Mercurial > repos > iuc > quast
comparison quast.xml @ 12:875d0f36d66f draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit f713a7853d074ca39057c680ebadba5cbecf5d86"
author | iuc |
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date | Sun, 06 Feb 2022 21:02:38 +0000 |
parents | 7594365c546b |
children | 675488238c96 |
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11:7594365c546b | 12:875d0f36d66f |
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188 <option value="nanopore">Nanopore reads</option> | 188 <option value="nanopore">Nanopore reads</option> |
189 </param> | 189 </param> |
190 <when value="disabled"/> | 190 <when value="disabled"/> |
191 | 191 |
192 <when value="single"> | 192 <when value="single"> |
193 <param name="input_1" format="fastq,fastq.gz" type="data" multiple="true" label="FASTQ file" /> | 193 <param name="input_1" format="fastq,fastq.gz,fasta,fasta.gz" type="data" multiple="true" label="FASTQ/FASTA file" /> |
194 </when> | 194 </when> |
195 | 195 |
196 <when value="paired"> | 196 <when value="paired"> |
197 <param name="input_1" format="fastq,fastq.gz" type="data" multiple="true" label="FASTQ file #1" /> | 197 <param name="input_1" format="fastq,fastq.gz,fasta,fasta.gz" type="data" multiple="true" label="FASTQ/FASTA file #1" /> |
198 <param name="input_2" format="fastq,fastq.gz" type="data" multiple="true" label="FASTQ file #2" /> | 198 <param name="input_2" format="fastq,fastq.gz,fasta,fasta.gz" type="data" multiple="true" label="FASTQ/FASTA file #2" /> |
199 </when> | 199 </when> |
200 | 200 |
201 <when value="paired_interlaced"> | 201 <when value="paired_interlaced"> |
202 <param name="input_1" format="fastq,fastq.gz" type="data" multiple="true" label="FASTQ file" /> | 202 <param name="input_1" format="fastq,fastq.gz,fasta,fasta.gz" type="data" multiple="true" label="FASTQ/FASTA file" /> |
203 </when> | 203 </when> |
204 | 204 |
205 <when value="mate_paired"> | 205 <when value="mate_paired"> |
206 <param name="input_1" format="fastq,fastq.gz" type="data" multiple="true" label="FASTQ file #1" /> | 206 <param name="input_1" format="fastq,fastq.gz,fasta,fasta.gz" type="data" multiple="true" label="FASTQ/FASTA file #1" /> |
207 <param name="input_2" format="fastq,fastq.gz" type="data" multiple="true" label="FASTQ file #2" /> | 207 <param name="input_2" format="fastq,fastq.gz,fasta,fasta.gz" type="data" multiple="true" label="FASTQ/FASTA file #2" /> |
208 </when> | 208 </when> |
209 | 209 |
210 <when value="pacbio"> | 210 <when value="pacbio"> |
211 <param name="input_1" format="fastq,fastq.gz" type="data" multiple="true" label="FASTQ file" /> | 211 <param name="input_1" format="fastq,fastq.gz,fasta,fasta.gz" type="data" multiple="true" label="FASTQ/FASTA file" /> |
212 </when> | 212 </when> |
213 | 213 |
214 <when value="nanopore"> | 214 <when value="nanopore"> |
215 <param name="input_1" format="fastq,fastq.gz" type="data" multiple="true" label="FASTQ file" /> | 215 <param name="input_1" format="fastq,fastq.gz,fasta,fasta.gz" type="data" multiple="true" label="FASTQ/FASTA file" /> |
216 </when> | 216 </when> |
217 </conditional> | 217 </conditional> |
218 | 218 |
219 <conditional name="assembly"> | 219 <conditional name="assembly"> |
220 <param name="type" type="select" label="Type of assembly"> | 220 <param name="type" type="select" label="Type of assembly"> |
411 <param name="skip_unaligned_mis_contigs" value="true"/> | 411 <param name="skip_unaligned_mis_contigs" value="true"/> |
412 <param name="fragmented_max_indent" value="50"/> | 412 <param name="fragmented_max_indent" value="50"/> |
413 </section> | 413 </section> |
414 <param name="output_files" value="html"/> | 414 <param name="output_files" value="html"/> |
415 <output name="report_html" file="test1_report.html" ftype="html" compare="sim_size"/> | 415 <output name="report_html" file="test1_report.html" ftype="html" compare="sim_size"/> |
416 <output name="circos_output" file="test1_circos.png" ftype="png"/> | 416 <output name="circos_output" file="test1_circos.png" ftype="png" compare="sim_size"/> |
417 </test> | 417 </test> |
418 <!-- Test 02: all outputs --> | 418 <!-- Test 02: all outputs --> |
419 <test expect_num_outputs="8"> | 419 <test expect_num_outputs="8"> |
420 <conditional name="in"> | 420 <conditional name="in"> |
421 <param name="custom" value="true"/> | 421 <param name="custom" value="true"/> |
587 <param name="reads_option" value="single"/> | 587 <param name="reads_option" value="single"/> |
588 <param name="input_1" value="pacbio_01.fastq.gz,pacbio_02.fastq.gz"/> | 588 <param name="input_1" value="pacbio_01.fastq.gz,pacbio_02.fastq.gz"/> |
589 </conditional> | 589 </conditional> |
590 <param name="output_files" value="tabular"/> | 590 <param name="output_files" value="tabular"/> |
591 <output name="quast_tabular" file="test6.tab" ftype="tabular"/> | 591 <output name="quast_tabular" file="test6.tab" ftype="tabular"/> |
592 </test> | |
593 <!-- Test 7: FASTA.gz read files --> | |
594 <test expect_num_outputs="1"> | |
595 <conditional name="in"> | |
596 <param name="custom" value="true"/> | |
597 <repeat name="inputs"> | |
598 <param name="input" value="contigs1.fna"/> | |
599 <param name="labels" value="contig1"/> | |
600 </repeat> | |
601 <repeat name="inputs"> | |
602 <param name="input" value="contigs2.fna"/> | |
603 <param name="labels" value="contig2"/> | |
604 </repeat> | |
605 </conditional> | |
606 <conditional name="reads"> | |
607 <param name="reads_option" value="single"/> | |
608 <param name="input_1" value="pacbio_01.fasta.gz,pacbio_02.fasta.gz"/> | |
609 </conditional> | |
610 <param name="output_files" value="tabular"/> | |
611 <output name="quast_tabular" file="test7.tab" ftype="tabular"/> | |
592 </test> | 612 </test> |
593 </tests> | 613 </tests> |
594 <help> | 614 <help> |
595 <![CDATA[ | 615 <![CDATA[ |
596 **What it does** | 616 **What it does** |