Mercurial > repos > iuc > tooldistillator
comparison tooldistillator.xml @ 2:a7387ce2a8ca draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit d7cada7ddf775e946e218fdc839e6e4c8aac6d80
| author | iuc |
|---|---|
| date | Wed, 03 Jul 2024 12:06:58 +0000 |
| parents | 65a69de1e294 |
| children | 8d6686664021 |
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| 1:65a69de1e294 | 2:a7387ce2a8ca |
|---|---|
| 77 #elif $tool.select_tool.tool_list == 'bandage': | 77 #elif $tool.select_tool.tool_list == 'bandage': |
| 78 #if $tool.select_tool.bandage_plot_path | 78 #if $tool.select_tool.bandage_plot_path |
| 79 --bandage_plot_path '$tool.select_tool.bandage_plot_path' | 79 --bandage_plot_path '$tool.select_tool.bandage_plot_path' |
| 80 --bandage_plot_hid '$tool.select_tool.bandage_plot_path.hid' | 80 --bandage_plot_hid '$tool.select_tool.bandage_plot_path.hid' |
| 81 #end if | 81 #end if |
| 82 #elif $tool.select_tool.tool_list == 'bwa': | |
| 83 #if $tool.select_tool.paired_second_file_path | |
| 84 --paired_second_file_path '$tool.select_tool.paired_second_file_path' | |
| 85 --paired_second_file_hid '$tool.select_tool.paired_second_file_path.hid' | |
| 86 #end if | |
| 82 #elif $tool.select_tool.tool_list == 'bracken': | 87 #elif $tool.select_tool.tool_list == 'bracken': |
| 83 #if $tool.select_tool.kraken_report_path | 88 #if $tool.select_tool.kraken_report_path |
| 84 --kraken_report_path '$tool.select_tool.kraken_report_path' | 89 --kraken_report_path '$tool.select_tool.kraken_report_path' |
| 85 --kraken_report_hid '$tool.select_tool.kraken_report_path.hid' | 90 --kraken_report_hid '$tool.select_tool.kraken_report_path.hid' |
| 86 #end if | 91 #end if |
| 97 --trimmed_reverse_R2_hid '$tool.select_tool.trimmed_reverse_R2_path.hid' | 102 --trimmed_reverse_R2_hid '$tool.select_tool.trimmed_reverse_R2_path.hid' |
| 98 #end if | 103 #end if |
| 99 #if $tool.select_tool.html_report_path | 104 #if $tool.select_tool.html_report_path |
| 100 --html_report_path '$tool.select_tool.html_report_path' | 105 --html_report_path '$tool.select_tool.html_report_path' |
| 101 --html_report_hid '$tool.select_tool.html_report_path.hid' | 106 --html_report_hid '$tool.select_tool.html_report_path.hid' |
| 107 #end if | |
| 108 #elif $tool.select_tool.tool_list == 'fastqc': | |
| 109 #if $tool.select_tool.html_report_path | |
| 110 --html_report_path '$tool.select_tool.html_report_path' | |
| 111 --html_report_hid '$tool.select_tool.html_report_path.hid' | |
| 112 #end if | |
| 113 #elif $tool.select_tool.tool_list == 'flye': | |
| 114 #if $tool.select_tool.contig_graph_path | |
| 115 --contig_graph_path '$tool.select_tool.contig_graph_path' | |
| 116 --contig_graph_hid '$tool.select_tool.contig_graph_path.hid' | |
| 117 #end if | |
| 118 #if $tool.select_tool.tsv_file_path | |
| 119 --tsv_file_path '$tool.select_tool.tsv_file_path' | |
| 120 --tsv_file_hid '$tool.select_tool.tsv_file_path.hid' | |
| 102 #end if | 121 #end if |
| 103 #elif $tool.select_tool.tool_list == 'integronfinder2': | 122 #elif $tool.select_tool.tool_list == 'integronfinder2': |
| 104 #if $tool.select_tool.summary_file_path | 123 #if $tool.select_tool.summary_file_path |
| 105 --summary_file_path '$tool.select_tool.summary_file_path' | 124 --summary_file_path '$tool.select_tool.summary_file_path' |
| 106 --summary_file_hid '$tool.select_tool.summary_file_path.hid' | 125 --summary_file_hid '$tool.select_tool.summary_file_path.hid' |
| 203 <option value="abricate">Abricate</option> | 222 <option value="abricate">Abricate</option> |
| 204 <option value="amrfinderplus">AMRFinderPlus</option> | 223 <option value="amrfinderplus">AMRFinderPlus</option> |
| 205 <option value="bakta">Bakta</option> | 224 <option value="bakta">Bakta</option> |
| 206 <option value="bandage">Bandage</option> | 225 <option value="bandage">Bandage</option> |
| 207 <option value="bracken">Bracken</option> | 226 <option value="bracken">Bracken</option> |
| 227 <option value="bwa">BWA</option> | |
| 208 <option value="fastp">Fastp</option> | 228 <option value="fastp">Fastp</option> |
| 229 <option value="fastqc">Fastqc</option> | |
| 230 <option value="filtlong">Filtlong</option> | |
| 231 <option value="flye">Flye</option> | |
| 209 <option value="integronfinder2">Integronfinder2</option> | 232 <option value="integronfinder2">Integronfinder2</option> |
| 210 <option value="isescan">ISEScan</option> | 233 <option value="isescan">ISEScan</option> |
| 211 <option value="kraken2">Kraken2</option> | 234 <option value="kraken2">Kraken2</option> |
| 212 <option value="multiqc">MultiQC</option> | 235 <option value="multiqc">MultiQC</option> |
| 213 <option value="plasmidfinder">PlasmidFinder</option> | 236 <option value="plasmidfinder">PlasmidFinder</option> |
| 237 <option value="polypolish">Polypolish</option> | |
| 214 <option value="quast">Quast</option> | 238 <option value="quast">Quast</option> |
| 215 <option value="recentrifuge">Recentrifuge</option> | 239 <option value="recentrifuge">Recentrifuge</option> |
| 216 <option value="refseqmasher">RefSeqMasher</option> | 240 <option value="refseqmasher">RefSeqMasher</option> |
| 217 <option value="shovill">Shovill</option> | 241 <option value="shovill">Shovill</option> |
| 218 <option value="staramr">Staramr</option> | 242 <option value="staramr">Staramr</option> |
| 268 <option value="G">Genus</option> | 292 <option value="G">Genus</option> |
| 269 <option value="S">Species</option> | 293 <option value="S">Species</option> |
| 270 <option value="S+">Subspecies</option> | 294 <option value="S+">Subspecies</option> |
| 271 </param> | 295 </param> |
| 272 </when> | 296 </when> |
| 297 <when value="bwa"> | |
| 298 <param name="input" type="data" format="bam" multiple="false" label="BWA bam file" help="Bam file from BWA output"/> | |
| 299 <param argument="--paired_second_file_path" type="data" format="bam" multiple="false" optional="true" label="BWA second bam file" help="If paired inputs are used for BWA"/> | |
| 300 <expand macro="analysis_software_version"/> | |
| 301 <expand macro="reference_database_version"/> | |
| 302 </when> | |
| 273 <when value="fastp"> | 303 <when value="fastp"> |
| 274 <param name="input" type="data" format="json" multiple="false" label="Fastp report file" help="Fastp result in json format"/> | 304 <param name="input" type="data" format="json" multiple="false" label="Fastp report file" help="Fastp result in json format"/> |
| 275 <param argument="--trimmed_forward_R1_path" type="data" format="fastq,fastq.gz" optional="true" multiple="false" label="Fastp trimmed R1" help="trimmed file R1"/> | 305 <param argument="--trimmed_forward_R1_path" type="data" format="fastq,fastq.gz" optional="true" multiple="false" label="Fastp trimmed R1" help="trimmed file R1"/> |
| 276 <param argument="--trimmed_reverse_R2_path" type="data" format="fastq,fastq.gz" optional="true" multiple="false" label="Fastp trimmed R2" help="trimmed file R2"/> | 306 <param argument="--trimmed_reverse_R2_path" type="data" format="fastq,fastq.gz" optional="true" multiple="false" label="Fastp trimmed R2" help="trimmed file R2"/> |
| 277 <param argument="--html_report_path" type="data" format="html" multiple="false" optional="true" label="Fastp report html" help="Fastp result in html format"/> | 307 <param argument="--html_report_path" type="data" format="html" multiple="false" optional="true" label="Fastp report html" help="Fastp result in html format"/> |
| 308 <expand macro="analysis_software_version"/> | |
| 309 <expand macro="reference_database_version"/> | |
| 310 </when> | |
| 311 <when value="fastqc"> | |
| 312 <param name="input" type="data" format="txt,tabular" multiple="false" label="Fastqc report file" help="Fastqc result in txt format"/> | |
| 313 <param argument="--html_report_path" type="data" format="html" multiple="false" optional="true" label="Fastqc report html" help="Fastqc result in html format"/> | |
| 314 <expand macro="analysis_software_version"/> | |
| 315 <expand macro="reference_database_version"/> | |
| 316 </when> | |
| 317 <when value="filtlong"> | |
| 318 <param name="input" type="data" format="fastq,fastq.gz" multiple="false" label="Filtered long reads from Filtlong" help="Filtlong reads in fastq format"/> | |
| 319 <expand macro="analysis_software_version"/> | |
| 320 <expand macro="reference_database_version"/> | |
| 321 </when> | |
| 322 <when value="flye"> | |
| 323 <param name="input" type="data" format="fasta" multiple="false" label="Contigs file" help="Contig fasta file from assembly"/> | |
| 324 <param argument="--contig_graph_path" type="data" format="html" multiple="false" optional="true" label="Flye Graphical Fragment Assembly file" help="Assembly graph file from Flye"/> | |
| 325 <param argument="--tsv_file_path" type="data" format="txt,tabular" multiple="false" optional="true" label="Flye Assembly info file" help="Assembly info file from Flye"/> | |
| 278 <expand macro="analysis_software_version"/> | 326 <expand macro="analysis_software_version"/> |
| 279 <expand macro="reference_database_version"/> | 327 <expand macro="reference_database_version"/> |
| 280 </when> | 328 </when> |
| 281 <when value="integronfinder2"> | 329 <when value="integronfinder2"> |
| 282 <param name="input" type="data" format="txt,tabular" multiple="false" label="Integronfinder report" help="Integron file from integronfinder2"/> | 330 <param name="input" type="data" format="txt,tabular" multiple="false" label="Integronfinder report" help="Integron file from integronfinder2"/> |
| 308 <when value="plasmidfinder"> | 356 <when value="plasmidfinder"> |
| 309 <param name="input" type="data" format="json" multiple="false" label="Json report" help="Plasmidfinder result from json file"/> | 357 <param name="input" type="data" format="json" multiple="false" label="Json report" help="Plasmidfinder result from json file"/> |
| 310 <param argument="--plasmid_result_tabular_path" type="data" format="tabular" optional="true" multiple="false" label="Result in tabular format" help="Plasmid result in tabular format"/> | 358 <param argument="--plasmid_result_tabular_path" type="data" format="tabular" optional="true" multiple="false" label="Result in tabular format" help="Plasmid result in tabular format"/> |
| 311 <param argument="--genome_hit_path" type="data" format="fasta" optional="true" multiple="false" label="Genome hits" help="Sequence hit in the analyzed genome"/> | 359 <param argument="--genome_hit_path" type="data" format="fasta" optional="true" multiple="false" label="Genome hits" help="Sequence hit in the analyzed genome"/> |
| 312 <param argument="--plasmid_hit_path" type="data" format="fasta" optional="true" multiple="false" label="Plasmid hits" help="Plasmid sequence identified"/> | 360 <param argument="--plasmid_hit_path" type="data" format="fasta" optional="true" multiple="false" label="Plasmid hits" help="Plasmid sequence identified"/> |
| 361 <expand macro="analysis_software_version"/> | |
| 362 <expand macro="reference_database_version"/> | |
| 363 </when> | |
| 364 <when value="polypolish"> | |
| 365 <param name="input" type="data" format="fasta" multiple="false" label="Contigs file" help="Contig fasta file from Polypolish"/> | |
| 313 <expand macro="analysis_software_version"/> | 366 <expand macro="analysis_software_version"/> |
| 314 <expand macro="reference_database_version"/> | 367 <expand macro="reference_database_version"/> |
| 315 </when> | 368 </when> |
| 316 <when value="quast"> | 369 <when value="quast"> |
| 317 <param name="input" type="data" format="txt,tabular" multiple="false" label="Quast report" help="Tabular Quast report"/> | 370 <param name="input" type="data" format="txt,tabular" multiple="false" label="Quast report" help="Tabular Quast report"/> |
| 484 <param name="reference_database_version" value="1.0"/> | 537 <param name="reference_database_version" value="1.0"/> |
| 485 </conditional> | 538 </conditional> |
| 486 </repeat> | 539 </repeat> |
| 487 <repeat name="tools"> | 540 <repeat name="tools"> |
| 488 <conditional name="select_tool"> | 541 <conditional name="select_tool"> |
| 542 <param name="tool_list" value="bwa"/> | |
| 543 <param name="input" value="bwa/aligned_R1.bam" ftype="bam"/> | |
| 544 <param name="paired_second_file_path" value="bwa/aligned_R1.bam"/> | |
| 545 <param name="analysis_software_version" value="2.2.1"/> | |
| 546 <param name="reference_database_version" value="tests/data/dummy/flye/assembly.fasta"/> | |
| 547 </conditional> | |
| 548 </repeat> | |
| 549 <repeat name="tools"> | |
| 550 <conditional name="select_tool"> | |
| 489 <param name="tool_list" value="fastp"/> | 551 <param name="tool_list" value="fastp"/> |
| 490 <param name="input" value="fastp/fastp_report.json" ftype="json"/> | 552 <param name="input" value="fastp/fastp_report.json" ftype="json"/> |
| 491 <param name="trimmed_forward_R1_path" value="fastp/trimmed_R1.fastq.gz"/> | 553 <param name="trimmed_forward_R1_path" value="fastp/trimmed_R1.fastq.gz"/> |
| 492 <param name="trimmed_reverse_R2_path" value="fastp/trimmed_R2.fastq.gz"/> | 554 <param name="trimmed_reverse_R2_path" value="fastp/trimmed_R2.fastq.gz"/> |
| 493 <param name="html_report_path" value="fastp/fastp_report.html"/> | 555 <param name="html_report_path" value="fastp/fastp_report.html"/> |
| 494 <param name="analysis_software_version" value="1.0"/> | 556 <param name="analysis_software_version" value="1.0"/> |
| 495 <param name="reference_database_version" value="1.0"/> | 557 <param name="reference_database_version" value="1.0"/> |
| 558 </conditional> | |
| 559 </repeat> | |
| 560 <repeat name="tools"> | |
| 561 <conditional name="select_tool"> | |
| 562 <param name="tool_list" value="fastqc"/> | |
| 563 <param name="input" value="fastqc/fastqc_report.txt" ftype="txt"/> | |
| 564 <param name="html_report_path" value="fastqc/fastqc_report.html"/> | |
| 565 <param name="analysis_software_version" value="0.12.1"/> | |
| 566 <param name="reference_database_version" value=""/> | |
| 567 </conditional> | |
| 568 </repeat> | |
| 569 <repeat name="tools"> | |
| 570 <conditional name="select_tool"> | |
| 571 <param name="tool_list" value="filtlong"/> | |
| 572 <param name="input" value="filtlong/filtered_sample.fastq.gz" ftype="fastq.gz"/> | |
| 573 <param name="analysis_software_version" value="0.2.1"/> | |
| 574 <param name="reference_database_version" value=""/> | |
| 575 </conditional> | |
| 576 </repeat> | |
| 577 <repeat name="tools"> | |
| 578 <conditional name="select_tool"> | |
| 579 <param name="tool_list" value="flye"/> | |
| 580 <param name="input" value="flye/assembly.fasta" ftype="fasta"/> | |
| 581 <param name="contig_graph_path" value="flye/assembly.gfa" ftype="txt"/> | |
| 582 <param name="tsv_file_path" value="flye/assembly_infos.tsv" ftype="tabular"/> | |
| 583 <param name="analysis_software_version" value="2.9.1"/> | |
| 584 <param name="reference_database_version" value=""/> | |
| 496 </conditional> | 585 </conditional> |
| 497 </repeat> | 586 </repeat> |
| 498 <repeat name="tools"> | 587 <repeat name="tools"> |
| 499 <conditional name="select_tool"> | 588 <conditional name="select_tool"> |
| 500 <param name="tool_list" value="integronfinder2"/> | 589 <param name="tool_list" value="integronfinder2"/> |
| 536 <param name="reference_database_version" value="1.0"/> | 625 <param name="reference_database_version" value="1.0"/> |
| 537 </conditional> | 626 </conditional> |
| 538 </repeat> | 627 </repeat> |
| 539 <repeat name="tools"> | 628 <repeat name="tools"> |
| 540 <conditional name="select_tool"> | 629 <conditional name="select_tool"> |
| 630 <param name="tool_list" value="polypolish"/> | |
| 631 <param name="input" value="polypolish/polished_assembly.fasta" ftype="fasta"/> | |
| 632 <param name="analysis_software_version" value="0.2.1"/> | |
| 633 <param name="reference_database_version" value=""/> | |
| 634 </conditional> | |
| 635 </repeat> | |
| 636 <repeat name="tools"> | |
| 637 <conditional name="select_tool"> | |
| 541 <param name="tool_list" value="quast"/> | 638 <param name="tool_list" value="quast"/> |
| 542 <param name="input" value="quast/quast_result.tsv" ftype="tabular"/> | 639 <param name="input" value="quast/quast_result.tsv" ftype="tabular"/> |
| 543 <param name="quast_html_path" value="quast/quast_report.html"/> | 640 <param name="quast_html_path" value="quast/quast_report.html"/> |
| 544 <param name="analysis_software_version" value="1.0"/> | 641 <param name="analysis_software_version" value="0.5.0"/> |
| 545 <param name="reference_database_version" value="1.0"/> | 642 <param name="reference_database_version" value=""/> |
| 546 </conditional> | 643 </conditional> |
| 547 </repeat> | 644 </repeat> |
| 548 <repeat name="tools"> | 645 <repeat name="tools"> |
| 549 <conditional name="select_tool"> | 646 <conditional name="select_tool"> |
| 550 <param name="tool_list" value="recentrifuge"/> | 647 <param name="tool_list" value="recentrifuge"/> |
| 593 <param name="analysis_software_version" value="1.0"/> | 690 <param name="analysis_software_version" value="1.0"/> |
| 594 <param name="reference_database_version" value="1.0"/> | 691 <param name="reference_database_version" value="1.0"/> |
| 595 </conditional> | 692 </conditional> |
| 596 </repeat> | 693 </repeat> |
| 597 </section> | 694 </section> |
| 598 <output_collection name="output_json" type="list" count="16"> | 695 <output_collection name="output_json" type="list" count="21"> |
| 599 <expand macro="element_assert" name="abricate_0_output" text="Enterococcus faecalis V583"/> | 696 <expand macro="element_assert" name="abricate_0_output" text="Enterococcus faecalis V583"/> |
| 600 <expand macro="element_assert" name="amrfinderplus_1_output" text="mercury resistance transcriptional regulator MerR"/> | 697 <expand macro="element_assert" name="amrfinderplus_1_output" text="mercury resistance transcriptional regulator MerR"/> |
| 601 <expand macro="element_assert" name="bakta_2_output" text="hypothetical protein"/> | 698 <expand macro="element_assert" name="bakta_2_output" text="hypothetical protein"/> |
| 602 <expand macro="element_assert" name="bandage_3_output" text="3042326"/> | 699 <expand macro="element_assert" name="bandage_3_output" text="3042326"/> |
| 603 <expand macro="element_assert" name="bracken_4_output" text="Staphylococcus_aureus"/> | 700 <expand macro="element_assert" name="bracken_4_output" text="Staphylococcus_aureus"/> |
| 604 <expand macro="element_assert" name="fastp_5_output" text="705053822"/> | 701 <expand macro="element_assert" name="bwa_5_output" text="bwa_report"/> |
| 605 <expand macro="element_assert" name="integronfinder2_6_output" text="2353.0"/> | 702 <expand macro="element_assert" name="fastp_6_output" text="705053822"/> |
| 606 <expand macro="element_assert" name="isescan_7_output" text="IS200/IS605"/> | 703 <expand macro="element_assert" name="fastqc_7_output" text="Sequences flagged as poor quality"/> |
| 607 <expand macro="element_assert" name="kraken2_8_output" text="Enterococcus_faecalis"/> | 704 <expand macro="element_assert" name="filtlong_8_output" text="filtlong_report"/> |
| 608 <expand macro="element_assert" name="plasmidfinder_9_output" text="repUS40_1_repB"/> | 705 <expand macro="element_assert" name="flye_9_output" text="contig_2"/> |
| 609 <expand macro="element_assert" name="quast_10_output" text="2944723"/> | 706 <expand macro="element_assert" name="integronfinder2_10_output" text="2353.0"/> |
| 610 <expand macro="element_assert" name="recentrifuge_11_output" text="6.4917947578"/> | 707 <expand macro="element_assert" name="isescan_11_output" text="IS200/IS605"/> |
| 611 <expand macro="element_assert" name="refseqmasher_12_output" text="GCF_000519925.1"/> | 708 <expand macro="element_assert" name="kraken2_12_output" text="Enterococcus_faecalis"/> |
| 612 <expand macro="element_assert" name="shovill_13_output" text="436224"/> | 709 <expand macro="element_assert" name="plasmidfinder_13_output" text="repUS40_1_repB"/> |
| 613 <expand macro="element_assert" name="staramr_14_output" text="10_Enterococcus_faecalis_S17_L001"/> | 710 <expand macro="element_assert" name="polypolish_14_output" text="320811"/> |
| 614 <expand macro="element_assert" name="tabular_file_15_output" text="NP_814691"/> | 711 <expand macro="element_assert" name="quast_15_output" text="2944723"/> |
| 712 <expand macro="element_assert" name="recentrifuge_16_output" text="6.4917947578"/> | |
| 713 <expand macro="element_assert" name="refseqmasher_17_output" text="GCF_000519925.1"/> | |
| 714 <expand macro="element_assert" name="shovill_18_output" text="436224"/> | |
| 715 <expand macro="element_assert" name="staramr_19_output" text="10_Enterococcus_faecalis_S17_L001"/> | |
| 716 <expand macro="element_assert" name="tabular_file_20_output" text="NP_814691"/> | |
| 615 </output_collection> | 717 </output_collection> |
| 616 </test> | 718 </test> |
| 617 | 719 |
| 618 </tests> | 720 </tests> |
| 619 <help><![CDATA[ | 721 <help><![CDATA[ |
| 622 ToolDistillator is a tool to extract information from output files of specific tools, expose it as JSON files, and aggregate over several tools. | 724 ToolDistillator is a tool to extract information from output files of specific tools, expose it as JSON files, and aggregate over several tools. |
| 623 | 725 |
| 624 This tool here is extracting information from output files of specific tools and exposing it as JSON files | 726 This tool here is extracting information from output files of specific tools and exposing it as JSON files |
| 625 ** Tool input** | 727 ** Tool input** |
| 626 | 728 |
| 627 ToolDistillator can use several input type from at least 15 different tools : | 729 ToolDistillator can use several input type from at least 21 different tools and 1 generic tool for tabular file: |
| 628 | 730 |
| 629 +----------------+----------------+-------------------+------------------------------------------------------------+ | 731 +----------------+----------------+-------------------+------------------------------------------------------------+ |
| 630 | Tools | Version | Default input file| Optional files | | 732 | Tools | Version | Default input file| Optional files | |
| 631 +----------------+----------------+-------------------+------------------------------------------------------------+ | 733 +----------------+----------------+-------------------+------------------------------------------------------------+ |
| 632 | Abricate | 1.0.1 | output.tsv | | | 734 | Abricate | 1.0.1 | output.tsv | | |
| 637 +----------------+----------------+-------------------+------------------------------------------------------------+ | 739 +----------------+----------------+-------------------+------------------------------------------------------------+ |
| 638 | Bandage | 0.8.1 | info.txt | | | 740 | Bandage | 0.8.1 | info.txt | | |
| 639 +----------------+----------------+-------------------+------------------------------------------------------------+ | 741 +----------------+----------------+-------------------+------------------------------------------------------------+ |
| 640 | Bracken | 2.8 | output.tsv | taxonomy.tsv | | 742 | Bracken | 2.8 | output.tsv | taxonomy.tsv | |
| 641 +----------------+----------------+-------------------+------------------------------------------------------------+ | 743 +----------------+----------------+-------------------+------------------------------------------------------------+ |
| 744 | BWA | 2.2.1 | input1.bam | input2.bam | | |
| 745 +----------------+----------------+-------------------+------------------------------------------------------------+ | |
| 642 | Fastp | 0.23.2 | output.json | | | 746 | Fastp | 0.23.2 | output.json | | |
| 643 +----------------+----------------+-------------------+------------------------------------------------------------+ | 747 +----------------+----------------+-------------------+------------------------------------------------------------+ |
| 748 | Fastqc | 0.12.1 | report.txt | report.html | | |
| 749 +----------------+----------------+-------------------+------------------------------------------------------------+ | |
| 750 | Filtlong | 0.2.1 | input.fastq | | | |
| 751 +----------------+----------------+-------------------+------------------------------------------------------------+ | |
| 752 | Flye | 2.9.1 | contig.fasta | contig.gfa, infos.tsv | | |
| 753 +----------------+----------------+-------------------+------------------------------------------------------------+ | |
| 644 | Integronfinder2| 2.0.2 | output.integrons | output.summary | | 754 | Integronfinder2| 2.0.2 | output.integrons | output.summary | |
| 645 +----------------+----------------+-------------------+------------------------------------------------------------+ | 755 +----------------+----------------+-------------------+------------------------------------------------------------+ |
| 646 | ISEScan | 1.7.2.3 | output.tsv | is.fna, orf.faa, orf.fna | | 756 | ISEScan | 1.7.2.3 | output.tsv | is.fna, orf.faa, orf.fna | |
| 647 +----------------+----------------+-------------------+------------------------------------------------------------+ | 757 +----------------+----------------+-------------------+------------------------------------------------------------+ |
| 648 | Kraken2 | 2.1.2 | taxonomy.tsv | reads_assignation.txt | | 758 | Kraken2 | 2.1.2 | taxonomy.tsv | reads_assignation.txt | |
| 649 +----------------+----------------+-------------------+------------------------------------------------------------+ | 759 +----------------+----------------+-------------------+------------------------------------------------------------+ |
| 760 | MultiQC | 1.11 | report.html | no optional files | | |
| 761 +----------------+----------------+-------------------+------------------------------------------------------------+ | |
| 650 | PlasmidFinder | 2.1.6 | output.json | genome_hits.fasta, plasmid_hits.fasta | | 762 | PlasmidFinder | 2.1.6 | output.json | genome_hits.fasta, plasmid_hits.fasta | |
| 763 +----------------+----------------+-------------------+------------------------------------------------------------+ | |
| 764 | Polypolish | 0.5.0 | contig.fasta | | | |
| 651 +----------------+----------------+-------------------+------------------------------------------------------------+ | 765 +----------------+----------------+-------------------+------------------------------------------------------------+ |
| 652 | Quast | 5.2.0 | output.tsv | | | 766 | Quast | 5.2.0 | output.tsv | | |
| 653 +----------------+----------------+-------------------+------------------------------------------------------------+ | 767 +----------------+----------------+-------------------+------------------------------------------------------------+ |
| 654 | Recentrifuge | 1.10.0 | data.tsv | report.html, stat.tsv | | 768 | Recentrifuge | 1.10.0 | data.tsv | report.html, stat.tsv | |
| 655 +----------------+----------------+-------------------+------------------------------------------------------------+ | 769 +----------------+----------------+-------------------+------------------------------------------------------------+ |