19" /> | 142 <param name="exclude" value="INFO/DP=19" /> |
131 <param name="soft_filter" value="XX" /> | 143 <section name="sec_filter"> |
144 <conditional name="conditional_soft_filter"> | |
145 <param name="selector" value="enabled"/> | |
146 <param name="soft_filter" value="XX" /> | |
147 </conditional> | |
148 </section> | |
132 <param name="output_type" value="v" /> | 149 <param name="output_type" value="v" /> |
133 <output name="output_file"> | 150 <output name="output_file"> |
134 <assert_contents> | 151 <assert_contents> |
135 <has_text_matching expression="\tXX\tDP=19" /> | 152 <has_text_matching expression="\tXX\tDP=19" /> |
136 <has_text_matching expression="\tq20\tAO" /> | 153 <has_text_matching expression="\tq20\tAO" /> |
138 </output> | 155 </output> |
139 </test> | 156 </test> |
140 <test> | 157 <test> |
141 <param name="input_file" ftype="vcf" value="filter.3.vcf" /> | 158 <param name="input_file" ftype="vcf" value="filter.3.vcf" /> |
142 <param name="exclude" value="INFO/DP=19" /> | 159 <param name="exclude" value="INFO/DP=19" /> |
143 <param name="soft_filter" value="XX" /> | 160 <section name="sec_filter"> |
144 <param name="mode" value="+" /> | 161 <conditional name="conditional_soft_filter"> |
145 <param name="output_type" value="v" /> | 162 <param name="selector" value="enabled"/> |
146 <output name="output_file"> | 163 <param name="soft_filter" value="XX" /> |
147 <assert_contents> | 164 <param name="mode" value="+" /> |
148 <has_text_matching expression="\tq20;XX\tDP=19" /> | 165 </conditional> |
166 </section> | |
167 <param name="output_type" value="v" /> | |
168 <output name="output_file"> | |
169 <assert_contents> | |
170 <has_text_matching expression="238\tXX\tDP=19" /> | |
149 <has_text_matching expression="\tq20\tAO" /> | 171 <has_text_matching expression="\tq20\tAO" /> |
150 </assert_contents> | 172 </assert_contents> |
151 </output> | 173 </output> |
152 </test> | 174 </test> |
153 <test> | 175 <test> |
154 <param name="input_file" ftype="vcf" value="filter.3.vcf" /> | 176 <param name="input_file" ftype="vcf" value="filter.3.vcf" /> |
155 <param name="exclude" value="INFO/DP=19" /> | 177 <param name="exclude" value="INFO/DP=19" /> |
156 <param name="soft_filter" value="XX" /> | 178 <section name="sec_filter"> |
157 <param name="mode" value="x" /> | 179 <conditional name="conditional_soft_filter"> |
180 <param name="selector" value="enabled"/> | |
181 <param name="soft_filter" value="XX" /> | |
182 <param name="mode" value="+" /> | |
183 </conditional> | |
184 </section> | |
158 <param name="output_type" value="v" /> | 185 <param name="output_type" value="v" /> |
159 <output name="output_file"> | 186 <output name="output_file"> |
160 <assert_contents> | 187 <assert_contents> |
161 <has_text_matching expression="\tXX\tDP=19" /> | 188 <has_text_matching expression="\tXX\tDP=19" /> |
162 <has_text_matching expression="\tPASS\tAO" /> | 189 <has_text_matching expression="\tq20\tAO=52101" /> |
163 </assert_contents> | 190 </assert_contents> |
164 </output> | 191 </output> |
165 </test> | 192 </test> |
166 <test> | 193 <test> |
167 <param name="input_file" ftype="vcf" value="filter.3.vcf" /> | 194 <param name="input_file" ftype="vcf" value="filter.3.vcf" /> |
168 <param name="exclude" value="INFO/DP=19" /> | 195 <param name="exclude" value="INFO/DP=19" /> |
169 <param name="soft_filter" value="XX" /> | 196 <section name="sec_filter"> |
170 <param name="mode" value="+,x" /> | 197 <conditional name="conditional_soft_filter"> |
198 <param name="selector" value="enabled"/> | |
199 <param name="soft_filter" value="XX" /> | |
200 <param name="mode" value="+" /> | |
201 </conditional> | |
202 </section> | |
203 <param name="output_type" value="v" /> | |
204 <output name="output_file"> | |
205 <assert_contents> | |
206 <has_text_matching expression="\t238\tXX\tDP=19" /> | |
207 <has_text_matching expression="\t238\tq20\tAO" /> | |
208 </assert_contents> | |
209 </output> | |
210 </test> | |
211 <test> | |
212 <param name="input_file" ftype="vcf" value="filter.3.vcf" /> | |
213 <param name="exclude" value="FMT/GT="0/2"" /> | |
214 <param name="output_type" value="v" /> | |
215 <output name="output_file"> | |
216 <assert_contents> | |
217 <not_has_text text="3162006" /> | |
218 <has_text text="3162007" /> | |
219 </assert_contents> | |
220 </output> | |
221 </test> | |
222 <test> | |
223 <param name="input_file" ftype="vcf" value="filter.2.vcf" /> | |
224 <param name="include" value="FMT/GT="0/0" && AC[*]=2" /> | |
225 <param name="output_type" value="v" /> | |
226 <output name="output_file"> | |
227 <assert_contents> | |
228 <has_text text="AN=4;AC=2" /> | |
229 <not_has_text text="AN=4;AC=0" /> | |
230 </assert_contents> | |
231 </output> | |
232 </test> | |
233 <!-- Test region overlap --> | |
234 <test> | |
235 <param name="input_file" ftype="vcf" value="filter.2.vcf" /> | |
236 <param name="include" value="FMT/GT="0/0" && AC[*]=2" /> | |
237 <param name="output_type" value="v" /> | |
238 <section name="sec_restrict"> | |
239 <param name="regions_overlap" value="1"/> | |
240 </section> | |
241 <output name="output_file"> | |
242 <assert_contents> | |
243 <has_text text="AN=4;AC=2" /> | |
244 <not_has_text text="AN=4;AC=0" /> | |
245 </assert_contents> | |
246 </output> | |
247 <assert_command> | |
248 <has_text text="--regions-overlap" /> | |
249 </assert_command> | |
250 </test> | |
251 <!-- Test mask options--> | |
252 <test> | |
253 <param name="input_file" ftype="vcf" value="filter.3.vcf" /> | |
254 <param name="exclude" value="INFO/DP=19" /> | |
255 <section name="sec_filter"> | |
256 <param name="mode" value="+,x" /> | |
257 <conditional name="conditional_soft_filter"> | |
258 <param name="selector" value="enabled"/> | |
259 <param name="soft_filter" value="XX" /> | |
260 <param name="masks_overlap" value="1"/> | |
261 </conditional> | |
262 </section> | |
263 | |
171 <param name="output_type" value="v" /> | 264 <param name="output_type" value="v" /> |
172 <output name="output_file"> | 265 <output name="output_file"> |
173 <assert_contents> | 266 <assert_contents> |
174 <has_text_matching expression="\tq20;XX\tDP=19" /> | 267 <has_text_matching expression="\tq20;XX\tDP=19" /> |
175 <has_text_matching expression="\tPASS\tAO" /> | 268 <has_text_matching expression="\tPASS\tAO" /> |
176 </assert_contents> | 269 </assert_contents> |
177 </output> | 270 </output> |
178 </test> | 271 <assert_command> |
179 <test> | 272 <has_text text="--mask-overlap" /> |
180 <param name="input_file" ftype="vcf" value="filter.3.vcf" /> | 273 </assert_command> |
181 <param name="exclude" value="FMT/GT="0/2"" /> | |
182 <param name="output_type" value="v" /> | |
183 <output name="output_file"> | |
184 <assert_contents> | |
185 <not_has_text text="3162006" /> | |
186 <has_text text="3162007" /> | |
187 </assert_contents> | |
188 </output> | |
189 </test> | |
190 <test> | |
191 <param name="input_file" ftype="vcf" value="filter.2.vcf" /> | |
192 <param name="include" value="FMT/GT="0/0" && AC[*]=2" /> | |
193 <param name="output_type" value="v" /> | |
194 <output name="output_file"> | |
195 <assert_contents> | |
196 <has_text text="AN=4;AC=2" /> | |
197 <not_has_text text="AN=4;AC=0" /> | |
198 </assert_contents> | |
199 </output> | |
200 </test> | 274 </test> |
201 </tests> | 275 </tests> |
202 <help><![CDATA[ | 276 <help><![CDATA[ |
203 ===================================== | 277 ===================================== |
204 bcftools @EXECUTABLE@ | 278 bcftools @EXECUTABLE@ |