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comparison featurecounts.xml @ 9:81e9f94f257c draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 4fb528145289ad4db04e4589c02e9ddaa1194138
author iuc
date Fri, 17 Nov 2017 06:02:40 -0500
parents bff059ad4d13
children 7d1e37c6ef85
comparison
equal deleted inserted replaced
8:bff059ad4d13 9:81e9f94f257c
1 <tool id="featurecounts" name="featureCounts" version="1.6.0" profile="16.04"> 1 <tool id="featurecounts" name="featureCounts" version="1.6.0.1" 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="1.6.0">subread</requirement> 4 <requirement type="package" version="1.6.0">subread</requirement>
5 </requirements> 5 </requirements>
6 6
382 <data format="tabular" 382 <data format="tabular"
383 name="output_medium" 383 name="output_medium"
384 label="${tool.name} on ${on_string}"> 384 label="${tool.name} on ${on_string}">
385 <filter>format == "tabdel_medium"</filter> 385 <filter>format == "tabdel_medium"</filter>
386 <actions> 386 <actions>
387 <action name="column_names" type="metadata" default="Geneid,${alignment.name},Length" /> 387 <action name="column_names" type="metadata" default="Geneid,${alignment.element_identifier},Length" />
388 </actions> 388 </actions>
389 </data> 389 </data>
390 390
391 <data format="tabular" 391 <data format="tabular"
392 name="output_short" 392 name="output_short"
393 label="${tool.name} on ${on_string}"> 393 label="${tool.name} on ${on_string}">
394 <filter>format == "tabdel_short"</filter> 394 <filter>format == "tabdel_short"</filter>
395 <actions> 395 <actions>
396 <action name="column_names" type="metadata" default="Geneid,${alignment.name}" /> 396 <action name="column_names" type="metadata" default="Geneid,${alignment.element_identifier}" />
397 </actions> 397 </actions>
398 </data> 398 </data>
399 399
400 <data format="tabular" 400 <data format="tabular"
401 name="output_full" 401 name="output_full"
402 label="${tool.name} on ${on_string}: count table"> 402 label="${tool.name} on ${on_string}: count table">
403 <filter>format == "tabdel_full"</filter> 403 <filter>format == "tabdel_full"</filter>
404 <actions> 404 <actions>
405 <action name="column_names" type="metadata" default="Geneid,Chr,Start,End,Strand,Length,${alignment.name}" /> 405 <action name="column_names" type="metadata" default="Geneid,Chr,Start,End,Strand,Length,${alignment.element_identifier}" />
406 </actions> 406 </actions>
407 </data> 407 </data>
408 408
409 <data format="tabular" 409 <data format="tabular"
410 name="output_summary" 410 name="output_summary"
411 hidden="true" 411 hidden="true"
412 label="${tool.name} on ${on_string}: summary"> 412 label="${tool.name} on ${on_string}: summary">
413 <actions> 413 <actions>
414 <action name="column_names" type="metadata" default="Status,${alignment.name}" /> 414 <action name="column_names" type="metadata" default="Status,${alignment.element_identifier}" />
415 </actions> 415 </actions>
416 </data> 416 </data>
417 417
418 <data format="tabular" 418 <data format="tabular"
419 name="output_feature_lengths" 419 name="output_feature_lengths"
426 426
427 <data name="output_jcounts" format="tabular" 427 <data name="output_jcounts" format="tabular"
428 label="${tool.name} on ${on_string}: junction counts"> 428 label="${tool.name} on ${on_string}: junction counts">
429 <filter>extended_parameters['exon_exon_junction_read_counting_enabled']['count_exon_exon_junction_reads']</filter> 429 <filter>extended_parameters['exon_exon_junction_read_counting_enabled']['count_exon_exon_junction_reads']</filter>
430 <actions> 430 <actions>
431 <action name="column_names" type="metadata" default="PrimaryGene,SecondaryGene,Site1_chr,Site1_location,Site1_strand,Site2_chr,Site2_location,Site2_strand,${alignment.name}" /> 431 <action name="column_names" type="metadata" default="PrimaryGene,SecondaryGene,Site1_chr,Site1_location,Site1_strand,Site2_chr,Site2_location,Site2_strand,${alignment.element_identifier}" />
432 </actions> 432 </actions>
433 </data> 433 </data>
434 </outputs> 434 </outputs>
435 <tests> 435 <tests>
436 <test expect_num_outputs="4"> 436 <test expect_num_outputs="4">