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comparison cutadapt.xml @ 18:5c7e7d905b33 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b58d6ff959a1d920fd0d9b02e43d2482667d61e8
author iuc
date Thu, 13 Dec 2018 20:54:04 -0500
parents 52ef1be47553
children 49370cb85f0f
comparison
equal deleted inserted replaced
17:52ef1be47553 18:5c7e7d905b33
80 #end if 80 #end if
81 81
82 #if str( $library.type ) == "single": 82 #if str( $library.type ) == "single":
83 @read1_options@ 83 @read1_options@
84 #if $output_options.multiple_output: 84 #if $output_options.multiple_output:
85 --output='split/{name}.fastq' 85 --output='split/{name}.${input_1.ext}'
86 #else: 86 #else:
87 --output='$out1' 87 --output='$out1'
88 #end if 88 #end if
89 #else: 89 #else:
90 @read1_options@ 90 @read1_options@
234 234
235 </inputs> 235 </inputs>
236 236
237 <outputs> 237 <outputs>
238 <data name="out1" format="fastqsanger" metadata_source="input_1" from_work_dir="out1*" label="${tool.name} on ${on_string}: Read 1 Output"> 238 <data name="out1" format="fastqsanger" metadata_source="input_1" from_work_dir="out1*" label="${tool.name} on ${on_string}: Read 1 Output">
239 <filter>(output_options['multiple_output'] is False)</filter>
239 <expand macro="inherit_format_1" /> 240 <expand macro="inherit_format_1" />
240 </data> 241 </data>
241 <data name="out2" format="fastqsanger" metadata_source="input_2" from_work_dir="out2*" label="${tool.name} on ${on_string}: Read 2 Output" > 242 <data name="out2" format="fastqsanger" metadata_source="input_2" from_work_dir="out2*" label="${tool.name} on ${on_string}: Read 2 Output" >
242 <filter>(library['type'] == 'paired' or library['type'] == 'paired_collection')</filter> 243 <filter>(library['type'] == 'paired' or library['type'] == 'paired_collection')</filter>
243 <expand macro="inherit_format_2" /> 244 <expand macro="inherit_format_2" />
288 <filter>(library['type'] == 'paired' or library['type'] == 'paired_collection')</filter> 289 <filter>(library['type'] == 'paired' or library['type'] == 'paired_collection')</filter>
289 <filter>(output_options['too_long_file'] is True)</filter> 290 <filter>(output_options['too_long_file'] is True)</filter>
290 <expand macro="inherit_format_2" /> 291 <expand macro="inherit_format_2" />
291 </data> 292 </data>
292 293
293 <collection name="split_output" type="list" format_source="input" label="${tool.name} on ${on_string}: Split outputs"> 294 <collection name="split_output" type="list" label="${tool.name} on ${on_string}: Split outputs" >
294 <discover_datasets pattern="__designation_and_ext__" directory="split" visible="false" /> 295 <discover_datasets pattern="(?P&lt;designation&gt;.+)\.(?P&lt;ext&gt;fastq.*)" directory="split" />
295 <filter>(output_options['multiple_output'] is True)</filter> 296 <filter>(output_options['multiple_output'] is True)</filter>
296 </collection> 297 </collection>
297 298
298 </outputs> 299 </outputs>
299 300
420 <param name="front_adapter" value="^AGGTCACT" /> 421 <param name="front_adapter" value="^AGGTCACT" />
421 </conditional> 422 </conditional>
422 </repeat> 423 </repeat>
423 </section> 424 </section>
424 </conditional> 425 </conditional>
425 <param name="report" value="True" /> 426 <param name="report" value="False" />
426 <param name="info_file" value="False" /> 427 <param name="info_file" value="False" />
427 <param name="multiple_output" value="True" /> 428 <param name="multiple_output" value="True" />
428 <output_collection name="split_output" type="list" count="3"> 429 <output_collection name="split_output" type="list" count="3">
429 <element name="A1" value="A1.fastq" ftype="fastq"> 430 <element name="A1" value="A1.fastq" ftype="fastq">
430 </element> 431 </element>
431 <element name="A2" value="A2.fastq" ftype="fastq"> 432 <element name="A2" value="A2.fastq" ftype="fastq">
432 </element> 433 </element>
433 <element name="unknown" value="unknown.fastq" ftype="fastq"> 434 <element name="unknown" value="unknown.fastq" ftype="fastq">
434 </element> 435 </element>
435 </output_collection> 436 </output_collection>
436 <output name="report"> 437 </test>
437 <assert_contents> 438
438 <has_text text="Summary"/> 439
439 </assert_contents> 440 <test>
440 </output> 441 <conditional name="library">
441 </test> 442 <param name="type" value="single" />
442 443 <param name="input_1" ftype="fastq.gz" value="cutadapt_in_split.fastq.gz" />
444 <section name="r1" >
445 <repeat name="front_adapters">
446 <conditional name="front_adapter_source">
447 <param name="front_adapter_source_list" value="user"/>
448 <param name="front_adapter_name" value="A1" />
449 <param name="front_adapter" value="^GTCGGTAA" />
450 </conditional>
451 </repeat>
452 <repeat name="front_adapters">
453 <conditional name="front_adapter_source">
454 <param name="front_adapter_source_list" value="user"/>
455 <param name="front_adapter_name" value="A2" />
456 <param name="front_adapter" value="^AGGTCACT" />
457 </conditional>
458 </repeat>
459 </section>
460 </conditional>
461 <param name="report" value="False" />
462 <param name="info_file" value="False" />
463 <param name="multiple_output" value="True" />
464 <output_collection name="split_output" type="list" count="3">
465 <element name="A1" decompress="True" file="A1.fastq.gz" ftype="fastq.gz">
466 </element>
467 <element name="A2" decompress="True" file="A2.fastq.gz" ftype="fastq.gz">
468 </element>
469 <element name="unknown" decompress="True" file="unknown.fastq.gz" ftype="fastq.gz">
470 </element>
471 </output_collection>
472 </test>
443 473
444 </tests> 474 </tests>
445 475
446 <help><![CDATA[ 476 <help><![CDATA[
447 477