Mercurial > repos > iuc > spades_coronaspades
comparison macros.xml @ 8:34305b013402 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 69c6e337e239e84ce8fec9cf9fb5d820136877b2
| author | iuc |
|---|---|
| date | Tue, 23 Aug 2022 08:01:45 +0000 |
| parents | ff41a00a6745 |
| children | 9678993ca5bd |
comparison
equal
deleted
inserted
replaced
| 7:ff41a00a6745 | 8:34305b013402 |
|---|---|
| 599 --> | 599 --> |
| 600 | 600 |
| 601 <xml name="out_ag"> | 601 <xml name="out_ag"> |
| 602 <data name="out_ag" format="fastg" from_work_dir="output/assembly_graph.fastg" label="${tool.name} on ${on_string}: Assembly graph"> | 602 <data name="out_ag" format="fastg" from_work_dir="output/assembly_graph.fastg" label="${tool.name} on ${on_string}: Assembly graph"> |
| 603 <filter>'ag' in optional_output</filter> | 603 <filter>'ag' in optional_output</filter> |
| 604 <filter> operation_mode != '--only-error-correction'</filter> | 604 <filter>'operation_mode' not in vars() or operation_mode != '--only-error-correction'</filter> |
| 605 </data> | 605 </data> |
| 606 </xml> | 606 </xml> |
| 607 <xml name="out_ags"> | 607 <xml name="out_ags"> |
| 608 <data name="out_ags" format="txt" from_work_dir="output/assembly_graph_with_scaffolds.gfa" label="${tool.name} on ${on_string}: Assembly graph with scaffolds"> | 608 <data name="out_ags" format="txt" from_work_dir="output/assembly_graph_with_scaffolds.gfa" label="${tool.name} on ${on_string}: Assembly graph with scaffolds"> |
| 609 <filter>'ags' in optional_output</filter> | 609 <filter>'ags' in optional_output</filter> |
| 610 <filter> operation_mode != '--only-error-correction'</filter> | 610 <filter>'operation_mode' not in vars() or operation_mode != '--only-error-correction'</filter> |
| 611 </data> | 611 </data> |
| 612 </xml> | 612 </xml> |
| 613 <xml name="out_cn"> | 613 <xml name="out_cn"> |
| 614 <data name="out_cn" format="fasta" from_work_dir="output/contigs.fasta" label="${tool.name} on ${on_string}: Contigs"> | 614 <data name="out_cn" format="fasta" from_work_dir="output/contigs.fasta" label="${tool.name} on ${on_string}: Contigs"> |
| 615 <filter>'cn' in optional_output</filter> | 615 <filter>'cn' in optional_output</filter> |
| 616 <filter> operation_mode != '--only-error-correction'</filter> | 616 <filter>'operation_mode' not in vars() or operation_mode != '--only-error-correction'</filter> |
| 617 </data> | 617 </data> |
| 618 </xml> | 618 </xml> |
| 619 <xml name="out_cp"> | 619 <xml name="out_cp"> |
| 620 <data name="out_cp" format="txt" from_work_dir="output/contigs.paths" label="${tool.name} on ${on_string}: Contigs paths"> | 620 <data name="out_cp" format="txt" from_work_dir="output/contigs.paths" label="${tool.name} on ${on_string}: Contigs paths"> |
| 621 <filter>'cp' in optional_output</filter> | 621 <filter>'cp' in optional_output</filter> |
| 622 <filter> operation_mode != '--only-error-correction'</filter> | 622 <filter>'operation_mode' not in vars() or operation_mode != '--only-error-correction'</filter> |
| 623 </data> | 623 </data> |
| 624 </xml> | 624 </xml> |
| 625 <xml name="out_cr"> | 625 <xml name="out_cr"> |
| 626 <!-- some mode combinations create fastq, some fasta --> | 626 <!-- some mode combinations create fastq, some fasta --> |
| 627 <collection name="out_cr" type="list" label="${tool.name} on ${on_string}: Corrected reads"> | 627 <collection name="out_cr" type="list" label="${tool.name} on ${on_string}: Corrected reads"> |
| 628 <filter>'cr' in optional_output</filter> | 628 <filter>'cr' in optional_output</filter> |
| 629 <filter> operation_mode != '--only-assembler'</filter> | 629 <filter>'operation_mode' not in vars() or operation_mode != '--only-assembler'</filter> |
| 630 <discover_datasets pattern="(?P<designation>.+)\.fastq\.gz" format="fastq" directory="output/corrected"/> | 630 <discover_datasets pattern="(?P<designation>.+)\.cor\.fastq\.gz" format="fastq" directory="output/corrected"/> |
| 631 <discover_datasets pattern="(?P<designation>.+)\.fasta\.gz" format="fasta" directory="output/corrected"/> | 631 <discover_datasets pattern="(?P<designation>.+)\.cor\.fasta\.gz" format="fasta" directory="output/corrected"/> |
| 632 </collection> | 632 </collection> |
| 633 </xml> | 633 </xml> |
| 634 <xml name="out_cs"> | 634 <xml name="out_cs"> |
| 635 <data name="out_cs" format="tabular" label="${tool.name} on ${on_string}: Contigs stats"> | 635 <data name="out_cs" format="tabular" label="${tool.name} on ${on_string}: Contigs stats"> |
| 636 <actions> | 636 <actions> |
| 637 <action name="column_names" type="metadata" default="name,length,coverage"/> | 637 <action name="column_names" type="metadata" default="name,length,coverage"/> |
| 638 </actions> | 638 </actions> |
| 639 <filter>'cs' in optional_output</filter> | 639 <filter>'cs' in optional_output</filter> |
| 640 <filter> operation_mode != '--only-error-correction'</filter> | 640 <filter>'operation_mode' not in vars() or operation_mode != '--only-error-correction'</filter> |
| 641 </data> | 641 </data> |
| 642 </xml> | 642 </xml> |
| 643 <xml name="out_l"> | 643 <xml name="out_l"> |
| 644 <data name="out_l" format="txt" from_work_dir="output/spades.log" label="${tool.name} on ${on_string}: Log"> | 644 <data name="out_l" format="txt" from_work_dir="output/spades.log" label="${tool.name} on ${on_string}: Log"> |
| 645 <filter>'l' in optional_output</filter> | 645 <filter>'l' in optional_output</filter> |
| 646 </data> | 646 </data> |
| 647 </xml> | 647 </xml> |
| 648 <xml name="out_sc"> | 648 <xml name="out_sc"> |
| 649 <data name="out_sc" format="fasta" from_work_dir="output/scaffolds.fasta" label="${tool.name} on ${on_string}: Scaffolds"> | 649 <data name="out_sc" format="fasta" from_work_dir="output/scaffolds.fasta" label="${tool.name} on ${on_string}: Scaffolds"> |
| 650 <filter>'sc' in optional_output</filter> | 650 <filter>'sc' in optional_output</filter> |
| 651 <filter> operation_mode != '--only-error-correction'</filter> | 651 <filter>'operation_mode' not in vars() or operation_mode != '--only-error-correction'</filter> |
| 652 </data> | 652 </data> |
| 653 </xml> | 653 </xml> |
| 654 <xml name="out_sp"> | 654 <xml name="out_sp"> |
| 655 <data name="out_sp" format="txt" from_work_dir="output/scaffolds.paths" label="${tool.name} on ${on_string}: Scaffolds paths"> | 655 <data name="out_sp" format="txt" from_work_dir="output/scaffolds.paths" label="${tool.name} on ${on_string}: Scaffolds paths"> |
| 656 <filter>'sp' in optional_output</filter> | 656 <filter>'sp' in optional_output</filter> |
| 657 <filter> operation_mode != '--only-error-correction'</filter> | 657 <filter>'operation_mode' not in vars() or operation_mode != '--only-error-correction'</filter> |
| 658 </data> | 658 </data> |
| 659 </xml> | 659 </xml> |
| 660 <xml name="out_ss"> | 660 <xml name="out_ss"> |
| 661 <data name="out_ss" format="tabular" label="${tool.name} on ${on_string}: Scaffolds stats"> | 661 <data name="out_ss" format="tabular" label="${tool.name} on ${on_string}: Scaffolds stats"> |
| 662 <actions> | 662 <actions> |
| 663 <action name="column_names" type="metadata" default="name,length,coverage"/> | 663 <action name="column_names" type="metadata" default="name,length,coverage"/> |
| 664 </actions> | 664 </actions> |
| 665 <filter>'ss' in optional_output</filter> | 665 <filter>'ss' in optional_output</filter> |
| 666 <filter> operation_mode != '--only-error-correction'</filter> | 666 <filter>'operation_mode' not in vars() or operation_mode != '--only-error-correction'</filter> |
| 667 </data> | 667 </data> |
| 668 </xml> | 668 </xml> |
| 669 <xml name="out_rs"> | 669 <xml name="out_rs"> |
| 670 <data name="out_rs" format="fasta" from_work_dir="output/raw_scaffolds.fasta" label="${tool.name} on ${on_string}: Raw scaffolds"> | 670 <data name="out_rs" format="fasta" from_work_dir="output/raw_scaffolds.fasta" label="${tool.name} on ${on_string}: Raw scaffolds"> |
| 671 <filter>'rs' in optional_output</filter> | 671 <filter>'rs' in optional_output</filter> |