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comparison bcftools_merge.xml @ 16:2215287d5cc9 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 13:10:15 +0000
parents 798c063f8fc9
children
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15:86296490704e 16:2215287d5cc9
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>Merge multiple VCF/BCF files from non-overlapping sample sets to create one multi-sample file</description> 3 <description>Merge multiple VCF/BCF files from non-overlapping sample sets to create one multi-sample file</description>
4 <macros> 4 <macros>
5 <token name="@EXECUTABLE@">merge</token> 5 <token name="@EXECUTABLE@">merge</token>
6 <import>macros.xml</import> 6 <import>macros.xml</import>
7 </macros> 7 </macros>
31 --info-rules "${section.info_rules}" 31 --info-rules "${section.info_rules}"
32 #end if 32 #end if
33 33
34 #if $section.merge: 34 #if $section.merge:
35 --merge "${section.merge}" 35 --merge "${section.merge}"
36 $section.no_index
36 #end if 37 #end if
37 38
38 #set $section = $sec_restrict 39 #set $section = $sec_restrict
39 @APPLY_FILTERS@ 40 @APPLY_FILTERS@
40 @REGIONS@ 41 @REGIONS@
63 <option value="indels">indels - allow multiallelic indel records</option> 64 <option value="indels">indels - allow multiallelic indel records</option>
64 <option value="both">both - both SNP and indel records can be multiallelic</option> 65 <option value="both">both - both SNP and indel records can be multiallelic</option>
65 <option value="all">all - SNP records can be merged with indel records</option> 66 <option value="all">all - SNP records can be merged with indel records</option>
66 <option value="id">id - merge by ID</option> 67 <option value="id">id - merge by ID</option>
67 </param> 68 </param>
69 <param argument="--no-index" type="boolean" truevalue="--no-index" falsevalue="" checked="false"
70 label="Allow merge unindexed files" help="Requires the input files to have chromosomes in th same order and consistent with the order of sequences in the header" />
68 </section> 71 </section>
69 <section name="sec_header" expanded="false" title="Header Options"> 72 <section name="sec_header" expanded="false" title="Header Options">
70 <param name="use_header" type="data" format="vcf" label="Use Header" optional="True" help="Use the provided header" /> 73 <param name="use_header" type="data" format="vcf" label="Use Header" optional="True" help="Use the provided header" />
71 <param name="print_header" type="boolean" truevalue="--print-header" falsevalue="" label="Print Header" help="Print only the merged header and exit" /> 74 <param name="print_header" type="boolean" truevalue="--print-header" falsevalue="" label="Print Header" help="Print only the merged header and exit" />
72 </section> 75 </section>
133 <has_text_matching expression="1\t3000000\t.\tC\t(CG,CCG|CCG,CG)\t"/> 136 <has_text_matching expression="1\t3000000\t.\tC\t(CG,CCG|CCG,CG)\t"/>
134 <has_text_matching expression="TR=[^;\t]*11"/> 137 <has_text_matching expression="TR=[^;\t]*11"/>
135 </assert_contents> 138 </assert_contents>
136 </output> 139 </output>
137 </test> 140 </test>
141 <!-- Test no_index option -->
138 <test> 142 <test>
139 <param name="input_files" ftype="vcf" value="merge.4.a.vcf,merge.4.b.vcf" /> 143 <param name="input_files" ftype="vcf" value="merge.4.a.vcf,merge.4.b.vcf" />
140 <param name="force_samples" value="true" /> 144 <param name="force_samples" value="true" />
141 <param name="merge" value="id" /> 145 <param name="merge" value="id" />
146 <param name="no_index" value="true"/>
142 <param name="output_type" value="v" /> 147 <param name="output_type" value="v" />
143 <output name="output_file"> 148 <output name="output_file">
144 <assert_contents> 149 <assert_contents>
145 <has_text_matching expression="1\t3000000\tid1\tC\t(A,CCG|CCG,A)\t"/> 150 <has_text_matching expression="1\t3000000\tid1\tC\t(A,CCG|CCG,A)\t"/>
146 </assert_contents> 151 </assert_contents>
147 </output> 152 </output>
153 <assert_command>
154 <has_text text="--no-index" />
155 </assert_command>
156 </test>
157 <!-- Test region overlap option -->
158 <test>
159 <param name="input_files" ftype="vcf" value="merge.4.a.vcf,merge.4.b.vcf" />
160 <param name="force_samples" value="true" />
161 <param name="merge" value="id" />
162 <param name="output_type" value="v" />
163 <section name="sec_restrict">
164 <param name="regions_overlap" value="1"/>
165 </section>
166 <output name="output_file">
167 <assert_contents>
168 <has_text_matching expression="1\t3000000\tid1\tC\t(A,CCG|CCG,A)\t"/>
169 </assert_contents>
170 </output>
171 <assert_command>
172 <has_text text="--regions-overlap" />
173 </assert_command>
148 </test> 174 </test>
149 </tests> 175 </tests>
150 <help><![CDATA[ 176 <help><![CDATA[
151 ===================================== 177 =====================================
152 bcftools @EXECUTABLE@ 178 bcftools @EXECUTABLE@