Mercurial > repos > devteam > bowtie2
comparison bowtie2_wrapper.xml @ 23:17062a0decb7 draft
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 |
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| 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 --> |