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comparison ragtag.xml @ 2:7ac8eea4245c draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 5b09d46d1096109a68a41ccd63813469ec8ea675
author iuc
date Fri, 14 Oct 2022 13:34:29 +0000
parents c877619c2de2
children
comparison
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1:c877619c2de2 2:7ac8eea4245c
234 <option value="log">Log file</option> 234 <option value="log">Log file</option>
235 </param> 235 </param>
236 </when> 236 </when>
237 <when value="merge"> 237 <when value="merge">
238 <param name="assembly_fasta" type="data" format="fasta" label="Assembly FASTA file"/> 238 <param name="assembly_fasta" type="data" format="fasta" label="Assembly FASTA file"/>
239 <param name="scaffold_files" type="data" format="agp" multiple="true" optional="true" label="Scaffold AGP files"/> 239 <param name="scaffold_files" type="data" format="agp" multiple="true" min="2" label="Scaffold AGP files" help="At least two AGP files are required."/>
240 <section name="merging_options" title="Merging options"> 240 <section name="merging_options" title="Merging options">
241 <param argument="-j" type="data" format="txt" optional="true" label="List of query headers to leave unplaced"/> 241 <param argument="-j" type="data" format="txt" optional="true" label="List of query headers to leave unplaced"/>
242 <param argument="-l" type="integer" min="0" value="100000" label="Minimum assembly sequence length" 242 <param argument="-l" type="integer" min="0" value="100000" label="Minimum assembly sequence length"
243 help="Assembly sequences shorter than -l will also be left unplaced."/> 243 help="Assembly sequences shorter than -l will also be left unplaced."/>
244 <param argument="-e" type="float" min="0" value="0" label="Minimum edge weight" 244 <param argument="-e" type="float" min="0" value="0" label="Minimum edge weight"
270 </when> 270 </when>
271 </conditional> 271 </conditional>
272 </inputs> 272 </inputs>
273 <outputs> 273 <outputs>
274 <!--Correct mode outputs--> 274 <!--Correct mode outputs-->
275 <data format="paf" name="correct_paf" from_work_dir="ragtag.correct.asm.paf" label="${tool.name} on ${on_string}: PAF"> 275 <data format="paf" name="correct_paf" from_work_dir="ragtag.correct.asm.paf" label="${tool.name} on ${on_string}: correct PAF">
276 <filter>mode_conditional["mode_option"] == "correct" and "paf" in mode_conditional["output_correct"]</filter> 276 <filter>mode_conditional["mode_option"] == "correct" and "paf" in mode_conditional["output_correct"]</filter>
277 </data> 277 </data>
278 <data format="agp" name="correct_agp" from_work_dir="ragtag.correct.agp" label="${tool.name} on ${on_string}: AGP"> 278 <data format="agp" name="correct_agp" from_work_dir="ragtag.correct.agp" label="${tool.name} on ${on_string}: correct AGP">
279 <filter>mode_conditional["mode_option"] == "correct" and "agp" in mode_conditional["output_correct"]</filter> 279 <filter>mode_conditional["mode_option"] == "correct" and "agp" in mode_conditional["output_correct"]</filter>
280 </data> 280 </data>
281 <data format="fasta" name="correct_fasta" from_work_dir="ragtag.correct.fasta" label="${tool.name} on ${on_string}: FASTA"> 281 <data format="fasta" name="correct_fasta" from_work_dir="ragtag.correct.fasta" label="${tool.name} on ${on_string}: correct FASTA">
282 <filter>mode_conditional["mode_option"] == "correct" and "fasta" in mode_conditional["output_correct"]</filter> 282 <filter>mode_conditional["mode_option"] == "correct" and "fasta" in mode_conditional["output_correct"]</filter>
283 </data> 283 </data>
284 <data format="txt" name="correct_log" from_work_dir="ragtag.correct.asm.paf.log" label="${tool.name} on ${on_string}: log"> 284 <data format="txt" name="correct_log" from_work_dir="ragtag.correct.asm.paf.log" label="${tool.name} on ${on_string}: correct log">
285 <filter>mode_conditional["mode_option"] == "correct" and "log" in mode_conditional["output_correct"]</filter> 285 <filter>mode_conditional["mode_option"] == "correct" and "log" in mode_conditional["output_correct"]</filter>
286 </data> 286 </data>
287 <!--Scaffold mode outputs--> 287 <!--Scaffold mode outputs-->
288 <data format="paf" name="scaffold_paf" from_work_dir="ragtag.scaffold.asm.paf" label="${tool.name} on ${on_string}: PAF"> 288 <data format="paf" name="scaffold_paf" from_work_dir="ragtag.scaffold.asm.paf" label="${tool.name} on ${on_string}: scaffold PAF">
289 <filter>mode_conditional["mode_option"] == "scaffold" and "paf" in mode_conditional["output_scaffold"]</filter> 289 <filter>mode_conditional["mode_option"] == "scaffold" and "paf" in mode_conditional["output_scaffold"]</filter>
290 </data> 290 </data>
291 <data format="agp" name="scaffold_agp" from_work_dir="ragtag.scaffold.agp" label="${tool.name} on ${on_string}: AGP"> 291 <data format="agp" name="scaffold_agp" from_work_dir="ragtag.scaffold.agp" label="${tool.name} on ${on_string}: scaffold AGP">
292 <filter>mode_conditional["mode_option"] == "scaffold" and "agp" in mode_conditional["output_scaffold"]</filter> 292 <filter>mode_conditional["mode_option"] == "scaffold" and "agp" in mode_conditional["output_scaffold"]</filter>
293 </data> 293 </data>
294 <data format="fasta" name="scaffold_fasta" from_work_dir="ragtag.scaffold.fasta" label="${tool.name} on ${on_string}: FASTA"> 294 <data format="fasta" name="scaffold_fasta" from_work_dir="ragtag.scaffold.fasta" label="${tool.name} on ${on_string}: scaffold FASTA">
295 <filter>mode_conditional["mode_option"] == "scaffold" and "fasta" in mode_conditional["output_scaffold"]</filter> 295 <filter>mode_conditional["mode_option"] == "scaffold" and "fasta" in mode_conditional["output_scaffold"]</filter>
296 </data> 296 </data>
297 <data format="txt" name="scaffold_log" from_work_dir="ragtag.scaffold.asm.paf.log" label="${tool.name} on ${on_string}: log"> 297 <data format="txt" name="scaffold_log" from_work_dir="ragtag.scaffold.asm.paf.log" label="${tool.name} on ${on_string}: scaffold log">
298 <filter>mode_conditional["mode_option"] == "scaffold" and "log" in mode_conditional["output_scaffold"]</filter> 298 <filter>mode_conditional["mode_option"] == "scaffold" and "log" in mode_conditional["output_scaffold"]</filter>
299 </data> 299 </data>
300 <data format="tabular" name="scaffold_stats" from_work_dir="ragtag.scaffold.stats" label="${tool.name} on ${on_string}: stats"> 300 <data format="tabular" name="scaffold_stats" from_work_dir="ragtag.scaffold.stats" label="${tool.name} on ${on_string}: scaffold stats">
301 <filter>mode_conditional["mode_option"] == "scaffold" and "stats" in mode_conditional["output_scaffold"]</filter> 301 <filter>mode_conditional["mode_option"] == "scaffold" and "stats" in mode_conditional["output_scaffold"]</filter>
302 </data> 302 </data>
303 <data format="tabular" name="scaffold_confidence" from_work_dir="ragtag.scaffold.confidence.txt" label="${tool.name} on ${on_string}: confidence"> 303 <data format="tabular" name="scaffold_confidence" from_work_dir="ragtag.scaffold.confidence.txt" label="${tool.name} on ${on_string}: scaffold confidence">
304 <filter>mode_conditional["mode_option"] == "scaffold" and "confidence" in mode_conditional["output_scaffold"]</filter> 304 <filter>mode_conditional["mode_option"] == "scaffold" and "confidence" in mode_conditional["output_scaffold"]</filter>
305 </data> 305 </data>
306 <!--Patch mode outputs--> 306 <!--Patch mode outputs-->
307 <data format="agp" name="patch_agp" from_work_dir="ragtag.patch.agp" label="${tool.name} on ${on_string}: final AGP"> 307 <data format="agp" name="patch_agp" from_work_dir="ragtag.patch.agp" label="${tool.name} on ${on_string}: patch final AGP">
308 <filter>mode_conditional["mode_option"] == "patch" and "final_agp" in mode_conditional["output_patch"]</filter> 308 <filter>mode_conditional["mode_option"] == "patch" and "final_agp" in mode_conditional["output_patch"]</filter>
309 </data> 309 </data>
310 <data format="paf" name="patch_paf" from_work_dir="ragtag.patch.asm.paf" label="${tool.name} on ${on_string}: final PAF"> 310 <data format="paf" name="patch_paf" from_work_dir="ragtag.patch.asm.paf" label="${tool.name} on ${on_string}: patch final PAF">
311 <filter>mode_conditional["mode_option"] == "patch" and "assembly_file" in mode_conditional["output_patch"]</filter> 311 <filter>mode_conditional["mode_option"] == "patch" and "assembly_file" in mode_conditional["output_patch"]</filter>
312 </data> 312 </data>
313 <data format="txt" name="patch_log" from_work_dir="ragtag.patch.log" label="${tool.name} on ${on_string}: log"> 313 <data format="txt" name="patch_log" from_work_dir="ragtag.patch.log" label="${tool.name} on ${on_string}: patch log">
314 <filter>mode_conditional["mode_option"] == "patch" and "log" in mode_conditional["output_patch"]</filter> 314 <filter>mode_conditional["mode_option"] == "patch" and "log" in mode_conditional["output_patch"]</filter>
315 </data> 315 </data>
316 <data format="fasta" name="patch_comps_fasta" from_work_dir="ragtag.patch.comps.fasta" label="${tool.name} on ${on_string}: components FASTA"> 316 <data format="fasta" name="patch_comps_fasta" from_work_dir="ragtag.patch.comps.fasta" label="${tool.name} on ${on_string}: patch components FASTA">
317 <filter>mode_conditional["mode_option"] == "patch" and "split_assembly" in mode_conditional["output_patch"]</filter> 317 <filter>mode_conditional["mode_option"] == "patch" and "split_assembly" in mode_conditional["output_patch"]</filter>
318 </data> 318 </data>
319 <data format="agp" name="patch_ctg_agp" from_work_dir="ragtag.patch.ctg.agp" label="${tool.name} on ${on_string}: contigs AGP"> 319 <data format="agp" name="patch_ctg_agp" from_work_dir="ragtag.patch.ctg.agp" label="${tool.name} on ${on_string}: patch contigs AGP">
320 <filter>mode_conditional["mode_option"] == "patch" and "split_description" in mode_conditional["output_patch"]</filter> 320 <filter>mode_conditional["mode_option"] == "patch" and "split_description" in mode_conditional["output_patch"]</filter>
321 </data> 321 </data>
322 <data format="fasta" name="patch_ctg_fasta" from_work_dir="ragtag.patch.ctg.fasta" label="${tool.name} on ${on_string}: contigs FASTA"> 322 <data format="fasta" name="patch_ctg_fasta" from_work_dir="ragtag.patch.ctg.fasta" label="${tool.name} on ${on_string}: patch contigs FASTA">
323 <filter>mode_conditional["mode_option"] == "patch" and "target_gaps" in mode_conditional["output_patch"]</filter> 323 <filter>mode_conditional["mode_option"] == "patch" and "target_gaps" in mode_conditional["output_patch"]</filter>
324 </data> 324 </data>
325 <data format="fasta" name="patch_fasta" from_work_dir="ragtag.patch.fasta" label="${tool.name} on ${on_string}: final FASTA"> 325 <data format="fasta" name="patch_fasta" from_work_dir="ragtag.patch.fasta" label="${tool.name} on ${on_string}: patch final FASTA">
326 <filter>mode_conditional["mode_option"] == "patch" and "final_fasta" in mode_conditional["output_patch"]</filter> 326 <filter>mode_conditional["mode_option"] == "patch" and "final_fasta" in mode_conditional["output_patch"]</filter>
327 </data> 327 </data>
328 <data format="agp" name="patch_rename_agp" from_work_dir="ragtag.patch.rename.agp" label="${tool.name} on ${on_string}: renamed AGP"> 328 <data format="agp" name="patch_rename_agp" from_work_dir="ragtag.patch.rename.agp" label="${tool.name} on ${on_string}: patch renamed AGP">
329 <filter>mode_conditional["mode_option"] == "patch" and "agp_renamed" in mode_conditional["output_patch"]</filter> 329 <filter>mode_conditional["mode_option"] == "patch" and "agp_renamed" in mode_conditional["output_patch"]</filter>
330 </data> 330 </data>
331 <data format="fasta" name="patch_rename_fasta" from_work_dir="ragtag.patch.rename.fasta" label="${tool.name} on ${on_string}: renamed FASTA"> 331 <data format="fasta" name="patch_rename_fasta" from_work_dir="ragtag.patch.rename.fasta" label="${tool.name} on ${on_string}: patch renamed FASTA">
332 <filter>mode_conditional["mode_option"] == "patch" and "fasta_renamed" in mode_conditional["output_patch"]</filter> 332 <filter>mode_conditional["mode_option"] == "patch" and "fasta_renamed" in mode_conditional["output_patch"]</filter>
333 </data> 333 </data>
334 <!-- Merge mode outputs--> 334 <!-- Merge mode outputs-->
335 <data format="agp" name="merge_agp" from_work_dir="ragtag.merge.agp" label="${tool.name} on ${on_string}: merged AGP"> 335 <data format="agp" name="merge_agp" from_work_dir="ragtag.merge.agp" label="${tool.name} on ${on_string}: merged AGP">
336 <filter>mode_conditional["mode_option"] == "merge"</filter> 336 <filter>mode_conditional["mode_option"] == "merge"</filter>