Mercurial > repos > iuc > srst2
comparison srst2.xml @ 2:81cea47ec685 draft
planemo upload for repository https://github.com/katholt/srst2 commit 13ef9da7b3f4b7a06deb5b3ce7331ae127ec7aba
| author | iuc |
|---|---|
| date | Mon, 18 Mar 2024 12:32:11 +0000 |
| parents | 46c5d7a0393b |
| children | f995ba9f1caa |
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| 1:46c5d7a0393b | 2:81cea47ec685 |
|---|---|
| 2 <description>Short Read Sequence Typing for Bacterial Pathogens</description> | 2 <description>Short Read Sequence Typing for Bacterial Pathogens</description> |
| 3 <macros> | 3 <macros> |
| 4 <import>macros.xml</import> | 4 <import>macros.xml</import> |
| 5 <token name="@FAST_A_Q_FORMATS@">fasta,fasta.gz,fastq,fastq.gz,fastqsanger,fastqsanger.gz</token> | 5 <token name="@FAST_A_Q_FORMATS@">fasta,fasta.gz,fastq,fastq.gz,fastqsanger,fastqsanger.gz</token> |
| 6 </macros> | 6 </macros> |
| 7 <expand macro="xrefs"/> | |
| 7 <expand macro="requirements"/> | 8 <expand macro="requirements"/> |
| 8 <version_command>srst2 --version</version_command> | 9 <version_command>srst2 --version</version_command> |
| 9 <command detect_errors="exit_code"><![CDATA[ | 10 <command detect_errors="exit_code"><![CDATA[ |
| 10 #if $input.selector == "single" | 11 #if $input.selector == "single" |
| 11 #set ext=$input.single_input.datatype.file_ext | 12 #set ext=$input.single_input.datatype.file_ext |
| 286 <assert_contents> | 287 <assert_contents> |
| 287 <has_text text="49__AmpC1_Ecoli_Bla__AmpC1__1670"/> | 288 <has_text text="49__AmpC1_Ecoli_Bla__AmpC1__1670"/> |
| 288 <has_n_lines n="2"/> | 289 <has_n_lines n="2"/> |
| 289 </assert_contents> | 290 </assert_contents> |
| 290 </output> | 291 </output> |
| 291 <output_collection name="new_consensus" type="list"> | 292 <output_collection name="new_consensus" type="list" count="1"> |
| 292 <element name="49__AmpC1_Ecoli_Bla__AmpC1__1670.output__input.0-gene_db.pileup"> | 293 <element name="49__AmpC1_Ecoli_Bla__AmpC1__1670.output__input.0-gene_db.pileup"> |
| 293 <assert_contents> | 294 <assert_contents> |
| 294 <has_text text="49__AmpC1_Ecoli_Bla__AmpC1__1670"/> | 295 <has_text text="49__AmpC1_Ecoli_Bla__AmpC1__1670"/> |
| 295 <has_n_lines n="1196"/> | 296 <has_n_lines n="1196"/> |
| 296 </assert_contents> | 297 </assert_contents> |
| 297 </element> | 298 </element> |
| 298 </output_collection> | 299 </output_collection> |
| 299 <output_collection name="samtools_pileup_alignment" type="list"> | 300 <output_collection name="samtools_pileup_alignment" type="list" count="1"> |
| 300 <element name="output__input.0-gene_db.pileup"> | 301 <element name="output__input.0-gene_db.pileup"> |
| 301 <assert_contents> | 302 <assert_contents> |
| 302 <has_text text="49__AmpC1_Ecoli_Bla__AmpC1__1670"/> | 303 <has_text text="49__AmpC1_Ecoli_Bla__AmpC1__1670"/> |
| 303 <has_n_lines n="1196"/> | 304 <has_n_lines n="1196"/> |
| 304 </assert_contents> | 305 </assert_contents> |
| 305 </element> | 306 </element> |
| 306 </output_collection> | 307 </output_collection> |
| 307 <output_collection name="bowtie2_alignment_output" type="list"> | 308 <output_collection name="bowtie2_alignment_output" type="list" count="1"> |
| 308 <element name="output__input.0-gene_db.sorted.bam"> | 309 <element name="output__input.0-gene_db.sorted.bam"> |
| 309 <assert_contents> | 310 <assert_contents> |
| 310 <has_size value="18500" delta="1000"/> | 311 <has_size value="18500" delta="1000"/> |
| 311 </assert_contents> | 312 </assert_contents> |
| 312 </element> | 313 </element> |
| 345 <output name="all_consensus"> | 346 <output name="all_consensus"> |
| 346 <assert_contents> | 347 <assert_contents> |
| 347 <has_size value="0" delta="0"/> | 348 <has_size value="0" delta="0"/> |
| 348 </assert_contents> | 349 </assert_contents> |
| 349 </output> | 350 </output> |
| 350 <output_collection name="new_consensus" type="list"> | 351 <output_collection name="new_consensus" type="list" count="0"/> |
| 351 </output_collection> | 352 <output_collection name="samtools_pileup_alignment" type="list" count="0"/> |
| 352 <output_collection name="samtools_pileup_alignment" type="list"> | 353 <output_collection name="bowtie2_alignment_output" type="list" count="0"/> |
| 353 </output_collection> | 354 <output_collection name="scores_ofEachAllele" type="list" count="0"/> |
| 354 <output_collection name="bowtie2_alignment_output" type="list"> | |
| 355 </output_collection> | |
| 356 <output_collection name="scores_ofEachAllele" type="list"> | |
| 357 </output_collection> | |
| 358 <output name="log_output"> | 355 <output name="log_output"> |
| 359 <assert_contents> | 356 <assert_contents> |
| 360 <has_text text="Total paired readsets found:1"/> | 357 <has_text text="Total paired readsets found:1"/> |
| 361 <has_n_lines n="4"/> | 358 <has_n_lines n="4"/> |
| 362 </assert_contents> | 359 </assert_contents> |