Mercurial > repos > iuc > snippy
comparison snippy.xml @ 11:5bbf9eada9c2 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snippy commit e3844d13b58d22b269b986e03177e6f5efb675b4"
| author | iuc |
|---|---|
| date | Wed, 11 Mar 2020 03:50:47 -0400 |
| parents | e4d0231d8595 |
| children | fa016f1eea1a |
comparison
equal
deleted
inserted
replaced
| 10:3fe8ef358d66 | 11:5bbf9eada9c2 |
|---|---|
| 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[ |