Mercurial > repos > iuc > stacks2_ustacks
comparison stacks_ustacks.xml @ 6:bb0475c884ff draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 2f4c9bfc48d63075ae18a1687e8d01ffea509084
| author | iuc |
|---|---|
| date | Wed, 11 May 2022 06:39:40 +0000 |
| parents | d1fda11e602f |
| children |
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| 5:d1fda11e602f | 6:bb0475c884ff |
|---|---|
| 9 @FASTQ_INPUT_FUNCTIONS@ | 9 @FASTQ_INPUT_FUNCTIONS@ |
| 10 | 10 |
| 11 trap ">&2 cat '$output_log'" err exit && | 11 trap ">&2 cat '$output_log'" err exit && |
| 12 mkdir stacks_inputs stacks_outputs && | 12 mkdir stacks_inputs stacks_outputs && |
| 13 | 13 |
| 14 #set $ID=1 | 14 #set $ID=int($processing_options.i) |
| 15 #for $sample in $input_type.fqinputs | 15 #for $sample in $input_type.fqinputs |
| 16 #set ($create_links, $data_path, $name, $inputype) = $fastq_input_foo($sample, "forward", ".1") | 16 #set ($create_links, $data_path, $name, $inputype) = $fastq_input_foo($sample, "forward", ".1") |
| 17 $create_links | 17 $create_links |
| 18 | 18 |
| 19 ustacks | 19 ustacks |
| 87 <expand macro="gap_options"/> | 87 <expand macro="gap_options"/> |
| 88 | 88 |
| 89 <!-- SNP Model options --> | 89 <!-- SNP Model options --> |
| 90 <section name="snp_options" title="SNP Model Options (ustacks options)" expanded="False"> | 90 <section name="snp_options" title="SNP Model Options (ustacks options)" expanded="False"> |
| 91 <expand macro="snp_options_full"/> | 91 <expand macro="snp_options_full"/> |
| 92 </section> | |
| 93 <section name="processing_options" title="Processing options" expanded="False"> | |
| 94 <param argument="-i" type="integer" value="1" label="Start identifier at" help="If you are combining multiple ustacks runs at the cstacks stage, use this option to avoid having different samples with the same identifier."/> | |
| 92 </section> | 95 </section> |
| 93 <expand macro="in_log"/> | 96 <expand macro="in_log"/> |
| 94 </inputs> | 97 </inputs> |
| 95 | 98 |
| 96 <outputs> | 99 <outputs> |
| 120 </param> | 123 </param> |
| 121 <param name="add_log" value="yes"/> | 124 <param name="add_log" value="yes"/> |
| 122 <output name="output_log"><assert_contents><has_text text="done."/></assert_contents></output> | 125 <output name="output_log"><assert_contents><has_text text="done."/></assert_contents></output> |
| 123 <!-- 1st test checks for file content allowing differences in the 2 comment lines that contain date and version --> | 126 <!-- 1st test checks for file content allowing differences in the 2 comment lines that contain date and version --> |
| 124 <output_collection name="tabs" type="list" count="6"> | 127 <output_collection name="tabs" type="list" count="6"> |
| 125 <element name="PopA_01.tags" ftype="tabular" file="ustacks/PopA_01.tags.tsv" lines_diff="4"/> | 128 <element name="PopA_01.tags"> |
| 126 <element name="PopA_01.snps" ftype="tabular" file="ustacks/PopA_01.snps.tsv" lines_diff="4"/> | 129 <assert_contents> |
| 127 <element name="PopA_01.alleles" ftype="tabular" file="ustacks/PopA_01.alleles.tsv" lines_diff="4"/> | 130 <has_text text="# ustacks version" /> |
| 128 <element name="PopA_02.tags" ftype="tabular" file="ustacks/PopA_02.tags.tsv" lines_diff="4"/> | 131 </assert_contents> |
| 129 <element name="PopA_02.snps" ftype="tabular" file="ustacks/PopA_02.snps.tsv" lines_diff="4"/> | 132 </element> |
| 130 <element name="PopA_02.alleles" ftype="tabular" file="ustacks/PopA_02.alleles.tsv" lines_diff="4"/> | 133 <element name="PopA_01.snps"> |
| 134 <assert_contents> | |
| 135 <has_text text="# ustacks version" /> | |
| 136 </assert_contents> | |
| 137 </element> | |
| 138 <expand macro="test_element_stacks_completed" element_name="PopA_01.alleles" /> | |
| 139 <element name="PopA_02.tags"> | |
| 140 <assert_contents> | |
| 141 <has_text text="# ustacks version" /> | |
| 142 </assert_contents> | |
| 143 </element> | |
| 144 <element name="PopA_02.snps"> | |
| 145 <assert_contents> | |
| 146 <has_text text="# ustacks version" /> | |
| 147 </assert_contents> | |
| 148 </element> | |
| 149 <expand macro="test_element_stacks_completed" element_name="PopA_02.alleles" /> | |
| 131 </output_collection> | 150 </output_collection> |
| 132 </test> | 151 </test> |
| 133 <!-- manual selected list of elements + default args, test for file equality --> | 152 <!-- manual selected list of elements + default args, test for file equality --> |
| 134 <test expect_num_outputs="2"> | 153 <test expect_num_outputs="2"> |
| 135 <param name="input_type|input_type_select" value="single"/> | 154 <param name="input_type|input_type_select" value="single"/> |
| 136 <param name="input_type|fqinputs" value="demultiplexed/PopA_01.1.fq,demultiplexed/PopA_02.1.fq" ftype="fastqsanger"/> | 155 <param name="input_type|fqinputs" value="demultiplexed/PopA_01.1.fq,demultiplexed/PopA_02.1.fq" ftype="fastqsanger"/> |
| 137 <param name="add_log" value="yes"/> | 156 <param name="add_log" value="yes"/> |
| 138 <output name="output_log" ftype="txt"><assert_contents><has_text text="ustacks is done."/></assert_contents></output> | 157 <output name="output_log" ftype="txt"><assert_contents><has_text text="ustacks is done."/></assert_contents></output> |
| 139 <output_collection name="tabs" count="6"> | 158 <output_collection name="tabs" count="6"> |
| 140 <element name="PopA_01.tags"><assert_contents><has_text text="# ustacks completed on "/></assert_contents></element> | 159 <expand macro="test_element_stacks_completed" element_name="PopA_01.tags" /> |
| 141 <element name="PopA_01.snps"><assert_contents><has_text text="# ustacks completed on "/></assert_contents></element> | 160 <expand macro="test_element_stacks_completed" element_name="PopA_01.snps" /> |
| 142 <element name="PopA_01.alleles"><assert_contents><has_text text="# ustacks completed on "/></assert_contents></element> | 161 <expand macro="test_element_stacks_completed" element_name="PopA_01.alleles" /> |
| 143 <element name="PopA_02.tags"><assert_contents><has_text text="# ustacks completed on "/></assert_contents></element> | 162 <expand macro="test_element_stacks_completed" element_name="PopA_02.tags" /> |
| 144 <element name="PopA_02.snps"><assert_contents><has_text text="# ustacks completed on "/></assert_contents></element> | 163 <expand macro="test_element_stacks_completed" element_name="PopA_02.snps" /> |
| 145 <element name="PopA_02.alleles"><assert_contents><has_text text="# ustacks completed on "/></assert_contents></element> | 164 <expand macro="test_element_stacks_completed" element_name="PopA_02.alleles" /> |
| 146 </output_collection> | 165 </output_collection> |
| 147 </test> | 166 </test> |
| 148 <!-- manual selected list of elements + non-default short args, test for file presence --> | 167 <!-- manual selected list of elements + non-default short args, test for file presence --> |
| 149 <test expect_num_outputs="2"> | 168 <test expect_num_outputs="2"> |
| 150 <param name="input_type|input_type_select" value="single"/> | 169 <param name="input_type|input_type_select" value="single"/> |
| 162 <has_text text="-R"/> | 181 <has_text text="-R"/> |
| 163 <has_text text="-H"/> | 182 <has_text text="-H"/> |
| 164 </assert_command> | 183 </assert_command> |
| 165 <output name="output_log" ftype="txt"><assert_contents><has_text text="ustacks is done."/></assert_contents></output> | 184 <output name="output_log" ftype="txt"><assert_contents><has_text text="ustacks is done."/></assert_contents></output> |
| 166 <output_collection name="tabs" count="6"> | 185 <output_collection name="tabs" count="6"> |
| 167 <element name="PopA_01.tags"><assert_contents><has_text text="# ustacks completed on "/></assert_contents></element> | 186 <expand macro="test_element_stacks_completed" element_name="PopA_01.tags" /> |
| 168 <element name="PopA_01.snps"><assert_contents><has_text text="# ustacks completed on "/></assert_contents></element> | 187 <expand macro="test_element_stacks_completed" element_name="PopA_01.snps" /> |
| 169 <element name="PopA_01.alleles"><assert_contents><has_text text="# ustacks completed on "/></assert_contents></element> | 188 <expand macro="test_element_stacks_completed" element_name="PopA_01.alleles" /> |
| 170 <element name="PopA_02.tags"><assert_contents><has_text text="# ustacks completed on "/></assert_contents></element> | 189 <expand macro="test_element_stacks_completed" element_name="PopA_02.tags" /> |
| 171 <element name="PopA_02.snps"><assert_contents><has_text text="# ustacks completed on "/></assert_contents></element> | 190 <expand macro="test_element_stacks_completed" element_name="PopA_02.snps" /> |
| 172 <element name="PopA_02.alleles"><assert_contents><has_text text="# ustacks completed on "/></assert_contents></element> | 191 <expand macro="test_element_stacks_completed" element_name="PopA_02.alleles" /> |
| 173 </output_collection> | 192 </output_collection> |
| 174 </test> | 193 </test> |
| 175 <!-- paired list, non-default model options, disabled gapped alignment, test for file presence --> | 194 <!-- paired list, non-default model options, disabled gapped alignment, test for file presence --> |
| 176 <test expect_num_outputs="2"> | 195 <test expect_num_outputs="2"> |
| 177 <param name="input_type|input_type_select" value="paired"/> | 196 <param name="input_type|input_type_select" value="paired"/> |
| 208 <not_has_text text="--bc_err_freq 0.1"/> | 227 <not_has_text text="--bc_err_freq 0.1"/> |
| 209 <has_text text="--disable-gapped"/> | 228 <has_text text="--disable-gapped"/> |
| 210 </assert_command> | 229 </assert_command> |
| 211 <output name="output_log" ftype="txt"><assert_contents><has_text text="ustacks is done."/></assert_contents></output> | 230 <output name="output_log" ftype="txt"><assert_contents><has_text text="ustacks is done."/></assert_contents></output> |
| 212 <output_collection name="tabs" count="6"> | 231 <output_collection name="tabs" count="6"> |
| 213 <element name="PopA_01.tags"><assert_contents><has_text text="# ustacks completed on "/></assert_contents></element> | 232 <expand macro="test_element_stacks_completed" element_name="PopA_01.tags" /> |
| 214 <element name="PopA_01.snps"><assert_contents><has_text text="# ustacks completed on "/></assert_contents></element> | 233 <expand macro="test_element_stacks_completed" element_name="PopA_01.snps" /> |
| 215 <element name="PopA_01.alleles"><assert_contents><has_text text="# ustacks completed on "/></assert_contents></element> | 234 <expand macro="test_element_stacks_completed" element_name="PopA_01.alleles" /> |
| 216 <element name="PopA_02.tags"><assert_contents><has_text text="# ustacks completed on "/></assert_contents></element> | 235 <expand macro="test_element_stacks_completed" element_name="PopA_02.tags" /> |
| 217 <element name="PopA_02.snps"><assert_contents><has_text text="# ustacks completed on "/></assert_contents></element> | 236 <expand macro="test_element_stacks_completed" element_name="PopA_02.snps" /> |
| 218 <element name="PopA_02.alleles"><assert_contents><has_text text="# ustacks completed on "/></assert_contents></element> | 237 <expand macro="test_element_stacks_completed" element_name="PopA_02.alleles" /> |
| 219 </output_collection> | 238 </output_collection> |
| 220 </test> | 239 </test> |
| 221 <!-- list of fwd reads, nondefault assembly and gapped alignment options, test for file presence --> | 240 <!-- list of fwd reads, nondefault assembly and gapped alignment options, test for file presence --> |
| 222 <test expect_num_outputs="2"> | 241 <test expect_num_outputs="2"> |
| 223 <param name="input_type|input_type_select" value="paired"/> | 242 <param name="input_type|input_type_select" value="paired"/> |
| 245 <has_text text="--max_gaps 3"/> | 264 <has_text text="--max_gaps 3"/> |
| 246 <has_text text="--min_aln_len 0.7"/> | 265 <has_text text="--min_aln_len 0.7"/> |
| 247 </assert_command> | 266 </assert_command> |
| 248 <output name="output_log" ftype="txt"><assert_contents><has_text text="ustacks is done."/></assert_contents></output> | 267 <output name="output_log" ftype="txt"><assert_contents><has_text text="ustacks is done."/></assert_contents></output> |
| 249 <output_collection name="tabs" count="6"> | 268 <output_collection name="tabs" count="6"> |
| 250 <element name="PopA_01.tags"><assert_contents><has_text text="# ustacks completed on "/></assert_contents></element> | 269 <expand macro="test_element_stacks_completed" element_name="PopA_01.tags" /> |
| 251 <element name="PopA_01.snps"><assert_contents><has_text text="# ustacks completed on "/></assert_contents></element> | 270 <expand macro="test_element_stacks_completed" element_name="PopA_01.snps" /> |
| 252 <element name="PopA_01.alleles"><assert_contents><has_text text="# ustacks completed on "/></assert_contents></element> | 271 <expand macro="test_element_stacks_completed" element_name="PopA_01.alleles" /> |
| 253 <element name="PopA_02.tags"><assert_contents><has_text text="# ustacks completed on "/></assert_contents></element> | 272 <expand macro="test_element_stacks_completed" element_name="PopA_02.tags" /> |
| 254 <element name="PopA_02.snps"><assert_contents><has_text text="# ustacks completed on "/></assert_contents></element> | 273 <expand macro="test_element_stacks_completed" element_name="PopA_02.snps" /> |
| 255 <element name="PopA_02.alleles"><assert_contents><has_text text="# ustacks completed on "/></assert_contents></element> | 274 <expand macro="test_element_stacks_completed" element_name="PopA_02.alleles" /> |
| 256 </output_collection> | 275 </output_collection> |
| 257 </test> | 276 </test> |
| 277 <!-- test setting i --> | |
| 278 <test expect_num_outputs="2"> | |
| 279 <param name="input_type|input_type_select" value="single"/> | |
| 280 <param name="input_type|fqinputs" value="demultiplexed/PopA_01.1.fq,demultiplexed/PopA_02.1.fq" ftype="fastqsanger"/> | |
| 281 <param name="add_log" value="yes"/> | |
| 282 <param name="i" value="42"/> | |
| 283 <output name="output_log" ftype="txt"><assert_contents><has_text text="ustacks is done."/></assert_contents></output> | |
| 284 <output_collection name="tabs" count="6"> | |
| 285 <expand macro="test_element_stacks_completed" element_name="PopA_01.tags" /> | |
| 286 <expand macro="test_element_stacks_completed" element_name="PopA_01.snps" /> | |
| 287 <expand macro="test_element_stacks_completed" element_name="PopA_01.alleles" /> | |
| 288 <expand macro="test_element_stacks_completed" element_name="PopA_02.tags" /> | |
| 289 <expand macro="test_element_stacks_completed" element_name="PopA_02.snps" /> | |
| 290 <expand macro="test_element_stacks_completed" element_name="PopA_02.alleles" /> | |
| 291 </output_collection> | |
| 292 </test> | |
| 293 | |
| 258 </tests> | 294 </tests> |
| 259 | 295 |
| 260 <help> | 296 <help> |
| 261 <![CDATA[ | 297 <![CDATA[ |
| 262 .. class:: infomark | 298 .. class:: infomark |