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comparison featurecounts.xml @ 4:2451333b004b draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 57dfb61ba50ecfbe8f1c624fdbe2d0a3a8deaa04
author iuc
date Thu, 26 Jan 2017 12:33:40 -0500
parents 711c80e57384
children e70afb590e50
comparison
equal deleted inserted replaced
3:711c80e57384 4:2451333b004b
384 <param name="alignment" value="featureCounts_input1.bam" ftype="bam" /> 384 <param name="alignment" value="featureCounts_input1.bam" ftype="bam" />
385 <param name="reference_gene_sets" value="featureCounts_guide.gff" ftype="gff" /> 385 <param name="reference_gene_sets" value="featureCounts_guide.gff" ftype="gff" />
386 <param name="format" value="tabdel_short" /> 386 <param name="format" value="tabdel_short" />
387 <param name="include_feature_length_file" value="true"/> 387 <param name="include_feature_length_file" value="true"/>
388 <param name="ref_source" value="history" /> 388 <param name="ref_source" value="history" />
389 <output name="output" file="output_1_short.tab"/> 389 <output name="output_short" file="output_1_short.tab">
390 <metadata name="column_names" value="Geneid,featureCounts_input1.bam"/>
391 </output>
390 <output name="output_summary" file="output_1_summary.tab"/> 392 <output name="output_summary" file="output_1_summary.tab"/>
391 </test> 393 </test>
392 <test> 394 <test>
393 <param name="alignment" value="featureCounts_input1.bam" ftype="bam" /> 395 <param name="alignment" value="featureCounts_input1.bam" ftype="bam" />
394 <param name="reference_gene_sets" value="featureCounts_guide.gff" ftype="gff" /> 396 <param name="reference_gene_sets" value="featureCounts_guide.gff" ftype="gff" />
395 <param name="format" value="tabdel_medium" /> 397 <param name="format" value="tabdel_medium" />
396 <param name="include_feature_length_file" value="true"/> 398 <param name="include_feature_length_file" value="true"/>
397 <param name="ref_source" value="history" /> 399 <param name="ref_source" value="history" />
398 <output name="output" file="output_1_medium.tab"/> 400 <output name="output_medium" file="output_1_medium.tab">
399 <output name="output_summary" file="output_1_summary.tab"/> 401 <metadata name="column_names" value="Geneid,featureCounts_input1.bam,Length"/>
402 </output>
403 <output name="output_summary" file="output_1_summary.tab">
404 <metadata name="column_names" value="Status,featureCounts_input1.bam"/>
405 </output>
400 </test> 406 </test>
401 <test> 407 <test>
402 <param name="alignment" value="featureCounts_input1.bam" ftype="bam" /> 408 <param name="alignment" value="featureCounts_input1.bam" ftype="bam" />
403 <param name="reference_gene_sets" value="featureCounts_guide.gff" ftype="gff" /> 409 <param name="reference_gene_sets" value="featureCounts_guide.gff" ftype="gff" />
404 <param name="format" value="tabdel_full" /> 410 <param name="format" value="tabdel_full" />
405 <param name="include_feature_length_file" value="true"/> 411 <param name="include_feature_length_file" value="true"/>
406 <param name="ref_source" value="history" /> 412 <param name="ref_source" value="history" />
407 <output name="output" file="output_1_full.tab"/> 413 <output name="output_full" file="output_1_full.tab">
408 <output name="output_summary" file="output_1_summary.tab"/> 414 <metadata name="column_names" value="Geneid,Chr,Start,End,Strand,Length,featureCounts_input1.bam"/>
409 <output name="output_feature_lengths" file="output_feature_lengths.tab"/> 415 </output>
416 <output name="output_summary" file="output_1_summary.tab">
417 <metadata name="column_names" value="Status,featureCounts_input1.bam"/>
418 </output>
419 <output name="output_feature_lengths" file="output_feature_lengths.tab">
420 <metadata name="column_names" value="Feature,Length"/>
421 </output>
410 </test> 422 </test>
411 423
412 <test> 424 <test>
413 <param name="alignment" value="featureCounts_input1.bam" ftype="bam" /> 425 <param name="alignment" value="featureCounts_input1.bam" ftype="bam" />
414 <param name="reference_gene_sets" value="featureCounts_guide.gff" ftype="gff" /> 426 <param name="reference_gene_sets" value="featureCounts_guide.gff" ftype="gff" />
415 <param name="format" value="tabdel_short" /> 427 <param name="format" value="tabdel_short" />
416 <param name="include_feature_length_file" value="true"/> 428 <param name="include_feature_length_file" value="true"/>
417 <param name="ref_source" value="history" /> 429 <param name="ref_source" value="history" />
418 <output name="output" file="output_2_short.tab"/> 430 <output name="output_short" file="output_2_short.tab">
419 <output name="output_summary" file="output_2_summary.tab"/> 431 <metadata name="column_names" value="Geneid,featureCounts_input1.bam"/>
432 </output>
433 <output name="output_summary" file="output_2_summary.tab">
434 <metadata name="column_names" value="Status,featureCounts_input1.bam"/>
435 </output>
420 </test> 436 </test>
421 <test> 437 <test>
422 <param name="alignment" value="featureCounts_input1.bam" ftype="bam" /> 438 <param name="alignment" value="featureCounts_input1.bam" ftype="bam" />
423 <param name="reference_gene_sets" value="featureCounts_guide.gff" ftype="gff" /> 439 <param name="reference_gene_sets" value="featureCounts_guide.gff" ftype="gff" />
424 <param name="format" value="tabdel_medium" /> 440 <param name="format" value="tabdel_medium" />
425 <param name="include_feature_length_file" value="true"/> 441 <param name="include_feature_length_file" value="true"/>
426 <param name="ref_source" value="history" /> 442 <param name="ref_source" value="history" />
427 <output name="output" file="output_2_medium.tab"/> 443 <output name="output_medium" file="output_2_medium.tab">
428 <output name="output_summary" file="output_2_summary.tab"/> 444 <metadata name="column_names" value="Geneid,featureCounts_input1.bam,Length"/>
445 </output>
446 <output name="output_summary" file="output_2_summary.tab">
447 <metadata name="column_names" value="Status,featureCounts_input1.bam"/>
448 </output>
429 </test> 449 </test>
430 <test> 450 <test>
431 <param name="alignment" value="featureCounts_input1.bam" ftype="bam" /> 451 <param name="alignment" value="featureCounts_input1.bam" ftype="bam" />
432 <param name="reference_gene_sets" value="featureCounts_guide.gff" ftype="gff" /> 452 <param name="reference_gene_sets" value="featureCounts_guide.gff" ftype="gff" />
433 <param name="format" value="tabdel_full" /> 453 <param name="format" value="tabdel_full" />
434 <param name="include_feature_length_file" value="true"/> 454 <param name="include_feature_length_file" value="true"/>
435 <param name="ref_source" value="history" /> 455 <param name="ref_source" value="history" />
436 <output name="output" file="output_2_full.tab"/> 456 <output name="output_full" file="output_2_full.tab">
437 <output name="output_summary" file="output_2_summary.tab"/> 457 <metadata name="column_names" value="Geneid,Chr,Start,End,Strand,Length,featureCounts_input1.bam"/>
438 <output name="output_feature_lengths" file="output_feature_lengths.tab"/> 458 </output>
459 <output name="output_summary" file="output_2_summary.tab">
460 <metadata name="column_names" value="Status,featureCounts_input1.bam"/>
461 </output>
462 <output name="output_feature_lengths" file="output_feature_lengths.tab">
463 <metadata name="column_names" value="Feature,Length"/>
464 </output>
439 </test> 465 </test>
440 </tests> 466 </tests>
441 467
442 <help><![CDATA[ 468 <help><![CDATA[
443 featureCounts 469 featureCounts