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comparison featurecounts.xml @ 20:b4f3420c2a70 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit c8c08f052bdffcbfd14eebd760af923486bcf8c5
author iuc
date Tue, 25 Sep 2018 04:28:07 -0400
parents 834c6a106740
children d4d69c4d0780
comparison
equal deleted inserted replaced
19:834c6a106740 20:b4f3420c2a70
1 <tool id="featurecounts" name="featureCounts" version="1.6.2" profile="16.04"> 1 <tool id="featurecounts" name="featureCounts" version="1.6.3" profile="16.04">
2 <description>Measure gene expression in RNA-Seq experiments from SAM or BAM files.</description> 2 <description>Measure gene expression in RNA-Seq experiments from SAM or BAM files.</description>
3 <requirements> 3 <requirements>
4 <requirement type="package" version="1.6.2">subread</requirement> 4 <requirement type="package" version="1.6.2">subread</requirement>
5 <requirement type="package" version="1.7">samtools</requirement> 5 <requirement type="package" version="1.7">samtools</requirement>
6 </requirements> 6 </requirements>
412 </section> 412 </section>
413 </inputs> 413 </inputs>
414 <outputs> 414 <outputs>
415 <data format="tabular" 415 <data format="tabular"
416 name="output_medium" 416 name="output_medium"
417 label="${tool.name} on ${on_string}"> 417 label="${tool.name} on ${on_string}: Counts (with length)">
418 <filter>format == "tabdel_medium"</filter> 418 <filter>format == "tabdel_medium"</filter>
419 <actions> 419 <actions>
420 <action name="column_names" type="metadata" default="Geneid,${alignment.element_identifier},Length" /> 420 <action name="column_names" type="metadata" default="Geneid,${alignment.element_identifier},Length" />
421 </actions> 421 </actions>
422 </data> 422 </data>
427 <filter>extended_parameters['R']</filter> 427 <filter>extended_parameters['R']</filter>
428 </data> 428 </data>
429 429
430 <data format="tabular" 430 <data format="tabular"
431 name="output_short" 431 name="output_short"
432 label="${tool.name} on ${on_string}"> 432 label="${tool.name} on ${on_string}: Counts">
433 <filter>format == "tabdel_short"</filter> 433 <filter>format == "tabdel_short"</filter>
434 <actions> 434 <actions>
435 <action name="column_names" type="metadata" default="Geneid,${alignment.element_identifier}" /> 435 <action name="column_names" type="metadata" default="Geneid,${alignment.element_identifier}" />
436 </actions> 436 </actions>
437 </data> 437 </data>
438 438
439 <data format="tabular" 439 <data format="tabular"
440 name="output_full" 440 name="output_full"
441 label="${tool.name} on ${on_string}: count table"> 441 label="${tool.name} on ${on_string}: Counts (with location)">
442 <filter>format == "tabdel_full"</filter> 442 <filter>format == "tabdel_full"</filter>
443 <actions> 443 <actions>
444 <action name="column_names" type="metadata" default="Geneid,Chr,Start,End,Strand,Length,${alignment.element_identifier}" /> 444 <action name="column_names" type="metadata" default="Geneid,Chr,Start,End,Strand,Length,${alignment.element_identifier}" />
445 </actions> 445 </actions>
446 </data> 446 </data>
447 447
448 <data format="tabular" 448 <data format="tabular"
449 name="output_summary" 449 name="output_summary"
450 label="${tool.name} on ${on_string}: summary"> 450 label="${tool.name} on ${on_string}: Summary">
451 <actions> 451 <actions>
452 <action name="column_names" type="metadata" default="Status,${alignment.element_identifier}" /> 452 <action name="column_names" type="metadata" default="Status,${alignment.element_identifier}" />
453 </actions> 453 </actions>
454 </data> 454 </data>
455 455
456 <data format="tabular" 456 <data format="tabular"
457 name="output_feature_lengths" 457 name="output_feature_lengths"
458 label="${tool.name} on ${on_string}: feature lengths"> 458 label="${tool.name} on ${on_string}: Feature lengths">
459 <filter>include_feature_length_file</filter> 459 <filter>include_feature_length_file</filter>
460 <actions> 460 <actions>
461 <action name="column_names" type="metadata" default="Feature,Length" /> 461 <action name="column_names" type="metadata" default="Feature,Length" />
462 </actions> 462 </actions>
463 </data> 463 </data>
464 464
465 <data name="output_jcounts" format="tabular" 465 <data name="output_jcounts" format="tabular"
466 label="${tool.name} on ${on_string}: junction counts"> 466 label="${tool.name} on ${on_string}: Junction counts">
467 <filter>extended_parameters['exon_exon_junction_read_counting_enabled']['count_exon_exon_junction_reads']</filter> 467 <filter>extended_parameters['exon_exon_junction_read_counting_enabled']['count_exon_exon_junction_reads']</filter>
468 <actions> 468 <actions>
469 <action name="column_names" type="metadata" 469 <action name="column_names" type="metadata"
470 default="PrimaryGene,SecondaryGene,Site1_chr,Site1_location,Site1_strand,Site2_chr,Site2_location,Site2_strand,${alignment.element_identifier}" /> 470 default="PrimaryGene,SecondaryGene,Site1_chr,Site1_location,Site1_strand,Site2_chr,Site2_location,Site2_strand,${alignment.element_identifier}" />
471 </actions> 471 </actions>