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comparison bcftools_filter.xml @ 16:e7452697afd9 draft

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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
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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=&quot;0/2&quot;" />
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=&quot;0/0&quot; &amp;&amp; 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=&quot;0/0&quot; &amp;&amp; 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=&quot;0/2&quot;" />
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=&quot;0/0&quot; &amp;&amp; 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@