Mercurial > repos > iuc > spades_metaplasmidspades

comparison macros.xml @ 7:e5a3b75a271f draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 69c6e337e239e84ce8fec9cf9fb5d820136877b2
author iuc
date Tue, 23 Aug 2022 08:01:19 +0000
parents 4a01e0d2892c
children 037f9927c4ff
comparison
equal deleted inserted replaced
6:4a01e0d2892c 7:e5a3b75a271f
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 ${on_string}: Corrected reads">
628 <filter>'cr' in optional_output</filter> 628 <filter>'cr' in optional_output</filter>
629 <filter> operation_mode != '--only-assembler'</filter> 629 <filter>'operation_mode' not in vars() or operation_mode != '--only-assembler'</filter>
630 <discover_datasets pattern="(?P&lt;designation&gt;.+)\.fastq\.gz" format="fastq" directory="output/corrected"/> 630 <discover_datasets pattern="(?P&lt;designation&gt;.+)\.cor\.fastq\.gz" format="fastq" directory="output/corrected"/>
631 <discover_datasets pattern="(?P&lt;designation&gt;.+)\.fasta\.gz" format="fasta" directory="output/corrected"/> 631 <discover_datasets pattern="(?P&lt;designation&gt;.+)\.cor\.fasta\.gz" format="fasta" directory="output/corrected"/>
632 </collection> 632 </collection>
633 </xml> 633 </xml>
634 <xml name="out_cs"> 634 <xml name="out_cs">
635 <data name="out_cs" format="tabular" label="${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>