Mercurial > repos > iuc > rgrnastar

comparison rg_rnaStar.xml @ 8:d5659efd66aa draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit be695260aa6fe507c80f932ea9b2e63b2662d167
author iuc
date Sat, 09 Jun 2018 14:33:39 -0400
parents a70a7eebb435
children 0a563fd2f22e
comparison
equal deleted inserted replaced
7:a70a7eebb435 8:d5659efd66aa
382 </when> 382 </when>
383 </conditional> 383 </conditional>
384 </inputs> 384 </inputs>
385 385
386 <outputs> 386 <outputs>
387 <data format="txt" name="output_log" label="${tool.name} on ${on_string}: log" from_work_dir="Log.final.out"/> 387 <data format="txt" name="output_log" label="${tool.name} on ${on_string}: log" from_work_dir="Log.final.out">
388 <expand macro="dbKeyActions" />
389 </data>
388 <data format="interval" name="chimeric_junctions" label="${tool.name} on ${on_string}: chimeric junctions" from_work_dir="Chimeric.out.junction"> 390 <data format="interval" name="chimeric_junctions" label="${tool.name} on ${on_string}: chimeric junctions" from_work_dir="Chimeric.out.junction">
389 <filter>params['settingsType'] == "star_fusion" or ( params['settingsType'] == "full" and params['chim']['chim_select'] == "yes" and params['chim']['chimSegmentMin'] > 0 )</filter> 391 <filter>params['settingsType'] == "star_fusion" or ( params['settingsType'] == "full" and params['chim']['chim_select'] == "yes" and params['chim']['chimSegmentMin'] > 0 )</filter>
390 <actions> 392 <expand macro="dbKeyActions" />
391 <conditional name="refGenomeSource.geneSource">
392 <when value="indexed">
393 <action type="metadata" name="dbkey">
394 <option type="from_data_table" name="rnastar_index" column="1" offset="0">
395 <filter type="param_value" column="0" value="#" compare="startswith" keep="False"/>
396 <filter type="param_value" ref="refGenomeSource.GTFconditional.genomeDir" column="0"/>
397 </option>
398 </action>
399 </when>
400 <when value="history">
401 <action type="metadata" name="dbkey">
402 <option type="from_param" name="refGenomeSource.genomeFastaFiles" param_attribute="dbkey" />
403 </action>
404 </when>
405 </conditional>
406 </actions>
407 </data> 393 </data>
408 394
409 <data format="bam" name="chimeric_reads" label="${tool.name} on ${on_string}: chimeric.bam" from_work_dir="ChimericSorted.bam"> 395 <data format="bam" name="chimeric_reads" label="${tool.name} on ${on_string}: chimeric.bam" from_work_dir="ChimericSorted.bam">
410 <filter>params['settingsType'] == "full" and params['chim']['chim_select'] == "yes" and params['chim']['chimSegmentMin'] > 0</filter> 396 <filter>params['settingsType'] == "full" and params['chim']['chim_select'] == "yes" and params['chim']['chimSegmentMin'] > 0</filter>
411 <actions> 397 <expand macro="dbKeyActions" />
412 <conditional name="refGenomeSource.geneSource">
413 <when value="indexed">
414 <action type="metadata" name="dbkey">
415 <option type="from_data_table" name="rnastar_index" column="1" offset="0">
416 <filter type="param_value" column="0" value="#" compare="startswith" keep="False"/>
417 <filter type="param_value" ref="refGenomeSource.GTFconditional.genomeDir" column="0"/>
418 </option>
419 </action>
420 </when>
421 <when value="history">
422 <action type="metadata" name="dbkey">
423 <option type="from_param" name="refGenomeSource.genomeFastaFiles" param_attribute="dbkey" />
424 </action>
425 </when>
426 </conditional>
427 </actions>
428 </data> 398 </data>
429 399
430 <data format="interval" name="splice_junctions" label="${tool.name} on ${on_string}: splice junctions.bed" from_work_dir="SJ.out.tab"> 400 <data format="interval" name="splice_junctions" label="${tool.name} on ${on_string}: splice junctions.bed" from_work_dir="SJ.out.tab">
431 <actions> 401 <expand macro="dbKeyActions" />
432 <conditional name="refGenomeSource.geneSource">
433 <when value="indexed">
434 <action type="metadata" name="dbkey">
435 <option type="from_data_table" name="rnastar_index" column="1" offset="0">
436 <filter type="param_value" column="0" value="#" compare="startswith" keep="False"/>
437 <filter type="param_value" ref="refGenomeSource.GTFconditional.genomeDir" column="0"/>
438 </option>
439 </action>
440 </when>
441 <when value="history">
442 <action type="metadata" name="dbkey">
443 <option type="from_param" name="refGenomeSource.genomeFastaFiles" param_attribute="dbkey" />
444 </action>
445 </when>
446 </conditional>
447 </actions>
448 </data> 402 </data>
449 403
450 <data name="mapped_reads" format="bam" label="${tool.name} on ${on_string}: mapped.bam" from_work_dir="Aligned.sortedByCoord.out.bam"> 404 <data name="mapped_reads" format="bam" label="${tool.name} on ${on_string}: mapped.bam" from_work_dir="Aligned.sortedByCoord.out.bam">
451 <actions> 405 <expand macro="dbKeyActions" />
452 <conditional name="refGenomeSource.geneSource">
453 <when value="indexed">
454 <action type="metadata" name="dbkey">
455 <option type="from_data_table" name="rnastar_index" column="1" offset="0">
456 <filter type="param_value" column="0" value="#" compare="startswith" keep="False"/>
457 <filter type="param_value" ref="refGenomeSource.GTFconditional.genomeDir" column="0"/>
458 </option>
459 </action>
460 </when>
461 <when value="history">
462 <action type="metadata" name="dbkey">
463 <option type="from_param" name="refGenomeSource.genomeFastaFiles" param_attribute="dbkey" />
464 </action>
465 </when>
466 </conditional>
467 </actions>
468 </data> 406 </data>
469 407
470 <data name="reads_per_gene" format="tabular" label="${tool.name} on ${on_string}: reads per gene" from_work_dir="ReadsPerGene.out.tab"> 408 <data name="reads_per_gene" format="tabular" label="${tool.name} on ${on_string}: reads per gene" from_work_dir="ReadsPerGene.out.tab">
471 <filter>quantMode is True</filter> 409 <filter>quantMode is True</filter>
410 <expand macro="dbKeyActions" />
472 </data> 411 </data>
473 </outputs> 412 </outputs>
474 413
475 <tests> 414 <tests>
476 <test> 415 <test>