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comparison snippy.xml @ 12:ac6e4444e3b8 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snippy commit e3844d13b58d22b269b986e03177e6f5efb675b4"
author iuc
date Wed, 11 Mar 2020 07:50:14 +0000
parents a3f95a688c47
children bd61e60350fd
comparison
equal deleted inserted replaced
11:96859e4292cb 12:ac6e4444e3b8
1 <tool id="snippy" name="snippy" version="@VERSION@+galaxy2"> 1 <tool id="snippy" name="snippy" version="@VERSION@">
2 <description> 2 <description>
3 Snippy finds SNPs between a haploid reference genome and your NGS sequence reads. 3 Snippy finds SNPs between a haploid reference genome and your NGS sequence reads.
4 </description> 4 </description>
5 <macros> 5 <macros>
6 <import>macros.xml</import> 6 <import>macros.xml</import>
151 <param name="fastq_input1" ftype="fastqsanger" value="a_1.fastq" /> 151 <param name="fastq_input1" ftype="fastqsanger" value="a_1.fastq" />
152 <param name="fastq_input2" ftype="fastqsanger" value="a_2.fastq" /> 152 <param name="fastq_input2" ftype="fastqsanger" value="a_2.fastq" />
153 <param name="mincov" value="2" /> 153 <param name="mincov" value="2" />
154 <param name="minqual" value="60" /> 154 <param name="minqual" value="60" />
155 <param name="outputs" value="outgff,outsum" /> 155 <param name="outputs" value="outgff,outsum" />
156 <output name="snpsum" ftype="tabular" file="a_fna_ref_mincov_2_minqual_60.snps.txt" lines_diff="6" /> 156 <output name="snpsum" ftype="tabular" file="a_fna_ref_mincov_2_minqual_60.snps.txt" lines_diff="8" />
157 <output name="snpgff" ftype="gff3" file="a_fna_ref_mincov_2_minqual_60.snps.gff" /> 157 <output name="snpgff" ftype="gff3" file="a_fna_ref_mincov_2_minqual_60.snps.gff" lines_diff="2"/>
158 </test> 158 </test>
159 159
160 <test> <!-- test 1 - fasta ref one snp --> 160 <test> <!-- test 1 - fasta ref one snp -->
161 <conditional name="reference_source"> 161 <conditional name="reference_source">
162 <param name="reference_source_selector" value="history"/> 162 <param name="reference_source_selector" value="history"/>
166 <param name="fastq_input1" ftype="fastqsanger" value="b_1.fastq" /> 166 <param name="fastq_input1" ftype="fastqsanger" value="b_1.fastq" />
167 <param name="fastq_input2" ftype="fastqsanger" value="b_2.fastq" /> 167 <param name="fastq_input2" ftype="fastqsanger" value="b_2.fastq" />
168 <param name="mincov" value="2" /> 168 <param name="mincov" value="2" />
169 <param name="minqual" value="60" /> 169 <param name="minqual" value="60" />
170 <param name="outputs" value="outgff,outsum" /> 170 <param name="outputs" value="outgff,outsum" />
171 <output name="snpsum" ftype="tabular" file="b_fna_ref_mincov_2_minqual_60.snps.txt" lines_diff="6" /> 171 <output name="snpsum" ftype="tabular" file="b_fna_ref_mincov_2_minqual_60.snps.txt" lines_diff="8" />
172 <output name="snpgff" ftype="gff3" file="b_fna_ref_mincov_2_minqual_60.snps.gff" /> 172 <output name="snpgff" ftype="gff3" file="b_fna_ref_mincov_2_minqual_60.snps.gff" lines_diff="2"/>
173 </test> 173 </test>
174 174
175 <test> <!-- test 2 - fasta ref one snp paired_collection --> 175 <test> <!-- test 2 - fasta ref one snp paired_collection -->
176 <conditional name="reference_source"> 176 <conditional name="reference_source">
177 <param name="reference_source_selector" value="history"/> 177 <param name="reference_source_selector" value="history"/>
185 </collection> 185 </collection>
186 </param> 186 </param>
187 <param name="mincov" value="2" /> 187 <param name="mincov" value="2" />
188 <param name="minqual" value="60" /> 188 <param name="minqual" value="60" />
189 <param name="outputs" value="outgff,outsum" /> 189 <param name="outputs" value="outgff,outsum" />
190 <output name="snpsum" ftype="tabular" file="b_fna_ref_mincov_2_minqual_60.snps.txt" lines_diff="6" /> 190 <output name="snpsum" ftype="tabular" file="b_fna_ref_mincov_2_minqual_60.snps.txt" lines_diff="8" />
191 <output name="snpgff" ftype="gff3" file="b_fna_ref_mincov_2_minqual_60.snps.gff" /> 191 <output name="snpgff" ftype="gff3" file="b_fna_ref_mincov_2_minqual_60.snps.gff" lines_diff="2"/>
192 </test> 192 </test>
193 193
194 <test> <!-- test 3 - fasta ref one snp single --> 194 <test> <!-- test 3 - fasta ref one snp single -->
195 <conditional name="reference_source"> 195 <conditional name="reference_source">
196 <param name="reference_source_selector" value="history"/> 196 <param name="reference_source_selector" value="history"/>
199 <param name="fastq_input_selector" value="single" /> 199 <param name="fastq_input_selector" value="single" />
200 <param name="fastq_input_single" value="b_2.fastq" ftype="fastqsanger" /> 200 <param name="fastq_input_single" value="b_2.fastq" ftype="fastqsanger" />
201 <param name="mincov" value="2" /> 201 <param name="mincov" value="2" />
202 <param name="minqual" value="60" /> 202 <param name="minqual" value="60" />
203 <param name="outputs" value="outgff,outsum" /> 203 <param name="outputs" value="outgff,outsum" />
204 <output name="snpsum" ftype="tabular" file="b_fna_ref_mincov_2_minqual_60.snps.txt" lines_diff="6" /> 204 <output name="snpsum" ftype="tabular" file="b_fna_ref_mincov_2_minqual_60.snps.txt" lines_diff="8" />
205 <output name="snpgff" ftype="gff3" file="b_2_fna_ref_mincov_2_minqual_60.snps.gff" /> 205 <output name="snpgff" ftype="gff3" file="b_2_fna_ref_mincov_2_minqual_60.snps.gff" lines_diff="2"/>
206 </test> 206 </test>
207 207
208 <test> <!-- test 4 - reference source as cached --> 208 <test> <!-- test 4 - reference source as cached -->
209 <conditional name="reference_source"> 209 <conditional name="reference_source">
210 <param name="reference_source_selector" value="cached"/> 210 <param name="reference_source_selector" value="cached"/>
213 <param name="fastq_input_selector" value="single" /> 213 <param name="fastq_input_selector" value="single" />
214 <param name="fastq_input_single" value="b_2.fastq" ftype="fastqsanger" /> 214 <param name="fastq_input_single" value="b_2.fastq" ftype="fastqsanger" />
215 <param name="mincov" value="2" /> 215 <param name="mincov" value="2" />
216 <param name="minqual" value="60" /> 216 <param name="minqual" value="60" />
217 <param name="outputs" value="outgff,outsum" /> 217 <param name="outputs" value="outgff,outsum" />
218 <output name="snpsum" ftype="tabular" file="b_fna_ref_mincov_2_minqual_60.snps.txt" lines_diff="6" /> 218 <output name="snpsum" ftype="tabular" file="b_fna_ref_mincov_2_minqual_60.snps.txt" lines_diff="8" />
219 <output name="snpgff" ftype="gff3" file="b_2_fna_ref_mincov_2_minqual_60.snps.gff" /> 219 <output name="snpgff" ftype="gff3" file="b_2_fna_ref_mincov_2_minqual_60.snps.gff" lines_diff="2"/>
220 </test> 220 </test>
221 </tests> 221 </tests>
222 222
223 223
224 <help><![CDATA[ 224 <help><![CDATA[