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comparison featurecounts.xml @ 7:889d2cd8a809 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit a705dfd329f2e917d549215715385f5ef5001d17
author iuc
date Mon, 30 Oct 2017 14:48:57 -0400
parents e70afb590e50
children bff059ad4d13
comparison
equal deleted inserted replaced
6:e70afb590e50 7:889d2cd8a809
28 $extended_parameters.multimapping_enabled.fraction 28 $extended_parameters.multimapping_enabled.fraction
29 #end if 29 #end if
30 30
31 $extended_parameters.exon_exon_junction_read_counting_enabled.count_exon_exon_junction_reads 31 $extended_parameters.exon_exon_junction_read_counting_enabled.count_exon_exon_junction_reads
32 #if str($extended_parameters.exon_exon_junction_read_counting_enabled.count_exon_exon_junction_reads) == "-J" 32 #if str($extended_parameters.exon_exon_junction_read_counting_enabled.count_exon_exon_junction_reads) == "-J"
33 -G '$extended_parameters.exon_exon_junction_read_counting_enabled.genome' 33 #if $extended_parameters.exon_exon_junction_read_counting_enabled.genome
34 -G '$extended_parameters.exon_exon_junction_read_counting_enabled.genome'
35 #end if
34 #end if 36 #end if
35 37
36 $extended_parameters.long_reads 38 $extended_parameters.long_reads
37 39
38 -Q $extended_parameters.mapping_quality 40 -Q $extended_parameters.mapping_quality
272 <conditional name="exon_exon_junction_read_counting_enabled"> 274 <conditional name="exon_exon_junction_read_counting_enabled">
273 <param name="count_exon_exon_junction_reads" argument="-J" type="boolean" truevalue="-J" falsevalue="" 275 <param name="count_exon_exon_junction_reads" argument="-J" type="boolean" truevalue="-J" falsevalue=""
274 label="Exon-exon junctions" 276 label="Exon-exon junctions"
275 help="If specified, reads supporting each exon-exon junction will be counted" /> 277 help="If specified, reads supporting each exon-exon junction will be counted" />
276 <when value="-J"> 278 <when value="-J">
277 <param name="genome" argument="-G" type="data" format="fasta" 279 <param name="genome" argument="-G" type="data" format="fasta" optional="true"
278 label="Reference sequence (genome) file" 280 label="Reference sequence file"
279 help="The FASTA-format file that contains the reference sequences used in read mapping can be used to improve read counting for junctions" /> 281 help="The FASTA-format file that contains the reference sequences used in read mapping can be used to improve read counting for junctions" />
280 </when> 282 </when>
281 <when value="" /> 283 <when value="" />
282 </conditional> 284 </conditional>
283 285
395 </actions> 397 </actions>
396 </data> 398 </data>
397 399
398 <data name="output_jcounts" format="tabular" 400 <data name="output_jcounts" format="tabular"
399 label="${tool.name} on ${on_string}: junction counts"> 401 label="${tool.name} on ${on_string}: junction counts">
400 <filter>extended_parameters.exon_exon_junction_read_counting_enabled.count_exon_exon_junction_reads == " -J"</filter> 402 <filter>extended_parameters['exon_exon_junction_read_counting_enabled']['count_exon_exon_junction_reads']</filter>
401 <actions> 403 <actions>
402 <action name="column_names" type="metadata" default="PrimaryGene,SecondaryGene,Site1_chr,Site1_location,Site1_strand,Site2_chr,Site2_location,Site2_strand,${alignment.name}" /> 404 <action name="column_names" type="metadata" default="PrimaryGene,SecondaryGene,Site1_chr,Site1_location,Site1_strand,Site2_chr,Site2_location,Site2_strand,${alignment.name}" />
403 </actions> 405 </actions>
404 </data> 406 </data>
405 </outputs> 407 </outputs>
406 <tests> 408 <tests>
407 <test> 409 <test expect_num_outputs="4">
408 <param name="alignment" value="featureCounts_input1.bam" ftype="bam" /> 410 <param name="alignment" value="featureCounts_input1.bam" ftype="bam" />
409 <param name="reference_gene_sets" value="featureCounts_guide.gff" ftype="gff" /> 411 <param name="reference_gene_sets" value="featureCounts_guide.gff" ftype="gff" />
410 <param name="format" value="tabdel_short" /> 412 <param name="format" value="tabdel_short" />
411 <param name="include_feature_length_file" value="true"/> 413 <param name="include_feature_length_file" value="true"/>
412 <param name="ref_source" value="history" /> 414 <param name="ref_source" value="history" />
415 <param name="count_exon_exon_junction_reads" value="-J"/>
413 <output name="output_short" file="output_1_short.tab"> 416 <output name="output_short" file="output_1_short.tab">
414 <metadata name="column_names" value="Geneid,featureCounts_input1.bam"/> 417 <metadata name="column_names" value="Geneid,featureCounts_input1.bam"/>
415 </output> 418 </output>
416 <output name="output_summary" file="output_1_summary.tab"/> 419 <output name="output_summary" file="output_1_summary.tab">
420 <metadata name="column_names" value="Status,featureCounts_input1.bam"/>
421 </output>
422 <output name="output_jcounts" file="output_1_jcounts.tab">
423 <metadata name="column_names" value="PrimaryGene,SecondaryGene,Site1_chr,Site1_location,Site1_strand,Site2_chr,Site2_location,Site2_strand,featureCounts_input1.bam"/>
424 </output>
417 </test> 425 </test>
418 <test> 426 <test expect_num_outputs="3">
419 <param name="alignment" value="featureCounts_input1.bam" ftype="bam" /> 427 <param name="alignment" value="featureCounts_input1.bam" ftype="bam" />
420 <param name="reference_gene_sets" value="featureCounts_guide.gff" ftype="gff" /> 428 <param name="reference_gene_sets" value="featureCounts_guide.gff" ftype="gff" />
421 <param name="format" value="tabdel_medium" /> 429 <param name="format" value="tabdel_medium" />
422 <param name="include_feature_length_file" value="true"/> 430 <param name="include_feature_length_file" value="true"/>
423 <param name="ref_source" value="history" /> 431 <param name="ref_source" value="history" />
426 </output> 434 </output>
427 <output name="output_summary" file="output_1_summary.tab"> 435 <output name="output_summary" file="output_1_summary.tab">
428 <metadata name="column_names" value="Status,featureCounts_input1.bam"/> 436 <metadata name="column_names" value="Status,featureCounts_input1.bam"/>
429 </output> 437 </output>
430 </test> 438 </test>
431 <test> 439 <test expect_num_outputs="3">
432 <param name="alignment" value="featureCounts_input1.bam" ftype="bam" /> 440 <param name="alignment" value="featureCounts_input1.bam" ftype="bam" />
433 <param name="reference_gene_sets" value="featureCounts_guide.gff" ftype="gff" /> 441 <param name="reference_gene_sets" value="featureCounts_guide.gff" ftype="gff" />
434 <param name="format" value="tabdel_full" /> 442 <param name="format" value="tabdel_full" />
435 <param name="include_feature_length_file" value="true"/> 443 <param name="include_feature_length_file" value="true"/>
436 <param name="ref_source" value="history" /> 444 <param name="ref_source" value="history" />
443 <output name="output_feature_lengths" file="output_feature_lengths.tab"> 451 <output name="output_feature_lengths" file="output_feature_lengths.tab">
444 <metadata name="column_names" value="Feature,Length"/> 452 <metadata name="column_names" value="Feature,Length"/>
445 </output> 453 </output>
446 </test> 454 </test>
447 455
448 <test>
449 <param name="alignment" value="featureCounts_input1.bam" ftype="bam" />
450 <param name="reference_gene_sets" value="featureCounts_guide.gff" ftype="gff" />
451 <param name="format" value="tabdel_short" />
452 <param name="include_feature_length_file" value="true"/>
453 <param name="ref_source" value="history" />
454 <output name="output_short" file="output_2_short.tab">
455 <metadata name="column_names" value="Geneid,featureCounts_input1.bam"/>
456 </output>
457 <output name="output_summary" file="output_2_summary.tab">
458 <metadata name="column_names" value="Status,featureCounts_input1.bam"/>
459 </output>
460 </test>
461 <test>
462 <param name="alignment" value="featureCounts_input1.bam" ftype="bam" />
463 <param name="reference_gene_sets" value="featureCounts_guide.gff" ftype="gff" />
464 <param name="format" value="tabdel_medium" />
465 <param name="include_feature_length_file" value="true"/>
466 <param name="ref_source" value="history" />
467 <output name="output_medium" file="output_2_medium.tab">
468 <metadata name="column_names" value="Geneid,featureCounts_input1.bam,Length"/>
469 </output>
470 <output name="output_summary" file="output_2_summary.tab">
471 <metadata name="column_names" value="Status,featureCounts_input1.bam"/>
472 </output>
473 </test>
474 <test>
475 <param name="alignment" value="featureCounts_input1.bam" ftype="bam" />
476 <param name="reference_gene_sets" value="featureCounts_guide.gff" ftype="gff" />
477 <param name="format" value="tabdel_full" />
478 <param name="include_feature_length_file" value="true"/>
479 <param name="ref_source" value="history" />
480 <output name="output_full" file="output_2_full.tab">
481 <metadata name="column_names" value="Geneid,Chr,Start,End,Strand,Length,featureCounts_input1.bam"/>
482 </output>
483 <output name="output_summary" file="output_2_summary.tab">
484 <metadata name="column_names" value="Status,featureCounts_input1.bam"/>
485 </output>
486 <output name="output_feature_lengths" file="output_feature_lengths.tab">
487 <metadata name="column_names" value="Feature,Length"/>
488 </output>
489 </test>
490 </tests> 456 </tests>
491 457
492 <help><![CDATA[ 458 <help><![CDATA[
493 featureCounts 459 featureCounts
494 ############# 460 #############