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comparison bowtie2_wrapper.xml @ 23:17062a0decb7 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit d611e968158b012c10d3f8b661af1f07313f06d7
author iuc
date Wed, 06 Jun 2018 17:23:32 -0400
parents c3dd1aeb7d07
children 017aba02828d
comparison
equal deleted inserted replaced
22:c3dd1aeb7d07 23:17062a0decb7
555 <action type="format"> 555 <action type="format">
556 <option type="from_param" name="library.input_1" param_attribute="forward.ext" /> 556 <option type="from_param" name="library.input_1" param_attribute="forward.ext" />
557 </action> 557 </action>
558 </when> 558 </when>
559 </conditional> 559 </conditional>
560 <expand macro="dbKeyActions" />
560 </actions> 561 </actions>
561 </data> 562 </data>
562 <data format="fastqsanger" name="output_aligned_reads_l" label="${tool.name} on ${on_string}: aligned reads (L)" > 563 <data format="fastqsanger" name="output_aligned_reads_l" label="${tool.name} on ${on_string}: aligned reads (L)" >
563 <filter>library['aligned_file'] is True</filter> 564 <filter>library['aligned_file'] is True</filter>
564 <actions> 565 <actions>
577 <action type="format"> 578 <action type="format">
578 <option type="from_param" name="library.input_1" param_attribute="forward.ext" /> 579 <option type="from_param" name="library.input_1" param_attribute="forward.ext" />
579 </action> 580 </action>
580 </when> 581 </when>
581 </conditional> 582 </conditional>
583 <expand macro="dbKeyActions" />
582 </actions> 584 </actions>
583 </data> 585 </data>
584 <data format="fastqsanger" name="output_aligned_reads_r" label="${tool.name} on ${on_string}: aligned reads (R)"> 586 <data format="fastqsanger" name="output_aligned_reads_r" label="${tool.name} on ${on_string}: aligned reads (R)">
585 <filter>( library['type'] == "paired" or library['type'] == "paired_collection" ) and library['aligned_file'] is True</filter> 587 <filter>( library['type'] == "paired" or library['type'] == "paired_collection" ) and library['aligned_file'] is True</filter>
586 <actions> 588 <actions>
594 <action type="format"> 596 <action type="format">
595 <option type="from_param" name="library.input_1" param_attribute="reverse.ext" /> 597 <option type="from_param" name="library.input_1" param_attribute="reverse.ext" />
596 </action> 598 </action>
597 </when> 599 </when>
598 </conditional> 600 </conditional>
601 <expand macro="dbKeyActions" />
599 </actions> 602 </actions>
600 </data> 603 </data>
601 <data format="fastqsanger" name="output_unaligned_reads_r" label="${tool.name} on ${on_string}: unaligned reads (R)"> 604 <data format="fastqsanger" name="output_unaligned_reads_r" label="${tool.name} on ${on_string}: unaligned reads (R)">
602 <filter>( library['type'] == "paired" or library['type'] == "paired_collection" ) and library['unaligned_file'] is True</filter> 605 <filter>( library['type'] == "paired" or library['type'] == "paired_collection" ) and library['unaligned_file'] is True</filter>
603 <actions> 606 <actions>
611 <action type="format"> 614 <action type="format">
612 <option type="from_param" name="library.input_1" param_attribute="reverse.ext" /> 615 <option type="from_param" name="library.input_1" param_attribute="reverse.ext" />
613 </action> 616 </action>
614 </when> 617 </when>
615 </conditional> 618 </conditional>
619 <expand macro="dbKeyActions" />
616 </actions> 620 </actions>
617 </data> 621 </data>
618 <data format="bam" name="output" label="${tool.name} on ${on_string}: aligned reads (BAM)"> 622 <data format="bam" name="output" label="${tool.name} on ${on_string}: aligned reads (BAM)">
619 <filter>analysis_type['analysis_type_selector'] == "simple" or analysis_type['sam_opt'] is False</filter> 623 <filter>analysis_type['analysis_type_selector'] == "simple" or analysis_type['sam_opt'] is False</filter>
620 <change_format> 624 <change_format>
634 <action type="metadata" name="dbkey"> 638 <action type="metadata" name="dbkey">
635 <option type="from_param" name="reference_genome.own_file" param_attribute="dbkey" /> 639 <option type="from_param" name="reference_genome.own_file" param_attribute="dbkey" />
636 </action> 640 </action>
637 </when> 641 </when>
638 </conditional> 642 </conditional>
643 <expand macro="dbKeyActions" />
639 </actions> 644 </actions>
640 </data> 645 </data>
641 <data format="sam" name="output_sam" label="${tool.name} on ${on_string}: aligned reads (SAM)"> 646 <data format="sam" name="output_sam" label="${tool.name} on ${on_string}: aligned reads (SAM)">
642 <filter>analysis_type['analysis_type_selector'] == "full" and analysis_type['sam_opt'] is True</filter> 647 <filter>analysis_type['analysis_type_selector'] == "full" and analysis_type['sam_opt'] is True</filter>
643 <actions> 648 <actions>
654 <action type="metadata" name="dbkey"> 659 <action type="metadata" name="dbkey">
655 <option type="from_param" name="reference_genome.own_file" param_attribute="dbkey" /> 660 <option type="from_param" name="reference_genome.own_file" param_attribute="dbkey" />
656 </action> 661 </action>
657 </when> 662 </when>
658 </conditional> 663 </conditional>
664 <expand macro="dbKeyActions" />
659 </actions> 665 </actions>
660 </data> 666 </data>
661 <data format="txt" name="mapping_stats" label="${tool.name} on ${on_string}: mapping stats"> 667 <data format="txt" name="mapping_stats" label="${tool.name} on ${on_string}: mapping stats">
662 <filter>save_mapping_stats is True</filter> 668 <filter>save_mapping_stats is True</filter>
669 <actions>
670 <expand macro="dbKeyActions" />
671 </actions>
663 </data> 672 </data>
664 </outputs> 673 </outputs>
665 <tests> 674 <tests>
666 <test> 675 <test>
667 <!-- test on paired-end datasets --> 676 <!-- test on paired-end datasets -->