abromics_galaxy_json_extractor: abromics_galaxy_json

annotate abromics_galaxy_json_extractor.xml @ 3:73aea20004ff draft default tip

planemo upload commit 8721cd95e02dd6b3a02e2eb549cd8ff6b1675ff8-dirty

author	pimarin
date	Sun, 23 Jul 2023 13:54:14 +0000
parents	421032d8dd5d
children

rev	line source
0 c49ec8c0b046 planemo upload commit bb69b191fe3ce756655bf90af4d69e4472f94ba9-dirty pimarin parents: diff changeset	1 <tool id="abromics_galaxy_json_extractor" name="abromics_galaxy_json_extractor" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
c49ec8c0b046 planemo upload commit bb69b191fe3ce756655bf90af4d69e4472f94ba9-dirty pimarin parents: diff changeset	2 <description>
c49ec8c0b046 planemo upload commit bb69b191fe3ce756655bf90af4d69e4472f94ba9-dirty pimarin parents: diff changeset	3 Result extractor to json format
c49ec8c0b046 planemo upload commit bb69b191fe3ce756655bf90af4d69e4472f94ba9-dirty pimarin parents: diff changeset	4 </description>
c49ec8c0b046 planemo upload commit bb69b191fe3ce756655bf90af4d69e4472f94ba9-dirty pimarin parents: diff changeset	5 <macros>
c49ec8c0b046 planemo upload commit bb69b191fe3ce756655bf90af4d69e4472f94ba9-dirty pimarin parents: diff changeset	6 <import>macro.xml</import>
c49ec8c0b046 planemo upload commit bb69b191fe3ce756655bf90af4d69e4472f94ba9-dirty pimarin parents: diff changeset	7 </macros>
c49ec8c0b046 planemo upload commit bb69b191fe3ce756655bf90af4d69e4472f94ba9-dirty pimarin parents: diff changeset	8 <expand macro='edam'/>
c49ec8c0b046 planemo upload commit bb69b191fe3ce756655bf90af4d69e4472f94ba9-dirty pimarin parents: diff changeset	9 <expand macro="requirements"/>
c49ec8c0b046 planemo upload commit bb69b191fe3ce756655bf90af4d69e4472f94ba9-dirty pimarin parents: diff changeset	10 <expand macro="version_command"/>
1 421032d8dd5d planemo upload commit 0a5fc6ee1a42b0c1c413de143a01559cb491c2e5-dirty pimarin parents: 0 diff changeset	11 <command detect_errors="aggressive"><![CDATA[
421032d8dd5d planemo upload commit 0a5fc6ee1a42b0c1c413de143a01559cb491c2e5-dirty pimarin parents: 0 diff changeset	12 #import re
421032d8dd5d planemo upload commit 0a5fc6ee1a42b0c1c413de143a01559cb491c2e5-dirty pimarin parents: 0 diff changeset	13 mkdir "abromics_extracted_folder" &&
421032d8dd5d planemo upload commit 0a5fc6ee1a42b0c1c413de143a01559cb491c2e5-dirty pimarin parents: 0 diff changeset	14 #*=================================================================
421032d8dd5d planemo upload commit 0a5fc6ee1a42b0c1c413de143a01559cb491c2e5-dirty pimarin parents: 0 diff changeset	15 Paramaters to add Database and tool version if available
421032d8dd5d planemo upload commit 0a5fc6ee1a42b0c1c413de143a01559cb491c2e5-dirty pimarin parents: 0 diff changeset	16 =================================================================*#
421032d8dd5d planemo upload commit 0a5fc6ee1a42b0c1c413de143a01559cb491c2e5-dirty pimarin parents: 0 diff changeset	17 #set $counter = len($tool_section.tools)-1
0 c49ec8c0b046 planemo upload commit bb69b191fe3ce756655bf90af4d69e4472f94ba9-dirty pimarin parents: diff changeset	18
1 421032d8dd5d planemo upload commit 0a5fc6ee1a42b0c1c413de143a01559cb491c2e5-dirty pimarin parents: 0 diff changeset	19 #*======================================================
421032d8dd5d planemo upload commit 0a5fc6ee1a42b0c1c413de143a01559cb491c2e5-dirty pimarin parents: 0 diff changeset	20 Loop to include some different tool in one time
421032d8dd5d planemo upload commit 0a5fc6ee1a42b0c1c413de143a01559cb491c2e5-dirty pimarin parents: 0 diff changeset	21 ======================================================*#
421032d8dd5d planemo upload commit 0a5fc6ee1a42b0c1c413de143a01559cb491c2e5-dirty pimarin parents: 0 diff changeset	22 #for $i, $tool in enumerate( $tool_section.tools )
421032d8dd5d planemo upload commit 0a5fc6ee1a42b0c1c413de143a01559cb491c2e5-dirty pimarin parents: 0 diff changeset	23 abromics_extract
421032d8dd5d planemo upload commit 0a5fc6ee1a42b0c1c413de143a01559cb491c2e5-dirty pimarin parents: 0 diff changeset	24 $tool.select_tool.tool_list
421032d8dd5d planemo upload commit 0a5fc6ee1a42b0c1c413de143a01559cb491c2e5-dirty pimarin parents: 0 diff changeset	25 --hid $tool.select_tool.input.hid
421032d8dd5d planemo upload commit 0a5fc6ee1a42b0c1c413de143a01559cb491c2e5-dirty pimarin parents: 0 diff changeset	26 "$tool.select_tool.input"
421032d8dd5d planemo upload commit 0a5fc6ee1a42b0c1c413de143a01559cb491c2e5-dirty pimarin parents: 0 diff changeset	27 --analysis_software_version "$tool.select_tool.analysis_software_version"
0 c49ec8c0b046 planemo upload commit bb69b191fe3ce756655bf90af4d69e4472f94ba9-dirty pimarin parents: diff changeset	28 --reference_database_version "$tool.select_tool.reference_database_version"
1 421032d8dd5d planemo upload commit 0a5fc6ee1a42b0c1c413de143a01559cb491c2e5-dirty pimarin parents: 0 diff changeset	29 #if $tool.select_tool.tool_list == "bakta"
421032d8dd5d planemo upload commit 0a5fc6ee1a42b0c1c413de143a01559cb491c2e5-dirty pimarin parents: 0 diff changeset	30 #if str($tool.select_tool.annotation_tabular_path) != 'None'
421032d8dd5d planemo upload commit 0a5fc6ee1a42b0c1c413de143a01559cb491c2e5-dirty pimarin parents: 0 diff changeset	31 --annotation_tabular_path '$tool.select_tool.annotation_tabular_path'
421032d8dd5d planemo upload commit 0a5fc6ee1a42b0c1c413de143a01559cb491c2e5-dirty pimarin parents: 0 diff changeset	32 --annotation_tabular_hid '$tool.select_tool.annotation_tabular_path.hid'
421032d8dd5d planemo upload commit 0a5fc6ee1a42b0c1c413de143a01559cb491c2e5-dirty pimarin parents: 0 diff changeset	33 #end if
421032d8dd5d planemo upload commit 0a5fc6ee1a42b0c1c413de143a01559cb491c2e5-dirty pimarin parents: 0 diff changeset	34 #if str($tool.select_tool.annotation_genbank_path) != 'None'
421032d8dd5d planemo upload commit 0a5fc6ee1a42b0c1c413de143a01559cb491c2e5-dirty pimarin parents: 0 diff changeset	35 --annotation_genbank_path '$tool.select_tool.annotation_genbank_path'
421032d8dd5d planemo upload commit 0a5fc6ee1a42b0c1c413de143a01559cb491c2e5-dirty pimarin parents: 0 diff changeset	36 --annotation_genbank_hid '$tool.select_tool.annotation_genbank_path.hid'
421032d8dd5d planemo upload commit 0a5fc6ee1a42b0c1c413de143a01559cb491c2e5-dirty pimarin parents: 0 diff changeset	37 #end if
421032d8dd5d planemo upload commit 0a5fc6ee1a42b0c1c413de143a01559cb491c2e5-dirty pimarin parents: 0 diff changeset	38 #if str($tool.select_tool.annotation_embl_path) != 'None'
421032d8dd5d planemo upload commit 0a5fc6ee1a42b0c1c413de143a01559cb491c2e5-dirty pimarin parents: 0 diff changeset	39 --annotation_embl_path '$tool.select_tool.annotation_embl_path'
421032d8dd5d planemo upload commit 0a5fc6ee1a42b0c1c413de143a01559cb491c2e5-dirty pimarin parents: 0 diff changeset	40 --annotation_embl_hid '$tool.select_tool.annotation_embl_path.hid'
421032d8dd5d planemo upload commit 0a5fc6ee1a42b0c1c413de143a01559cb491c2e5-dirty pimarin parents: 0 diff changeset	41 #end if
421032d8dd5d planemo upload commit 0a5fc6ee1a42b0c1c413de143a01559cb491c2e5-dirty pimarin parents: 0 diff changeset	42 #if str($tool.select_tool.contig_sequences_path) != 'None'
421032d8dd5d planemo upload commit 0a5fc6ee1a42b0c1c413de143a01559cb491c2e5-dirty pimarin parents: 0 diff changeset	43 --contig_sequences_path '$tool.select_tool.contig_sequences_path'
421032d8dd5d planemo upload commit 0a5fc6ee1a42b0c1c413de143a01559cb491c2e5-dirty pimarin parents: 0 diff changeset	44 --contig_sequences_hid '$tool.select_tool.contig_sequences_path.hid'
421032d8dd5d planemo upload commit 0a5fc6ee1a42b0c1c413de143a01559cb491c2e5-dirty pimarin parents: 0 diff changeset	45 #end if
421032d8dd5d planemo upload commit 0a5fc6ee1a42b0c1c413de143a01559cb491c2e5-dirty pimarin parents: 0 diff changeset	46 #if str($tool.select_tool.nucleotide_annotation_path) != 'None'
421032d8dd5d planemo upload commit 0a5fc6ee1a42b0c1c413de143a01559cb491c2e5-dirty pimarin parents: 0 diff changeset	47 --nucleotide_annotation_path '$tool.select_tool.nucleotide_annotation_path'
421032d8dd5d planemo upload commit 0a5fc6ee1a42b0c1c413de143a01559cb491c2e5-dirty pimarin parents: 0 diff changeset	48 --nucleotide_annotation_hid '$tool.select_tool.nucleotide_annotation_path.hid'
421032d8dd5d planemo upload commit 0a5fc6ee1a42b0c1c413de143a01559cb491c2e5-dirty pimarin parents: 0 diff changeset	49 #end if
421032d8dd5d planemo upload commit 0a5fc6ee1a42b0c1c413de143a01559cb491c2e5-dirty pimarin parents: 0 diff changeset	50 #if str($tool.select_tool.amino_acid_annotation_path) != 'None'
421032d8dd5d planemo upload commit 0a5fc6ee1a42b0c1c413de143a01559cb491c2e5-dirty pimarin parents: 0 diff changeset	51 --amino_acid_annotation_path '$tool.select_tool.amino_acid_annotation_path'
421032d8dd5d planemo upload commit 0a5fc6ee1a42b0c1c413de143a01559cb491c2e5-dirty pimarin parents: 0 diff changeset	52 --amino_acid_annotation_hid '$tool.select_tool.amino_acid_annotation_path.hid'
421032d8dd5d planemo upload commit 0a5fc6ee1a42b0c1c413de143a01559cb491c2e5-dirty pimarin parents: 0 diff changeset	53 #end if
421032d8dd5d planemo upload commit 0a5fc6ee1a42b0c1c413de143a01559cb491c2e5-dirty pimarin parents: 0 diff changeset	54 #if str($tool.select_tool.summary_result_path) != 'None'
421032d8dd5d planemo upload commit 0a5fc6ee1a42b0c1c413de143a01559cb491c2e5-dirty pimarin parents: 0 diff changeset	55 --summary_result_path '$tool.select_tool.summary_result_path'
421032d8dd5d planemo upload commit 0a5fc6ee1a42b0c1c413de143a01559cb491c2e5-dirty pimarin parents: 0 diff changeset	56 --summary_result_hid '$tool.select_tool.summary_result_path.hid'
421032d8dd5d planemo upload commit 0a5fc6ee1a42b0c1c413de143a01559cb491c2e5-dirty pimarin parents: 0 diff changeset	57 #end if
421032d8dd5d planemo upload commit 0a5fc6ee1a42b0c1c413de143a01559cb491c2e5-dirty pimarin parents: 0 diff changeset	58 #if str($tool.select_tool.gff_file_path) != 'None'
421032d8dd5d planemo upload commit 0a5fc6ee1a42b0c1c413de143a01559cb491c2e5-dirty pimarin parents: 0 diff changeset	59 --gff_file_path "$tool.select_tool.gff_file_path"
421032d8dd5d planemo upload commit 0a5fc6ee1a42b0c1c413de143a01559cb491c2e5-dirty pimarin parents: 0 diff changeset	60 --gff_file_hid "$tool.select_tool.gff_file_path.hid"
421032d8dd5d planemo upload commit 0a5fc6ee1a42b0c1c413de143a01559cb491c2e5-dirty pimarin parents: 0 diff changeset	61 #end if
421032d8dd5d planemo upload commit 0a5fc6ee1a42b0c1c413de143a01559cb491c2e5-dirty pimarin parents: 0 diff changeset	62 #if str($tool.select_tool.hypothetical_protein_path) != 'None'
421032d8dd5d planemo upload commit 0a5fc6ee1a42b0c1c413de143a01559cb491c2e5-dirty pimarin parents: 0 diff changeset	63 --hypothetical_protein_path '$tool.select_tool.hypothetical_protein_path'
421032d8dd5d planemo upload commit 0a5fc6ee1a42b0c1c413de143a01559cb491c2e5-dirty pimarin parents: 0 diff changeset	64 --hypothetical_protein_hid '$tool.select_tool.hypothetical_protein_path.hid'
421032d8dd5d planemo upload commit 0a5fc6ee1a42b0c1c413de143a01559cb491c2e5-dirty pimarin parents: 0 diff changeset	65 #end if
421032d8dd5d planemo upload commit 0a5fc6ee1a42b0c1c413de143a01559cb491c2e5-dirty pimarin parents: 0 diff changeset	66 #if str($tool.select_tool.hypothetical_tabular_path) != 'None'
421032d8dd5d planemo upload commit 0a5fc6ee1a42b0c1c413de143a01559cb491c2e5-dirty pimarin parents: 0 diff changeset	67 --hypothetical_tabular_path '$tool.select_tool.hypothetical_tabular_path'
421032d8dd5d planemo upload commit 0a5fc6ee1a42b0c1c413de143a01559cb491c2e5-dirty pimarin parents: 0 diff changeset	68 --hypothetical_tabular_hid '$tool.select_tool.hypothetical_tabular_path.hid'
421032d8dd5d planemo upload commit 0a5fc6ee1a42b0c1c413de143a01559cb491c2e5-dirty pimarin parents: 0 diff changeset	69 #end if
421032d8dd5d planemo upload commit 0a5fc6ee1a42b0c1c413de143a01559cb491c2e5-dirty pimarin parents: 0 diff changeset	70 #if str($tool.select_tool.plot_file_path) != 'None'
421032d8dd5d planemo upload commit 0a5fc6ee1a42b0c1c413de143a01559cb491c2e5-dirty pimarin parents: 0 diff changeset	71 --plot_file_path '$tool.select_tool.plot_file_path'
421032d8dd5d planemo upload commit 0a5fc6ee1a42b0c1c413de143a01559cb491c2e5-dirty pimarin parents: 0 diff changeset	72 --plot_file_hid '$tool.select_tool.plot_file_path.hid'
3 73aea20004ff planemo upload commit 8721cd95e02dd6b3a02e2eb549cd8ff6b1675ff8-dirty pimarin parents: 1 diff changeset	73 #end if
1 421032d8dd5d planemo upload commit 0a5fc6ee1a42b0c1c413de143a01559cb491c2e5-dirty pimarin parents: 0 diff changeset	74 #elif $tool.select_tool.tool_list == "bandage"
421032d8dd5d planemo upload commit 0a5fc6ee1a42b0c1c413de143a01559cb491c2e5-dirty pimarin parents: 0 diff changeset	75 #if str($tool.select_tool.bandage_plot_path) != 'None'
421032d8dd5d planemo upload commit 0a5fc6ee1a42b0c1c413de143a01559cb491c2e5-dirty pimarin parents: 0 diff changeset	76 --bandage_plot_path '$tool.select_tool.bandage_plot_path'
421032d8dd5d planemo upload commit 0a5fc6ee1a42b0c1c413de143a01559cb491c2e5-dirty pimarin parents: 0 diff changeset	77 --bandage_plot_hid '$tool.select_tool.bandage_plot_path.hid'
3 73aea20004ff planemo upload commit 8721cd95e02dd6b3a02e2eb549cd8ff6b1675ff8-dirty pimarin parents: 1 diff changeset	78 #end if
1 421032d8dd5d planemo upload commit 0a5fc6ee1a42b0c1c413de143a01559cb491c2e5-dirty pimarin parents: 0 diff changeset	79 #elif $tool.select_tool.tool_list == "bracken"
421032d8dd5d planemo upload commit 0a5fc6ee1a42b0c1c413de143a01559cb491c2e5-dirty pimarin parents: 0 diff changeset	80 #if str($tool.select_tool.kraken_report_path) != 'None'
421032d8dd5d planemo upload commit 0a5fc6ee1a42b0c1c413de143a01559cb491c2e5-dirty pimarin parents: 0 diff changeset	81 --kraken_report_path "$tool.select_tool.kraken_report_path"
421032d8dd5d planemo upload commit 0a5fc6ee1a42b0c1c413de143a01559cb491c2e5-dirty pimarin parents: 0 diff changeset	82 --kraken_report_hid "$tool.select_tool.kraken_report_path.hid"
421032d8dd5d planemo upload commit 0a5fc6ee1a42b0c1c413de143a01559cb491c2e5-dirty pimarin parents: 0 diff changeset	83 #end if
421032d8dd5d planemo upload commit 0a5fc6ee1a42b0c1c413de143a01559cb491c2e5-dirty pimarin parents: 0 diff changeset	84 --threshold "$tool.select_tool.threshold"
421032d8dd5d planemo upload commit 0a5fc6ee1a42b0c1c413de143a01559cb491c2e5-dirty pimarin parents: 0 diff changeset	85 --read_len "$tool.select_tool.read_len"
421032d8dd5d planemo upload commit 0a5fc6ee1a42b0c1c413de143a01559cb491c2e5-dirty pimarin parents: 0 diff changeset	86 --level "$tool.select_tool.level"
421032d8dd5d planemo upload commit 0a5fc6ee1a42b0c1c413de143a01559cb491c2e5-dirty pimarin parents: 0 diff changeset	87 #elif $tool.select_tool.tool_list == "fastp"
421032d8dd5d planemo upload commit 0a5fc6ee1a42b0c1c413de143a01559cb491c2e5-dirty pimarin parents: 0 diff changeset	88 #if str($tool.select_tool.trimmed_forward_R1_path) != 'None'
421032d8dd5d planemo upload commit 0a5fc6ee1a42b0c1c413de143a01559cb491c2e5-dirty pimarin parents: 0 diff changeset	89 --trimmed_forward_R1_path '$tool.select_tool.trimmed_forward_R1_path'
421032d8dd5d planemo upload commit 0a5fc6ee1a42b0c1c413de143a01559cb491c2e5-dirty pimarin parents: 0 diff changeset	90 --trimmed_forward_R1_hid '$tool.select_tool.trimmed_forward_R1_path.hid'
421032d8dd5d planemo upload commit 0a5fc6ee1a42b0c1c413de143a01559cb491c2e5-dirty pimarin parents: 0 diff changeset	91 #end if
421032d8dd5d planemo upload commit 0a5fc6ee1a42b0c1c413de143a01559cb491c2e5-dirty pimarin parents: 0 diff changeset	92 #if str($tool.select_tool.trimmed_reverse_R2_path) != 'None'
421032d8dd5d planemo upload commit 0a5fc6ee1a42b0c1c413de143a01559cb491c2e5-dirty pimarin parents: 0 diff changeset	93 --trimmed_reverse_R2_path '$tool.select_tool.trimmed_reverse_R2_path'
421032d8dd5d planemo upload commit 0a5fc6ee1a42b0c1c413de143a01559cb491c2e5-dirty pimarin parents: 0 diff changeset	94 --trimmed_reverse_R2_hid '$tool.select_tool.trimmed_reverse_R2_path.hid'
421032d8dd5d planemo upload commit 0a5fc6ee1a42b0c1c413de143a01559cb491c2e5-dirty pimarin parents: 0 diff changeset	95 #end if
421032d8dd5d planemo upload commit 0a5fc6ee1a42b0c1c413de143a01559cb491c2e5-dirty pimarin parents: 0 diff changeset	96 #if str($tool.select_tool.html_report_path) != 'None'
421032d8dd5d planemo upload commit 0a5fc6ee1a42b0c1c413de143a01559cb491c2e5-dirty pimarin parents: 0 diff changeset	97 --html_report_path '$tool.select_tool.html_report_path'
421032d8dd5d planemo upload commit 0a5fc6ee1a42b0c1c413de143a01559cb491c2e5-dirty pimarin parents: 0 diff changeset	98 --html_report_hid '$tool.select_tool.html_report_path.hid'
421032d8dd5d planemo upload commit 0a5fc6ee1a42b0c1c413de143a01559cb491c2e5-dirty pimarin parents: 0 diff changeset	99 #end if
421032d8dd5d planemo upload commit 0a5fc6ee1a42b0c1c413de143a01559cb491c2e5-dirty pimarin parents: 0 diff changeset	100 #elif $tool.select_tool.tool_list == "integronfinder2"
421032d8dd5d planemo upload commit 0a5fc6ee1a42b0c1c413de143a01559cb491c2e5-dirty pimarin parents: 0 diff changeset	101 #if str($tool.select_tool.summary_file_path) != 'None'
421032d8dd5d planemo upload commit 0a5fc6ee1a42b0c1c413de143a01559cb491c2e5-dirty pimarin parents: 0 diff changeset	102 --summary_file_path "$tool.select_tool.summary_file_path"
421032d8dd5d planemo upload commit 0a5fc6ee1a42b0c1c413de143a01559cb491c2e5-dirty pimarin parents: 0 diff changeset	103 --summary_file_hid "$tool.select_tool.summary_file_path.hid"
421032d8dd5d planemo upload commit 0a5fc6ee1a42b0c1c413de143a01559cb491c2e5-dirty pimarin parents: 0 diff changeset	104 #end if
421032d8dd5d planemo upload commit 0a5fc6ee1a42b0c1c413de143a01559cb491c2e5-dirty pimarin parents: 0 diff changeset	105 #elif $tool.select_tool.tool_list == "isescan"
421032d8dd5d planemo upload commit 0a5fc6ee1a42b0c1c413de143a01559cb491c2e5-dirty pimarin parents: 0 diff changeset	106 #if str($tool.select_tool.summary_path) != 'None'
421032d8dd5d planemo upload commit 0a5fc6ee1a42b0c1c413de143a01559cb491c2e5-dirty pimarin parents: 0 diff changeset	107 --summary_path '$tool.select_tool.summary_path'
421032d8dd5d planemo upload commit 0a5fc6ee1a42b0c1c413de143a01559cb491c2e5-dirty pimarin parents: 0 diff changeset	108 --summary_hid '$tool.select_tool.summary_path.hid'
421032d8dd5d planemo upload commit 0a5fc6ee1a42b0c1c413de143a01559cb491c2e5-dirty pimarin parents: 0 diff changeset	109 #end if
421032d8dd5d planemo upload commit 0a5fc6ee1a42b0c1c413de143a01559cb491c2e5-dirty pimarin parents: 0 diff changeset	110 #if str($tool.select_tool.annotation_path) != 'None'
421032d8dd5d planemo upload commit 0a5fc6ee1a42b0c1c413de143a01559cb491c2e5-dirty pimarin parents: 0 diff changeset	111 --annotation_path '$tool.select_tool.annotation_path'
421032d8dd5d planemo upload commit 0a5fc6ee1a42b0c1c413de143a01559cb491c2e5-dirty pimarin parents: 0 diff changeset	112 --annotation_hid '$tool.select_tool.annotation_path.hid'
421032d8dd5d planemo upload commit 0a5fc6ee1a42b0c1c413de143a01559cb491c2e5-dirty pimarin parents: 0 diff changeset	113 #end if
421032d8dd5d planemo upload commit 0a5fc6ee1a42b0c1c413de143a01559cb491c2e5-dirty pimarin parents: 0 diff changeset	114 #if str($tool.select_tool.orf_fna_path) != 'None'
421032d8dd5d planemo upload commit 0a5fc6ee1a42b0c1c413de143a01559cb491c2e5-dirty pimarin parents: 0 diff changeset	115 --orf_fna_path "$tool.select_tool.orf_fna_path"
421032d8dd5d planemo upload commit 0a5fc6ee1a42b0c1c413de143a01559cb491c2e5-dirty pimarin parents: 0 diff changeset	116 --orf_fna_hid "$tool.select_tool.orf_fna_path.hid"
421032d8dd5d planemo upload commit 0a5fc6ee1a42b0c1c413de143a01559cb491c2e5-dirty pimarin parents: 0 diff changeset	117 #end if
421032d8dd5d planemo upload commit 0a5fc6ee1a42b0c1c413de143a01559cb491c2e5-dirty pimarin parents: 0 diff changeset	118 #if str($tool.select_tool.orf_faa_path) != 'None'
421032d8dd5d planemo upload commit 0a5fc6ee1a42b0c1c413de143a01559cb491c2e5-dirty pimarin parents: 0 diff changeset	119 --orf_faa_path "$tool.select_tool.orf_faa_path"
421032d8dd5d planemo upload commit 0a5fc6ee1a42b0c1c413de143a01559cb491c2e5-dirty pimarin parents: 0 diff changeset	120 --orf_faa_hid "$tool.select_tool.orf_faa_path.hid"
421032d8dd5d planemo upload commit 0a5fc6ee1a42b0c1c413de143a01559cb491c2e5-dirty pimarin parents: 0 diff changeset	121 #end if
421032d8dd5d planemo upload commit 0a5fc6ee1a42b0c1c413de143a01559cb491c2e5-dirty pimarin parents: 0 diff changeset	122 #if str($tool.select_tool.is_fna_path) != 'None'
421032d8dd5d planemo upload commit 0a5fc6ee1a42b0c1c413de143a01559cb491c2e5-dirty pimarin parents: 0 diff changeset	123 --is_fna_path "$tool.select_tool.is_fna_path"
421032d8dd5d planemo upload commit 0a5fc6ee1a42b0c1c413de143a01559cb491c2e5-dirty pimarin parents: 0 diff changeset	124 --is_fna_hid "$tool.select_tool.is_fna_path.hid"
421032d8dd5d planemo upload commit 0a5fc6ee1a42b0c1c413de143a01559cb491c2e5-dirty pimarin parents: 0 diff changeset	125 #end if
421032d8dd5d planemo upload commit 0a5fc6ee1a42b0c1c413de143a01559cb491c2e5-dirty pimarin parents: 0 diff changeset	126 #elif $tool.select_tool.tool_list == "kraken2"
421032d8dd5d planemo upload commit 0a5fc6ee1a42b0c1c413de143a01559cb491c2e5-dirty pimarin parents: 0 diff changeset	127 #if str($tool.select_tool.seq_classification_file_path) != 'None'
421032d8dd5d planemo upload commit 0a5fc6ee1a42b0c1c413de143a01559cb491c2e5-dirty pimarin parents: 0 diff changeset	128 --seq_classification_file_path "$tool.select_tool.seq_classification_file_path"
3 73aea20004ff planemo upload commit 8721cd95e02dd6b3a02e2eb549cd8ff6b1675ff8-dirty pimarin parents: 1 diff changeset	129 --seq_classification_file_hid "$tool.select_tool.seq_classification_file_path.hid"
1 421032d8dd5d planemo upload commit 0a5fc6ee1a42b0c1c413de143a01559cb491c2e5-dirty pimarin parents: 0 diff changeset	130 #end if
421032d8dd5d planemo upload commit 0a5fc6ee1a42b0c1c413de143a01559cb491c2e5-dirty pimarin parents: 0 diff changeset	131 #elif $tool.select_tool.tool_list == "plasmidfinder"
421032d8dd5d planemo upload commit 0a5fc6ee1a42b0c1c413de143a01559cb491c2e5-dirty pimarin parents: 0 diff changeset	132 #if str($tool.select_tool.genome_hit_path) != 'None'
421032d8dd5d planemo upload commit 0a5fc6ee1a42b0c1c413de143a01559cb491c2e5-dirty pimarin parents: 0 diff changeset	133 --genome_hit_path "$tool.select_tool.genome_hit_path"
421032d8dd5d planemo upload commit 0a5fc6ee1a42b0c1c413de143a01559cb491c2e5-dirty pimarin parents: 0 diff changeset	134 --genome_hit_hid "$tool.select_tool.genome_hit_path.hid"
421032d8dd5d planemo upload commit 0a5fc6ee1a42b0c1c413de143a01559cb491c2e5-dirty pimarin parents: 0 diff changeset	135 #end if
421032d8dd5d planemo upload commit 0a5fc6ee1a42b0c1c413de143a01559cb491c2e5-dirty pimarin parents: 0 diff changeset	136 #if str($tool.select_tool.plasmid_hit_path) != 'None'
421032d8dd5d planemo upload commit 0a5fc6ee1a42b0c1c413de143a01559cb491c2e5-dirty pimarin parents: 0 diff changeset	137 --plasmid_hit_path "$tool.select_tool.plasmid_hit_path"
421032d8dd5d planemo upload commit 0a5fc6ee1a42b0c1c413de143a01559cb491c2e5-dirty pimarin parents: 0 diff changeset	138 --plasmid_hit_hid "$tool.select_tool.plasmid_hit_path.hid"
421032d8dd5d planemo upload commit 0a5fc6ee1a42b0c1c413de143a01559cb491c2e5-dirty pimarin parents: 0 diff changeset	139 #end if
421032d8dd5d planemo upload commit 0a5fc6ee1a42b0c1c413de143a01559cb491c2e5-dirty pimarin parents: 0 diff changeset	140 #elif $tool.select_tool.tool_list == "quast"
421032d8dd5d planemo upload commit 0a5fc6ee1a42b0c1c413de143a01559cb491c2e5-dirty pimarin parents: 0 diff changeset	141 #if str($tool.select_tool.quast_html_path) != 'None'
421032d8dd5d planemo upload commit 0a5fc6ee1a42b0c1c413de143a01559cb491c2e5-dirty pimarin parents: 0 diff changeset	142 --quast_html_path "$tool.select_tool.quast_html_path"
421032d8dd5d planemo upload commit 0a5fc6ee1a42b0c1c413de143a01559cb491c2e5-dirty pimarin parents: 0 diff changeset	143 --quast_html_hid "$tool.select_tool.quast_html_path.hid"
421032d8dd5d planemo upload commit 0a5fc6ee1a42b0c1c413de143a01559cb491c2e5-dirty pimarin parents: 0 diff changeset	144 #end if
421032d8dd5d planemo upload commit 0a5fc6ee1a42b0c1c413de143a01559cb491c2e5-dirty pimarin parents: 0 diff changeset	145 #elif $tool.select_tool.tool_list == "recentrifuge"
421032d8dd5d planemo upload commit 0a5fc6ee1a42b0c1c413de143a01559cb491c2e5-dirty pimarin parents: 0 diff changeset	146 #if str($tool.select_tool.rcf_stat_path) != 'None'
421032d8dd5d planemo upload commit 0a5fc6ee1a42b0c1c413de143a01559cb491c2e5-dirty pimarin parents: 0 diff changeset	147 --rcf_stat_path "$tool.select_tool.rcf_stat_path"
421032d8dd5d planemo upload commit 0a5fc6ee1a42b0c1c413de143a01559cb491c2e5-dirty pimarin parents: 0 diff changeset	148 --rcf_stat_hid "$tool.select_tool.rcf_stat_path.hid"
421032d8dd5d planemo upload commit 0a5fc6ee1a42b0c1c413de143a01559cb491c2e5-dirty pimarin parents: 0 diff changeset	149 #end if
421032d8dd5d planemo upload commit 0a5fc6ee1a42b0c1c413de143a01559cb491c2e5-dirty pimarin parents: 0 diff changeset	150 #if str($tool.select_tool.rcf_html_path) != 'None'
421032d8dd5d planemo upload commit 0a5fc6ee1a42b0c1c413de143a01559cb491c2e5-dirty pimarin parents: 0 diff changeset	151 --rcf_html_path "$tool.select_tool.rcf_html_path"
421032d8dd5d planemo upload commit 0a5fc6ee1a42b0c1c413de143a01559cb491c2e5-dirty pimarin parents: 0 diff changeset	152 --rcf_html_hid "$tool.select_tool.rcf_html_path.hid"
421032d8dd5d planemo upload commit 0a5fc6ee1a42b0c1c413de143a01559cb491c2e5-dirty pimarin parents: 0 diff changeset	153 #end if
421032d8dd5d planemo upload commit 0a5fc6ee1a42b0c1c413de143a01559cb491c2e5-dirty pimarin parents: 0 diff changeset	154 #elif $tool.select_tool.tool_list == "shovill"
421032d8dd5d planemo upload commit 0a5fc6ee1a42b0c1c413de143a01559cb491c2e5-dirty pimarin parents: 0 diff changeset	155 #if str($tool.select_tool.contig_graph_path) != 'None'
421032d8dd5d planemo upload commit 0a5fc6ee1a42b0c1c413de143a01559cb491c2e5-dirty pimarin parents: 0 diff changeset	156 --contig_graph_path "$tool.select_tool.contig_graph_path"
421032d8dd5d planemo upload commit 0a5fc6ee1a42b0c1c413de143a01559cb491c2e5-dirty pimarin parents: 0 diff changeset	157 --contig_graph_hid "$tool.select_tool.contig_graph_path.hid"
421032d8dd5d planemo upload commit 0a5fc6ee1a42b0c1c413de143a01559cb491c2e5-dirty pimarin parents: 0 diff changeset	158 #end if
421032d8dd5d planemo upload commit 0a5fc6ee1a42b0c1c413de143a01559cb491c2e5-dirty pimarin parents: 0 diff changeset	159 #if str($tool.select_tool.bam_file_path) != 'None'
421032d8dd5d planemo upload commit 0a5fc6ee1a42b0c1c413de143a01559cb491c2e5-dirty pimarin parents: 0 diff changeset	160 --bam_file_path "$tool.select_tool.bam_file_path"
421032d8dd5d planemo upload commit 0a5fc6ee1a42b0c1c413de143a01559cb491c2e5-dirty pimarin parents: 0 diff changeset	161 --bam_file_hid "$tool.select_tool.bam_file_path.hid"
421032d8dd5d planemo upload commit 0a5fc6ee1a42b0c1c413de143a01559cb491c2e5-dirty pimarin parents: 0 diff changeset	162 #end if
421032d8dd5d planemo upload commit 0a5fc6ee1a42b0c1c413de143a01559cb491c2e5-dirty pimarin parents: 0 diff changeset	163 #elif $tool.select_tool.tool_list == "staramr"
421032d8dd5d planemo upload commit 0a5fc6ee1a42b0c1c413de143a01559cb491c2e5-dirty pimarin parents: 0 diff changeset	164 #if str($tool.select_tool.mlst_file_path) != 'None'
421032d8dd5d planemo upload commit 0a5fc6ee1a42b0c1c413de143a01559cb491c2e5-dirty pimarin parents: 0 diff changeset	165 --mlst_file_path "$tool.select_tool.mlst_file_path"
421032d8dd5d planemo upload commit 0a5fc6ee1a42b0c1c413de143a01559cb491c2e5-dirty pimarin parents: 0 diff changeset	166 --mlst_hid "$tool.select_tool.mlst_file_path.hid"
421032d8dd5d planemo upload commit 0a5fc6ee1a42b0c1c413de143a01559cb491c2e5-dirty pimarin parents: 0 diff changeset	167 #end if
421032d8dd5d planemo upload commit 0a5fc6ee1a42b0c1c413de143a01559cb491c2e5-dirty pimarin parents: 0 diff changeset	168 #if str($tool.select_tool.plasmidfinder_file_path) != 'None'
421032d8dd5d planemo upload commit 0a5fc6ee1a42b0c1c413de143a01559cb491c2e5-dirty pimarin parents: 0 diff changeset	169 --plasmidfinder_file_path "$tool.select_tool.plasmidfinder_file_path"
421032d8dd5d planemo upload commit 0a5fc6ee1a42b0c1c413de143a01559cb491c2e5-dirty pimarin parents: 0 diff changeset	170 --plasmidfinder_hid "$tool.select_tool.plasmidfinder_file_path.hid"
421032d8dd5d planemo upload commit 0a5fc6ee1a42b0c1c413de143a01559cb491c2e5-dirty pimarin parents: 0 diff changeset	171 #end if
421032d8dd5d planemo upload commit 0a5fc6ee1a42b0c1c413de143a01559cb491c2e5-dirty pimarin parents: 0 diff changeset	172 #if str($tool.select_tool.pointfinder_file_path) != 'None'
421032d8dd5d planemo upload commit 0a5fc6ee1a42b0c1c413de143a01559cb491c2e5-dirty pimarin parents: 0 diff changeset	173 --pointfinder_file_path "$tool.select_tool.pointfinder_file_path"
421032d8dd5d planemo upload commit 0a5fc6ee1a42b0c1c413de143a01559cb491c2e5-dirty pimarin parents: 0 diff changeset	174 --pointfinder_hid "$tool.select_tool.pointfinder_file_path.hid"
421032d8dd5d planemo upload commit 0a5fc6ee1a42b0c1c413de143a01559cb491c2e5-dirty pimarin parents: 0 diff changeset	175 #end if
421032d8dd5d planemo upload commit 0a5fc6ee1a42b0c1c413de143a01559cb491c2e5-dirty pimarin parents: 0 diff changeset	176 #if str($tool.select_tool.setting_file_path) != 'None'
421032d8dd5d planemo upload commit 0a5fc6ee1a42b0c1c413de143a01559cb491c2e5-dirty pimarin parents: 0 diff changeset	177 --setting_file_path "$tool.select_tool.setting_file_path"
421032d8dd5d planemo upload commit 0a5fc6ee1a42b0c1c413de143a01559cb491c2e5-dirty pimarin parents: 0 diff changeset	178 --setting_hid "$tool.select_tool.setting_file_path.hid"
421032d8dd5d planemo upload commit 0a5fc6ee1a42b0c1c413de143a01559cb491c2e5-dirty pimarin parents: 0 diff changeset	179 #end if
421032d8dd5d planemo upload commit 0a5fc6ee1a42b0c1c413de143a01559cb491c2e5-dirty pimarin parents: 0 diff changeset	180 #elif $tool.select_tool.tool_list == "tabular_file"
421032d8dd5d planemo upload commit 0a5fc6ee1a42b0c1c413de143a01559cb491c2e5-dirty pimarin parents: 0 diff changeset	181 --analysis_software_name "$tool.select_tool.analysis_software_name"
421032d8dd5d planemo upload commit 0a5fc6ee1a42b0c1c413de143a01559cb491c2e5-dirty pimarin parents: 0 diff changeset	182 #end if
421032d8dd5d planemo upload commit 0a5fc6ee1a42b0c1c413de143a01559cb491c2e5-dirty pimarin parents: 0 diff changeset	183 -o "abromics_extracted_folder/$($tool.select_tool.tool_list)_$(i)_output.json"
421032d8dd5d planemo upload commit 0a5fc6ee1a42b0c1c413de143a01559cb491c2e5-dirty pimarin parents: 0 diff changeset	184 \| tee "$logfile"
421032d8dd5d planemo upload commit 0a5fc6ee1a42b0c1c413de143a01559cb491c2e5-dirty pimarin parents: 0 diff changeset	185 #if $i < $counter
421032d8dd5d planemo upload commit 0a5fc6ee1a42b0c1c413de143a01559cb491c2e5-dirty pimarin parents: 0 diff changeset	186 &&
421032d8dd5d planemo upload commit 0a5fc6ee1a42b0c1c413de143a01559cb491c2e5-dirty pimarin parents: 0 diff changeset	187 #end if
421032d8dd5d planemo upload commit 0a5fc6ee1a42b0c1c413de143a01559cb491c2e5-dirty pimarin parents: 0 diff changeset	188 #end for
3 73aea20004ff planemo upload commit 8721cd95e02dd6b3a02e2eb549cd8ff6b1675ff8-dirty pimarin parents: 1 diff changeset	189 && ls abromics_extracted_folder
0 c49ec8c0b046 planemo upload commit bb69b191fe3ce756655bf90af4d69e4472f94ba9-dirty pimarin parents: diff changeset	190 ]]>
c49ec8c0b046 planemo upload commit bb69b191fe3ce756655bf90af4d69e4472f94ba9-dirty pimarin parents: diff changeset	191 </command>
c49ec8c0b046 planemo upload commit bb69b191fe3ce756655bf90af4d69e4472f94ba9-dirty pimarin parents: diff changeset	192 <inputs>
c49ec8c0b046 planemo upload commit bb69b191fe3ce756655bf90af4d69e4472f94ba9-dirty pimarin parents: diff changeset	193 <section name="tool_section" title="Available tools" expanded="true">
c49ec8c0b046 planemo upload commit bb69b191fe3ce756655bf90af4d69e4472f94ba9-dirty pimarin parents: diff changeset	194 <repeat name="tools" title="Tool" min="0">
c49ec8c0b046 planemo upload commit bb69b191fe3ce756655bf90af4d69e4472f94ba9-dirty pimarin parents: diff changeset	195 <conditional name="select_tool">
c49ec8c0b046 planemo upload commit bb69b191fe3ce756655bf90af4d69e4472f94ba9-dirty pimarin parents: diff changeset	196 <param name="tool_list" type="select" label="Available tools">
c49ec8c0b046 planemo upload commit bb69b191fe3ce756655bf90af4d69e4472f94ba9-dirty pimarin parents: diff changeset	197 <option value="abricate">abricate</option>
c49ec8c0b046 planemo upload commit bb69b191fe3ce756655bf90af4d69e4472f94ba9-dirty pimarin parents: diff changeset	198 <option value="bakta">bakta</option>
c49ec8c0b046 planemo upload commit bb69b191fe3ce756655bf90af4d69e4472f94ba9-dirty pimarin parents: diff changeset	199 <option value="bandage">bandage</option>
c49ec8c0b046 planemo upload commit bb69b191fe3ce756655bf90af4d69e4472f94ba9-dirty pimarin parents: diff changeset	200 <option value="bracken">bracken</option>
c49ec8c0b046 planemo upload commit bb69b191fe3ce756655bf90af4d69e4472f94ba9-dirty pimarin parents: diff changeset	201 <option value="fastp">fastp</option>
c49ec8c0b046 planemo upload commit bb69b191fe3ce756655bf90af4d69e4472f94ba9-dirty pimarin parents: diff changeset	202 <option value="integronfinder2">integronfinder2</option>
c49ec8c0b046 planemo upload commit bb69b191fe3ce756655bf90af4d69e4472f94ba9-dirty pimarin parents: diff changeset	203 <option value="isescan">isescan</option>
c49ec8c0b046 planemo upload commit bb69b191fe3ce756655bf90af4d69e4472f94ba9-dirty pimarin parents: diff changeset	204 <option value="kraken2">kraken2</option>
1 421032d8dd5d planemo upload commit 0a5fc6ee1a42b0c1c413de143a01559cb491c2e5-dirty pimarin parents: 0 diff changeset	205 <option value="multiqc">MultiQC</option>
0 c49ec8c0b046 planemo upload commit bb69b191fe3ce756655bf90af4d69e4472f94ba9-dirty pimarin parents: diff changeset	206 <option value="plasmidfinder">plasmidfinder</option>
c49ec8c0b046 planemo upload commit bb69b191fe3ce756655bf90af4d69e4472f94ba9-dirty pimarin parents: diff changeset	207 <option value="quast">quast</option>
c49ec8c0b046 planemo upload commit bb69b191fe3ce756655bf90af4d69e4472f94ba9-dirty pimarin parents: diff changeset	208 <option value="recentrifuge">recentrifuge</option>
c49ec8c0b046 planemo upload commit bb69b191fe3ce756655bf90af4d69e4472f94ba9-dirty pimarin parents: diff changeset	209 <option value="refseqmasher">refseqmasher</option>
c49ec8c0b046 planemo upload commit bb69b191fe3ce756655bf90af4d69e4472f94ba9-dirty pimarin parents: diff changeset	210 <option value="shovill">shovill</option>
c49ec8c0b046 planemo upload commit bb69b191fe3ce756655bf90af4d69e4472f94ba9-dirty pimarin parents: diff changeset	211 <option value="staramr">staramr</option>
c49ec8c0b046 planemo upload commit bb69b191fe3ce756655bf90af4d69e4472f94ba9-dirty pimarin parents: diff changeset	212 <option value="tabular_file">tabular_generic_file</option>
c49ec8c0b046 planemo upload commit bb69b191fe3ce756655bf90af4d69e4472f94ba9-dirty pimarin parents: diff changeset	213 </param>
c49ec8c0b046 planemo upload commit bb69b191fe3ce756655bf90af4d69e4472f94ba9-dirty pimarin parents: diff changeset	214 <when value="abricate">
c49ec8c0b046 planemo upload commit bb69b191fe3ce756655bf90af4d69e4472f94ba9-dirty pimarin parents: diff changeset	215 <param name="input" type="data" format="tabular" multiple="false" label="Abricate report file" help="Tabular file from abricate output"/>
c49ec8c0b046 planemo upload commit bb69b191fe3ce756655bf90af4d69e4472f94ba9-dirty pimarin parents: diff changeset	216 <expand macro="analysis_software_version"/>
c49ec8c0b046 planemo upload commit bb69b191fe3ce756655bf90af4d69e4472f94ba9-dirty pimarin parents: diff changeset	217 <expand macro="reference_database_version"/>
c49ec8c0b046 planemo upload commit bb69b191fe3ce756655bf90af4d69e4472f94ba9-dirty pimarin parents: diff changeset	218 </when>
c49ec8c0b046 planemo upload commit bb69b191fe3ce756655bf90af4d69e4472f94ba9-dirty pimarin parents: diff changeset	219 <when value="bakta">
c49ec8c0b046 planemo upload commit bb69b191fe3ce756655bf90af4d69e4472f94ba9-dirty pimarin parents: diff changeset	220 <param name="input" type="data" format="json" multiple="false" label="Bakta report file" help="Json file from bakta output"/>
1 421032d8dd5d planemo upload commit 0a5fc6ee1a42b0c1c413de143a01559cb491c2e5-dirty pimarin parents: 0 diff changeset	221 <param argument="--annotation_tabular_path" type="data" format="tabular" multiple="false" optional="true" label="Bakta annotation file" help="Tabular annotation file"/>
421032d8dd5d planemo upload commit 0a5fc6ee1a42b0c1c413de143a01559cb491c2e5-dirty pimarin parents: 0 diff changeset	222 <param argument="--annotation_genbank_path" type="data" format="txt" multiple="false" optional="true" label="Bakta genbank file" help="Genbank annotation file"/>
421032d8dd5d planemo upload commit 0a5fc6ee1a42b0c1c413de143a01559cb491c2e5-dirty pimarin parents: 0 diff changeset	223 <param argument="--annotation_embl_path" type="data" format="txt" multiple="false" optional="true" label="Bakta embl file" help="EMBL annotation file"/>
421032d8dd5d planemo upload commit 0a5fc6ee1a42b0c1c413de143a01559cb491c2e5-dirty pimarin parents: 0 diff changeset	224 <param argument="--contig_sequences_path" type="data" format="fasta" multiple="false" optional="true" label="Contig sequences" help="Contig sequences files"/>
421032d8dd5d planemo upload commit 0a5fc6ee1a42b0c1c413de143a01559cb491c2e5-dirty pimarin parents: 0 diff changeset	225 <param argument="--hypothetical_protein_path" type="data" format="fasta" multiple="false" optional="true" label="Hypothetical protein" help="Hypothetical protein fasta file"/>
421032d8dd5d planemo upload commit 0a5fc6ee1a42b0c1c413de143a01559cb491c2e5-dirty pimarin parents: 0 diff changeset	226 <param argument="--hypothetical_tabular_path" type="data" format="tabular" multiple="false" optional="true" label="Hypothetical annotation" help="Hypothetical protein annotation"/>
421032d8dd5d planemo upload commit 0a5fc6ee1a42b0c1c413de143a01559cb491c2e5-dirty pimarin parents: 0 diff changeset	227 <param argument="--plot_file_path" type="data" format="svg" multiple="false" optional="true" label="Contig sequences" help="Contig sequences files"/>
0 c49ec8c0b046 planemo upload commit bb69b191fe3ce756655bf90af4d69e4472f94ba9-dirty pimarin parents: diff changeset	228 <param argument="--summary_result_path" type="data" format="txt" multiple="false" optional="true" label="Bakta summary file" help="Summary file from bakta output"/>
1 421032d8dd5d planemo upload commit 0a5fc6ee1a42b0c1c413de143a01559cb491c2e5-dirty pimarin parents: 0 diff changeset	229 <param argument="--nucleotide_annotation_path" type="data" format="fasta" multiple="false" optional="true" label="Bakta nucleotide annotation" help="Nucleotide sequence annotation file"/>
421032d8dd5d planemo upload commit 0a5fc6ee1a42b0c1c413de143a01559cb491c2e5-dirty pimarin parents: 0 diff changeset	230 <param argument="--amino_acid_annotation_path" type="data" format="fasta" multiple="false" optional="true" label="Bakta protein annotation" help="Amino acid sequence annotation file"/>
0 c49ec8c0b046 planemo upload commit bb69b191fe3ce756655bf90af4d69e4472f94ba9-dirty pimarin parents: diff changeset	231 <param argument="--gff_file_path" type="data" format="gff3" multiple="false" optional="true" label="Bakta annotation file" help="Annotation file"/>
c49ec8c0b046 planemo upload commit bb69b191fe3ce756655bf90af4d69e4472f94ba9-dirty pimarin parents: diff changeset	232 <expand macro="analysis_software_version"/>
c49ec8c0b046 planemo upload commit bb69b191fe3ce756655bf90af4d69e4472f94ba9-dirty pimarin parents: diff changeset	233 <expand macro="reference_database_version"/>
c49ec8c0b046 planemo upload commit bb69b191fe3ce756655bf90af4d69e4472f94ba9-dirty pimarin parents: diff changeset	234 </when>
c49ec8c0b046 planemo upload commit bb69b191fe3ce756655bf90af4d69e4472f94ba9-dirty pimarin parents: diff changeset	235 <when value="bandage">
c49ec8c0b046 planemo upload commit bb69b191fe3ce756655bf90af4d69e4472f94ba9-dirty pimarin parents: diff changeset	236 <param name="input" type="data" format="txt,tabular" multiple="false" label="Bandage report file" help="Tabular file from bandage output"/>
1 421032d8dd5d planemo upload commit 0a5fc6ee1a42b0c1c413de143a01559cb491c2e5-dirty pimarin parents: 0 diff changeset	237 <param argument="--bandage_plot_path" type="data" format="svg" multiple="false" optional="true" label="Bandage plot" help="Bandage visualisation file"/>
0 c49ec8c0b046 planemo upload commit bb69b191fe3ce756655bf90af4d69e4472f94ba9-dirty pimarin parents: diff changeset	238 <expand macro="analysis_software_version"/>
1 421032d8dd5d planemo upload commit 0a5fc6ee1a42b0c1c413de143a01559cb491c2e5-dirty pimarin parents: 0 diff changeset	239 <expand macro="reference_database_version"/>
0 c49ec8c0b046 planemo upload commit bb69b191fe3ce756655bf90af4d69e4472f94ba9-dirty pimarin parents: diff changeset	240 </when>
c49ec8c0b046 planemo upload commit bb69b191fe3ce756655bf90af4d69e4472f94ba9-dirty pimarin parents: diff changeset	241 <when value="bracken">
c49ec8c0b046 planemo upload commit bb69b191fe3ce756655bf90af4d69e4472f94ba9-dirty pimarin parents: diff changeset	242 <param name="input" type="data" format="txt,tabular" multiple="false" label="Bracken report file" help="Tabular file from bracken output"/>
c49ec8c0b046 planemo upload commit bb69b191fe3ce756655bf90af4d69e4472f94ba9-dirty pimarin parents: diff changeset	243 <expand macro="analysis_software_version"/>
c49ec8c0b046 planemo upload commit bb69b191fe3ce756655bf90af4d69e4472f94ba9-dirty pimarin parents: diff changeset	244 <expand macro="reference_database_version"/>
3 73aea20004ff planemo upload commit 8721cd95e02dd6b3a02e2eb549cd8ff6b1675ff8-dirty pimarin parents: 1 diff changeset	245 <param argument="--kraken_report_path" type="data" format="txt,tabular" multiple="false" optional="true" label="Kraken re-estimated report" help="New kraken report from bracken tool"/>
0 c49ec8c0b046 planemo upload commit bb69b191fe3ce756655bf90af4d69e4472f94ba9-dirty pimarin parents: diff changeset	246 <param argument="--threshold" type="integer" min="0" optional="true" label="PRIOR on read numbers" help="Prior of read for estimation, default is 0"/>
1 421032d8dd5d planemo upload commit 0a5fc6ee1a42b0c1c413de143a01559cb491c2e5-dirty pimarin parents: 0 diff changeset	247 <param argument="--read_len" type="integer" min="0" optional="true" label="Read length"/>
3 73aea20004ff planemo upload commit 8721cd95e02dd6b3a02e2eb549cd8ff6b1675ff8-dirty pimarin parents: 1 diff changeset	248 <param argument="--level" type="select" label="Taxonomic level estimation" optional="true" help="Level of final abundance (from Domain to subspecies, default on species)">
0 c49ec8c0b046 planemo upload commit bb69b191fe3ce756655bf90af4d69e4472f94ba9-dirty pimarin parents: diff changeset	249 <option value="D">Domain</option>
c49ec8c0b046 planemo upload commit bb69b191fe3ce756655bf90af4d69e4472f94ba9-dirty pimarin parents: diff changeset	250 <option value="P">Phylum</option>
c49ec8c0b046 planemo upload commit bb69b191fe3ce756655bf90af4d69e4472f94ba9-dirty pimarin parents: diff changeset	251 <option value="C">Class</option>
c49ec8c0b046 planemo upload commit bb69b191fe3ce756655bf90af4d69e4472f94ba9-dirty pimarin parents: diff changeset	252 <option value="O">Order</option>
c49ec8c0b046 planemo upload commit bb69b191fe3ce756655bf90af4d69e4472f94ba9-dirty pimarin parents: diff changeset	253 <option value="F">Family</option>
c49ec8c0b046 planemo upload commit bb69b191fe3ce756655bf90af4d69e4472f94ba9-dirty pimarin parents: diff changeset	254 <option value="G">Genus</option>
c49ec8c0b046 planemo upload commit bb69b191fe3ce756655bf90af4d69e4472f94ba9-dirty pimarin parents: diff changeset	255 <option value="S">Species</option>
c49ec8c0b046 planemo upload commit bb69b191fe3ce756655bf90af4d69e4472f94ba9-dirty pimarin parents: diff changeset	256 <option value="S+">Subspecies</option>
c49ec8c0b046 planemo upload commit bb69b191fe3ce756655bf90af4d69e4472f94ba9-dirty pimarin parents: diff changeset	257 </param>
c49ec8c0b046 planemo upload commit bb69b191fe3ce756655bf90af4d69e4472f94ba9-dirty pimarin parents: diff changeset	258 </when>
c49ec8c0b046 planemo upload commit bb69b191fe3ce756655bf90af4d69e4472f94ba9-dirty pimarin parents: diff changeset	259 <when value="fastp">
c49ec8c0b046 planemo upload commit bb69b191fe3ce756655bf90af4d69e4472f94ba9-dirty pimarin parents: diff changeset	260 <param name="input" type="data" format="json" multiple="false" label="Fastp report file" help="Fastp result in json format"/>
1 421032d8dd5d planemo upload commit 0a5fc6ee1a42b0c1c413de143a01559cb491c2e5-dirty pimarin parents: 0 diff changeset	261 <param argument="--trimmed_forward_R1_path" type="data" format="fastq,fastq.gz" optional="true" multiple="false" label="Fastp trimmed R1" help="trimmed file R1"/>
421032d8dd5d planemo upload commit 0a5fc6ee1a42b0c1c413de143a01559cb491c2e5-dirty pimarin parents: 0 diff changeset	262 <param argument="--trimmed_reverse_R2_path" type="data" format="fastq,fastq.gz" optional="true" multiple="false" label="Fastp trimmed R2" help="trimmed file R2"/>
3 73aea20004ff planemo upload commit 8721cd95e02dd6b3a02e2eb549cd8ff6b1675ff8-dirty pimarin parents: 1 diff changeset	263 <param argument="--html_report_path" type="data" format="html" multiple="false" optional="true" label="Fastp report html" help="Fastp result in html format"/>
0 c49ec8c0b046 planemo upload commit bb69b191fe3ce756655bf90af4d69e4472f94ba9-dirty pimarin parents: diff changeset	264 <expand macro="analysis_software_version"/>
1 421032d8dd5d planemo upload commit 0a5fc6ee1a42b0c1c413de143a01559cb491c2e5-dirty pimarin parents: 0 diff changeset	265 <expand macro="reference_database_version"/>
0 c49ec8c0b046 planemo upload commit bb69b191fe3ce756655bf90af4d69e4472f94ba9-dirty pimarin parents: diff changeset	266 </when>
c49ec8c0b046 planemo upload commit bb69b191fe3ce756655bf90af4d69e4472f94ba9-dirty pimarin parents: diff changeset	267 <when value="integronfinder2">
c49ec8c0b046 planemo upload commit bb69b191fe3ce756655bf90af4d69e4472f94ba9-dirty pimarin parents: diff changeset	268 <param name="input" type="data" format="txt,tabular" multiple="false" label="Integronfinder report" help="Integron file from integronfinder2"/>
3 73aea20004ff planemo upload commit 8721cd95e02dd6b3a02e2eb549cd8ff6b1675ff8-dirty pimarin parents: 1 diff changeset	269 <param argument="--summary_file_path" type="data" format="txt,tabular" multiple="false" optional="true" label="Summary report" help="Summary file from integronfinder2"/>
0 c49ec8c0b046 planemo upload commit bb69b191fe3ce756655bf90af4d69e4472f94ba9-dirty pimarin parents: diff changeset	270 <expand macro="analysis_software_version"/>
1 421032d8dd5d planemo upload commit 0a5fc6ee1a42b0c1c413de143a01559cb491c2e5-dirty pimarin parents: 0 diff changeset	271 <expand macro="reference_database_version"/>
0 c49ec8c0b046 planemo upload commit bb69b191fe3ce756655bf90af4d69e4472f94ba9-dirty pimarin parents: diff changeset	272 </when>
c49ec8c0b046 planemo upload commit bb69b191fe3ce756655bf90af4d69e4472f94ba9-dirty pimarin parents: diff changeset	273 <when value="isescan">
c49ec8c0b046 planemo upload commit bb69b191fe3ce756655bf90af4d69e4472f94ba9-dirty pimarin parents: diff changeset	274 <param name="input" type="data" format="txt,tabular" multiple="false" label="Isescan report" help="IseScan file from integronfinder2"/>
1 421032d8dd5d planemo upload commit 0a5fc6ee1a42b0c1c413de143a01559cb491c2e5-dirty pimarin parents: 0 diff changeset	275 <param argument="--summary_path" type="data" format="tabular" optional="true" multiple="false" label="summary file" help="ISEscan summary"/>
421032d8dd5d planemo upload commit 0a5fc6ee1a42b0c1c413de143a01559cb491c2e5-dirty pimarin parents: 0 diff changeset	276 <param argument="--annotation_path" type="data" format="gff" optional="true" multiple="false" label="annotation results" help="Annotation in gff file format"/>
421032d8dd5d planemo upload commit 0a5fc6ee1a42b0c1c413de143a01559cb491c2e5-dirty pimarin parents: 0 diff changeset	277 <param argument="--orf_fna_path" type="data" format="fasta" optional="true" multiple="false" label="ORF fna file" help="Nuleotide sequence to the ORFs"/>
421032d8dd5d planemo upload commit 0a5fc6ee1a42b0c1c413de143a01559cb491c2e5-dirty pimarin parents: 0 diff changeset	278 <param argument="--orf_faa_path" type="data" format="fasta" optional="true" multiple="false" label="ORF faa file" help="Amino acid sequence to the ORFs"/>
421032d8dd5d planemo upload commit 0a5fc6ee1a42b0c1c413de143a01559cb491c2e5-dirty pimarin parents: 0 diff changeset	279 <param argument="--is_fna_path" type="data" format="fasta" optional="true" multiple="false" label="IS fna file" help="Nuleotide sequence to the inserted elements"/>
0 c49ec8c0b046 planemo upload commit bb69b191fe3ce756655bf90af4d69e4472f94ba9-dirty pimarin parents: diff changeset	280 <expand macro="analysis_software_version"/>
1 421032d8dd5d planemo upload commit 0a5fc6ee1a42b0c1c413de143a01559cb491c2e5-dirty pimarin parents: 0 diff changeset	281 <expand macro="reference_database_version"/>
0 c49ec8c0b046 planemo upload commit bb69b191fe3ce756655bf90af4d69e4472f94ba9-dirty pimarin parents: diff changeset	282 </when>
c49ec8c0b046 planemo upload commit bb69b191fe3ce756655bf90af4d69e4472f94ba9-dirty pimarin parents: diff changeset	283 <when value="kraken2">
c49ec8c0b046 planemo upload commit bb69b191fe3ce756655bf90af4d69e4472f94ba9-dirty pimarin parents: diff changeset	284 <param name="input" type="data" format="txt,tabular" multiple="false" label="kraken report" help="Taxonomic assignation file from kraken2"/>
c49ec8c0b046 planemo upload commit bb69b191fe3ce756655bf90af4d69e4472f94ba9-dirty pimarin parents: diff changeset	285 <param argument="--seq_classification_file_path" type="data" format="txt,tabular" optional="true" multiple="false" label="Sequence assignation" help="Reads assignation file"/>
c49ec8c0b046 planemo upload commit bb69b191fe3ce756655bf90af4d69e4472f94ba9-dirty pimarin parents: diff changeset	286 <expand macro="analysis_software_version"/>
c49ec8c0b046 planemo upload commit bb69b191fe3ce756655bf90af4d69e4472f94ba9-dirty pimarin parents: diff changeset	287 <expand macro="reference_database_version"/>
c49ec8c0b046 planemo upload commit bb69b191fe3ce756655bf90af4d69e4472f94ba9-dirty pimarin parents: diff changeset	288 </when>
1 421032d8dd5d planemo upload commit 0a5fc6ee1a42b0c1c413de143a01559cb491c2e5-dirty pimarin parents: 0 diff changeset	289 <when value="multiqc">
421032d8dd5d planemo upload commit 0a5fc6ee1a42b0c1c413de143a01559cb491c2e5-dirty pimarin parents: 0 diff changeset	290 <param name="input" type="data" format="html" multiple="false" label="MultiQC report" help="Html report from MultiQC"/>
421032d8dd5d planemo upload commit 0a5fc6ee1a42b0c1c413de143a01559cb491c2e5-dirty pimarin parents: 0 diff changeset	291 <expand macro="analysis_software_version"/>
421032d8dd5d planemo upload commit 0a5fc6ee1a42b0c1c413de143a01559cb491c2e5-dirty pimarin parents: 0 diff changeset	292 <expand macro="reference_database_version"/>
421032d8dd5d planemo upload commit 0a5fc6ee1a42b0c1c413de143a01559cb491c2e5-dirty pimarin parents: 0 diff changeset	293 </when>
0 c49ec8c0b046 planemo upload commit bb69b191fe3ce756655bf90af4d69e4472f94ba9-dirty pimarin parents: diff changeset	294 <when value="plasmidfinder">
c49ec8c0b046 planemo upload commit bb69b191fe3ce756655bf90af4d69e4472f94ba9-dirty pimarin parents: diff changeset	295 <param name="input" type="data" format="json" multiple="false" label="Json report" help="Plasmidfinder result from json file"/>
1 421032d8dd5d planemo upload commit 0a5fc6ee1a42b0c1c413de143a01559cb491c2e5-dirty pimarin parents: 0 diff changeset	296 <param argument="--genome_hit_path" type="data" format="fasta" optional="true" multiple="false" label="Genome hits" help="Sequence hit in the analyzed genome"/>
421032d8dd5d planemo upload commit 0a5fc6ee1a42b0c1c413de143a01559cb491c2e5-dirty pimarin parents: 0 diff changeset	297 <param argument="--plasmid_hit_path" type="data" format="fasta" optional="true" multiple="false" label="Plasmid hits" help="Plasmid sequence identified"/>
0 c49ec8c0b046 planemo upload commit bb69b191fe3ce756655bf90af4d69e4472f94ba9-dirty pimarin parents: diff changeset	298 <expand macro="analysis_software_version"/>
c49ec8c0b046 planemo upload commit bb69b191fe3ce756655bf90af4d69e4472f94ba9-dirty pimarin parents: diff changeset	299 <expand macro="reference_database_version"/>
c49ec8c0b046 planemo upload commit bb69b191fe3ce756655bf90af4d69e4472f94ba9-dirty pimarin parents: diff changeset	300 </when>
c49ec8c0b046 planemo upload commit bb69b191fe3ce756655bf90af4d69e4472f94ba9-dirty pimarin parents: diff changeset	301 <when value="quast">
c49ec8c0b046 planemo upload commit bb69b191fe3ce756655bf90af4d69e4472f94ba9-dirty pimarin parents: diff changeset	302 <param name="input" type="data" format="txt,tabular" multiple="false" label="Quast report" help="Tabular Quast report"/>
3 73aea20004ff planemo upload commit 8721cd95e02dd6b3a02e2eb549cd8ff6b1675ff8-dirty pimarin parents: 1 diff changeset	303 <param argument="--quast_html_path" type="data" format="html" multiple="false" optional="true" label="Quast html report" help="Quast html report"/>
0 c49ec8c0b046 planemo upload commit bb69b191fe3ce756655bf90af4d69e4472f94ba9-dirty pimarin parents: diff changeset	304 <expand macro="analysis_software_version"/>
1 421032d8dd5d planemo upload commit 0a5fc6ee1a42b0c1c413de143a01559cb491c2e5-dirty pimarin parents: 0 diff changeset	305 <expand macro="reference_database_version"/>
0 c49ec8c0b046 planemo upload commit bb69b191fe3ce756655bf90af4d69e4472f94ba9-dirty pimarin parents: diff changeset	306 </when>
c49ec8c0b046 planemo upload commit bb69b191fe3ce756655bf90af4d69e4472f94ba9-dirty pimarin parents: diff changeset	307 <when value="recentrifuge">
c49ec8c0b046 planemo upload commit bb69b191fe3ce756655bf90af4d69e4472f94ba9-dirty pimarin parents: diff changeset	308 <param name="input" type="data" format="txt,tabular" multiple="false" label="Recentrifuge data file"/>
1 421032d8dd5d planemo upload commit 0a5fc6ee1a42b0c1c413de143a01559cb491c2e5-dirty pimarin parents: 0 diff changeset	309 <param argument="--rcf_stat_path" type="data" format="txt,tabular" optional="true" multiple="false" label="Recentrifuge stat file"/>
0 c49ec8c0b046 planemo upload commit bb69b191fe3ce756655bf90af4d69e4472f94ba9-dirty pimarin parents: diff changeset	310 <param argument="--rcf_html_path" type="data" format="html" optional="true" multiple="false" label="Recentrifuge html report file"/>
c49ec8c0b046 planemo upload commit bb69b191fe3ce756655bf90af4d69e4472f94ba9-dirty pimarin parents: diff changeset	311 <expand macro="analysis_software_version"/>
c49ec8c0b046 planemo upload commit bb69b191fe3ce756655bf90af4d69e4472f94ba9-dirty pimarin parents: diff changeset	312 <expand macro="reference_database_version"/>
c49ec8c0b046 planemo upload commit bb69b191fe3ce756655bf90af4d69e4472f94ba9-dirty pimarin parents: diff changeset	313 </when>
c49ec8c0b046 planemo upload commit bb69b191fe3ce756655bf90af4d69e4472f94ba9-dirty pimarin parents: diff changeset	314 <when value="refseqmasher">
c49ec8c0b046 planemo upload commit bb69b191fe3ce756655bf90af4d69e4472f94ba9-dirty pimarin parents: diff changeset	315 <param name="input" type="data" format="txt,tabular" multiple="false" label="RefsesMasher results"/>
c49ec8c0b046 planemo upload commit bb69b191fe3ce756655bf90af4d69e4472f94ba9-dirty pimarin parents: diff changeset	316 <expand macro="analysis_software_version"/>
1 421032d8dd5d planemo upload commit 0a5fc6ee1a42b0c1c413de143a01559cb491c2e5-dirty pimarin parents: 0 diff changeset	317 <expand macro="reference_database_version"/>
0 c49ec8c0b046 planemo upload commit bb69b191fe3ce756655bf90af4d69e4472f94ba9-dirty pimarin parents: diff changeset	318 </when>
c49ec8c0b046 planemo upload commit bb69b191fe3ce756655bf90af4d69e4472f94ba9-dirty pimarin parents: diff changeset	319 <when value="shovill">
c49ec8c0b046 planemo upload commit bb69b191fe3ce756655bf90af4d69e4472f94ba9-dirty pimarin parents: diff changeset	320 <param name="input" type="data" format="fasta" multiple="false" label="Contigs file" help="Contig fasta file from assembly"/>
c49ec8c0b046 planemo upload commit bb69b191fe3ce756655bf90af4d69e4472f94ba9-dirty pimarin parents: diff changeset	321 <param argument="--contig_graph_path" type="data" format="txt" optional="true" multiple="false" label="Contig graph file" help="Graphic file assembly"/>
c49ec8c0b046 planemo upload commit bb69b191fe3ce756655bf90af4d69e4472f94ba9-dirty pimarin parents: diff changeset	322 <param argument="--bam_file_path" type="data" format="bam" optional="true" multiple="false" label="Bam file" help="Alignemnt file in bam format"/>
c49ec8c0b046 planemo upload commit bb69b191fe3ce756655bf90af4d69e4472f94ba9-dirty pimarin parents: diff changeset	323 <expand macro="analysis_software_version"/>
1 421032d8dd5d planemo upload commit 0a5fc6ee1a42b0c1c413de143a01559cb491c2e5-dirty pimarin parents: 0 diff changeset	324 <expand macro="reference_database_version"/>
0 c49ec8c0b046 planemo upload commit bb69b191fe3ce756655bf90af4d69e4472f94ba9-dirty pimarin parents: diff changeset	325 </when>
c49ec8c0b046 planemo upload commit bb69b191fe3ce756655bf90af4d69e4472f94ba9-dirty pimarin parents: diff changeset	326 <when value="staramr">
c49ec8c0b046 planemo upload commit bb69b191fe3ce756655bf90af4d69e4472f94ba9-dirty pimarin parents: diff changeset	327 <param name="input" type="data" format="txt,tabular" multiple="false" label="Resfinder report" help="Resfinder result from starAMR"/>
c49ec8c0b046 planemo upload commit bb69b191fe3ce756655bf90af4d69e4472f94ba9-dirty pimarin parents: diff changeset	328 <param argument="--mlst_file_path" type="data" format="txt,tabular" optional="true" multiple="false" label="MLST results" help="mlst scheme file result from starAMR"/>
c49ec8c0b046 planemo upload commit bb69b191fe3ce756655bf90af4d69e4472f94ba9-dirty pimarin parents: diff changeset	329 <param argument="--plasmidfinder_file_path" type="data" optional="true" format="txt,tabular" multiple="false" label="Plasmid results" help="Plasmidfinder result from starAMR"/>
c49ec8c0b046 planemo upload commit bb69b191fe3ce756655bf90af4d69e4472f94ba9-dirty pimarin parents: diff changeset	330 <param argument="--pointfinder_file_path" type="data" optional="true" format="txt,tabular" multiple="false" label="Pointfinder results" help="PointFinder result from starAMR"/>
c49ec8c0b046 planemo upload commit bb69b191fe3ce756655bf90af4d69e4472f94ba9-dirty pimarin parents: diff changeset	331 <param argument="--setting_file_path" type="data" optional="true" format="txt,tabular" multiple="false" label="Setting informations" help="Settings file from starAMR"/>
c49ec8c0b046 planemo upload commit bb69b191fe3ce756655bf90af4d69e4472f94ba9-dirty pimarin parents: diff changeset	332 <expand macro="analysis_software_version"/>
1 421032d8dd5d planemo upload commit 0a5fc6ee1a42b0c1c413de143a01559cb491c2e5-dirty pimarin parents: 0 diff changeset	333 <expand macro="reference_database_version"/>
0 c49ec8c0b046 planemo upload commit bb69b191fe3ce756655bf90af4d69e4472f94ba9-dirty pimarin parents: diff changeset	334 </when>
c49ec8c0b046 planemo upload commit bb69b191fe3ce756655bf90af4d69e4472f94ba9-dirty pimarin parents: diff changeset	335 <when value="tabular_file">
c49ec8c0b046 planemo upload commit bb69b191fe3ce756655bf90af4d69e4472f94ba9-dirty pimarin parents: diff changeset	336 <param name="input" type="data" format="txt,tabular" multiple="false" label="Tabular file type" help="Generic result file in tabular format with header"/>
3 73aea20004ff planemo upload commit 8721cd95e02dd6b3a02e2eb549cd8ff6b1675ff8-dirty pimarin parents: 1 diff changeset	337 <param argument="--analysis_software_name" type="text" multiple="false" optional="true" label="Tool name" help="Tool name which generated the result file"/>
0 c49ec8c0b046 planemo upload commit bb69b191fe3ce756655bf90af4d69e4472f94ba9-dirty pimarin parents: diff changeset	338 <expand macro="analysis_software_version"/>
1 421032d8dd5d planemo upload commit 0a5fc6ee1a42b0c1c413de143a01559cb491c2e5-dirty pimarin parents: 0 diff changeset	339 <expand macro="reference_database_version"/>
0 c49ec8c0b046 planemo upload commit bb69b191fe3ce756655bf90af4d69e4472f94ba9-dirty pimarin parents: diff changeset	340 </when>
c49ec8c0b046 planemo upload commit bb69b191fe3ce756655bf90af4d69e4472f94ba9-dirty pimarin parents: diff changeset	341 </conditional>
c49ec8c0b046 planemo upload commit bb69b191fe3ce756655bf90af4d69e4472f94ba9-dirty pimarin parents: diff changeset	342 </repeat>
c49ec8c0b046 planemo upload commit bb69b191fe3ce756655bf90af4d69e4472f94ba9-dirty pimarin parents: diff changeset	343 </section>
c49ec8c0b046 planemo upload commit bb69b191fe3ce756655bf90af4d69e4472f94ba9-dirty pimarin parents: diff changeset	344 <param name="log" type="boolean" truevalue="true" falsevalue="" label="Add log" help="Activate/Deactivate the log"/>
c49ec8c0b046 planemo upload commit bb69b191fe3ce756655bf90af4d69e4472f94ba9-dirty pimarin parents: diff changeset	345 </inputs>
c49ec8c0b046 planemo upload commit bb69b191fe3ce756655bf90af4d69e4472f94ba9-dirty pimarin parents: diff changeset	346 <outputs>
c49ec8c0b046 planemo upload commit bb69b191fe3ce756655bf90af4d69e4472f94ba9-dirty pimarin parents: diff changeset	347 <collection name="output_json" type="list" label="${tool.name} on ${on_string}: abromics formated json results">
c49ec8c0b046 planemo upload commit bb69b191fe3ce756655bf90af4d69e4472f94ba9-dirty pimarin parents: diff changeset	348 <discover_datasets pattern="(?P<designation>.+)\.json" format="json" directory="abromics_extracted_folder" />
c49ec8c0b046 planemo upload commit bb69b191fe3ce756655bf90af4d69e4472f94ba9-dirty pimarin parents: diff changeset	349 </collection>
c49ec8c0b046 planemo upload commit bb69b191fe3ce756655bf90af4d69e4472f94ba9-dirty pimarin parents: diff changeset	350 <data name="logfile" format="txt" label="${tool.name} on ${on_string}: log file">
c49ec8c0b046 planemo upload commit bb69b191fe3ce756655bf90af4d69e4472f94ba9-dirty pimarin parents: diff changeset	351 <filter> log == True </filter>
c49ec8c0b046 planemo upload commit bb69b191fe3ce756655bf90af4d69e4472f94ba9-dirty pimarin parents: diff changeset	352 </data>
c49ec8c0b046 planemo upload commit bb69b191fe3ce756655bf90af4d69e4472f94ba9-dirty pimarin parents: diff changeset	353 </outputs>
c49ec8c0b046 planemo upload commit bb69b191fe3ce756655bf90af4d69e4472f94ba9-dirty pimarin parents: diff changeset	354 <tests>
c49ec8c0b046 planemo upload commit bb69b191fe3ce756655bf90af4d69e4472f94ba9-dirty pimarin parents: diff changeset	355 <test expect_num_outputs="2"> <!-- TEST_1 abricate with logfile -->
c49ec8c0b046 planemo upload commit bb69b191fe3ce756655bf90af4d69e4472f94ba9-dirty pimarin parents: diff changeset	356 <section name="tool_section">
c49ec8c0b046 planemo upload commit bb69b191fe3ce756655bf90af4d69e4472f94ba9-dirty pimarin parents: diff changeset	357 <repeat name="tools">
c49ec8c0b046 planemo upload commit bb69b191fe3ce756655bf90af4d69e4472f94ba9-dirty pimarin parents: diff changeset	358 <conditional name="select_tool">
c49ec8c0b046 planemo upload commit bb69b191fe3ce756655bf90af4d69e4472f94ba9-dirty pimarin parents: diff changeset	359 <param name="tool_list" value="abricate"/>
c49ec8c0b046 planemo upload commit bb69b191fe3ce756655bf90af4d69e4472f94ba9-dirty pimarin parents: diff changeset	360 <param name="input" value="abricate/report.tsv" ftype="tabular"/>
c49ec8c0b046 planemo upload commit bb69b191fe3ce756655bf90af4d69e4472f94ba9-dirty pimarin parents: diff changeset	361 <param name="analysis_software_version" value="1.0"/>
c49ec8c0b046 planemo upload commit bb69b191fe3ce756655bf90af4d69e4472f94ba9-dirty pimarin parents: diff changeset	362 <param name="reference_database_version" value="2.0" />
c49ec8c0b046 planemo upload commit bb69b191fe3ce756655bf90af4d69e4472f94ba9-dirty pimarin parents: diff changeset	363 </conditional>
c49ec8c0b046 planemo upload commit bb69b191fe3ce756655bf90af4d69e4472f94ba9-dirty pimarin parents: diff changeset	364 </repeat>
c49ec8c0b046 planemo upload commit bb69b191fe3ce756655bf90af4d69e4472f94ba9-dirty pimarin parents: diff changeset	365 </section>
c49ec8c0b046 planemo upload commit bb69b191fe3ce756655bf90af4d69e4472f94ba9-dirty pimarin parents: diff changeset	366 <param name="log" value="true"/>
c49ec8c0b046 planemo upload commit bb69b191fe3ce756655bf90af4d69e4472f94ba9-dirty pimarin parents: diff changeset	367 <output_collection name="output_json" type="list">
c49ec8c0b046 planemo upload commit bb69b191fe3ce756655bf90af4d69e4472f94ba9-dirty pimarin parents: diff changeset	368 <expand macro="element_assert" name="abricate_0_output" text="Enterococcus faecalis V583"/>
c49ec8c0b046 planemo upload commit bb69b191fe3ce756655bf90af4d69e4472f94ba9-dirty pimarin parents: diff changeset	369 </output_collection>
c49ec8c0b046 planemo upload commit bb69b191fe3ce756655bf90af4d69e4472f94ba9-dirty pimarin parents: diff changeset	370 <output name="logfile" value="abricate_logfile.txt"/>
c49ec8c0b046 planemo upload commit bb69b191fe3ce756655bf90af4d69e4472f94ba9-dirty pimarin parents: diff changeset	371 </test>
c49ec8c0b046 planemo upload commit bb69b191fe3ce756655bf90af4d69e4472f94ba9-dirty pimarin parents: diff changeset	372 <test expect_num_outputs="1"> <!-- TEST_2 bakta all files -->
c49ec8c0b046 planemo upload commit bb69b191fe3ce756655bf90af4d69e4472f94ba9-dirty pimarin parents: diff changeset	373 <section name="tool_section">
c49ec8c0b046 planemo upload commit bb69b191fe3ce756655bf90af4d69e4472f94ba9-dirty pimarin parents: diff changeset	374 <repeat name="tools">
c49ec8c0b046 planemo upload commit bb69b191fe3ce756655bf90af4d69e4472f94ba9-dirty pimarin parents: diff changeset	375 <conditional name="select_tool">
c49ec8c0b046 planemo upload commit bb69b191fe3ce756655bf90af4d69e4472f94ba9-dirty pimarin parents: diff changeset	376 <param name="tool_list" value="bakta"/>
c49ec8c0b046 planemo upload commit bb69b191fe3ce756655bf90af4d69e4472f94ba9-dirty pimarin parents: diff changeset	377 <param name="input" value="bakta/bakta.json" ftype="json"/>
1 421032d8dd5d planemo upload commit 0a5fc6ee1a42b0c1c413de143a01559cb491c2e5-dirty pimarin parents: 0 diff changeset	378 <param name="annotation_tabular_path" value="bakta/bakta_summary.txt" ftype="txt"/>
421032d8dd5d planemo upload commit 0a5fc6ee1a42b0c1c413de143a01559cb491c2e5-dirty pimarin parents: 0 diff changeset	379 <param name="annotation_genbank_path" value="bakta/bakta_summary.txt" ftype="txt"/>
421032d8dd5d planemo upload commit 0a5fc6ee1a42b0c1c413de143a01559cb491c2e5-dirty pimarin parents: 0 diff changeset	380 <param name="annotation_embl_path" value="bakta/bakta_summary.txt" ftype="txt"/>
421032d8dd5d planemo upload commit 0a5fc6ee1a42b0c1c413de143a01559cb491c2e5-dirty pimarin parents: 0 diff changeset	381 <param name="contig_sequences_path" value="bakta/bakta_summary.txt" ftype="txt"/>
421032d8dd5d planemo upload commit 0a5fc6ee1a42b0c1c413de143a01559cb491c2e5-dirty pimarin parents: 0 diff changeset	382 <param name="hypothetical_protein_path" value="bakta/bakta_summary.txt" ftype="txt"/>
421032d8dd5d planemo upload commit 0a5fc6ee1a42b0c1c413de143a01559cb491c2e5-dirty pimarin parents: 0 diff changeset	383 <param name="hypothetical_tabular_path" value="bakta/bakta_summary.txt" ftype="txt"/>
0 c49ec8c0b046 planemo upload commit bb69b191fe3ce756655bf90af4d69e4472f94ba9-dirty pimarin parents: diff changeset	384 <param name="summary_result_path" value="bakta/bakta_summary.txt" ftype="txt"/>
1 421032d8dd5d planemo upload commit 0a5fc6ee1a42b0c1c413de143a01559cb491c2e5-dirty pimarin parents: 0 diff changeset	385 <param name="nucleotide_annotation_path" value="bakta/bakta_nucleotide_annotation.ffn" ftype="fasta"/>
0 c49ec8c0b046 planemo upload commit bb69b191fe3ce756655bf90af4d69e4472f94ba9-dirty pimarin parents: diff changeset	386 <param name="amino_acid_annotation_path" value="bakta/bakta_aminoacid.faa" ftype="fasta"/>
c49ec8c0b046 planemo upload commit bb69b191fe3ce756655bf90af4d69e4472f94ba9-dirty pimarin parents: diff changeset	387 <param name="gff_file_path" value="bakta/bakta_annotation.gff3" ftype="gff3"/>
1 421032d8dd5d planemo upload commit 0a5fc6ee1a42b0c1c413de143a01559cb491c2e5-dirty pimarin parents: 0 diff changeset	388 <param name="analysis_software_version" value="1.8.1"/>
421032d8dd5d planemo upload commit 0a5fc6ee1a42b0c1c413de143a01559cb491c2e5-dirty pimarin parents: 0 diff changeset	389 <param name="reference_database_version" value="5.0"/>
0 c49ec8c0b046 planemo upload commit bb69b191fe3ce756655bf90af4d69e4472f94ba9-dirty pimarin parents: diff changeset	390 </conditional>
c49ec8c0b046 planemo upload commit bb69b191fe3ce756655bf90af4d69e4472f94ba9-dirty pimarin parents: diff changeset	391 </repeat>
c49ec8c0b046 planemo upload commit bb69b191fe3ce756655bf90af4d69e4472f94ba9-dirty pimarin parents: diff changeset	392 </section>
c49ec8c0b046 planemo upload commit bb69b191fe3ce756655bf90af4d69e4472f94ba9-dirty pimarin parents: diff changeset	393 <output_collection name="output_json" type="list" count="1">
c49ec8c0b046 planemo upload commit bb69b191fe3ce756655bf90af4d69e4472f94ba9-dirty pimarin parents: diff changeset	394 <expand macro="element_assert" name="bakta_0_output" text="UniRef50_A0A0H2ZNL3"/>
c49ec8c0b046 planemo upload commit bb69b191fe3ce756655bf90af4d69e4472f94ba9-dirty pimarin parents: diff changeset	395 </output_collection>
c49ec8c0b046 planemo upload commit bb69b191fe3ce756655bf90af4d69e4472f94ba9-dirty pimarin parents: diff changeset	396 </test>
1 421032d8dd5d planemo upload commit 0a5fc6ee1a42b0c1c413de143a01559cb491c2e5-dirty pimarin parents: 0 diff changeset	397 <test expect_num_outputs="1"> <!-- TEST_3 bakta with no files -->
421032d8dd5d planemo upload commit 0a5fc6ee1a42b0c1c413de143a01559cb491c2e5-dirty pimarin parents: 0 diff changeset	398 <section name="tool_section">
421032d8dd5d planemo upload commit 0a5fc6ee1a42b0c1c413de143a01559cb491c2e5-dirty pimarin parents: 0 diff changeset	399 <repeat name="tools">
421032d8dd5d planemo upload commit 0a5fc6ee1a42b0c1c413de143a01559cb491c2e5-dirty pimarin parents: 0 diff changeset	400 <conditional name="select_tool">
421032d8dd5d planemo upload commit 0a5fc6ee1a42b0c1c413de143a01559cb491c2e5-dirty pimarin parents: 0 diff changeset	401 <param name="tool_list" value="bakta"/>
421032d8dd5d planemo upload commit 0a5fc6ee1a42b0c1c413de143a01559cb491c2e5-dirty pimarin parents: 0 diff changeset	402 <param name="input" value="bakta/bakta.json" ftype="json"/>
421032d8dd5d planemo upload commit 0a5fc6ee1a42b0c1c413de143a01559cb491c2e5-dirty pimarin parents: 0 diff changeset	403 </conditional>
421032d8dd5d planemo upload commit 0a5fc6ee1a42b0c1c413de143a01559cb491c2e5-dirty pimarin parents: 0 diff changeset	404 </repeat>
421032d8dd5d planemo upload commit 0a5fc6ee1a42b0c1c413de143a01559cb491c2e5-dirty pimarin parents: 0 diff changeset	405 </section>
421032d8dd5d planemo upload commit 0a5fc6ee1a42b0c1c413de143a01559cb491c2e5-dirty pimarin parents: 0 diff changeset	406 <output_collection name="output_json" type="list" count="1">
421032d8dd5d planemo upload commit 0a5fc6ee1a42b0c1c413de143a01559cb491c2e5-dirty pimarin parents: 0 diff changeset	407 <expand macro="element_assert" name="bakta_0_output" text="UniRef50_A0A0H2ZNL3"/>
421032d8dd5d planemo upload commit 0a5fc6ee1a42b0c1c413de143a01559cb491c2e5-dirty pimarin parents: 0 diff changeset	408 </output_collection>
421032d8dd5d planemo upload commit 0a5fc6ee1a42b0c1c413de143a01559cb491c2e5-dirty pimarin parents: 0 diff changeset	409 </test>
421032d8dd5d planemo upload commit 0a5fc6ee1a42b0c1c413de143a01559cb491c2e5-dirty pimarin parents: 0 diff changeset	410 <test expect_num_outputs="1"> <!-- TEST_4 All tool in repeat -->
0 c49ec8c0b046 planemo upload commit bb69b191fe3ce756655bf90af4d69e4472f94ba9-dirty pimarin parents: diff changeset	411 <section name="tool_section">
c49ec8c0b046 planemo upload commit bb69b191fe3ce756655bf90af4d69e4472f94ba9-dirty pimarin parents: diff changeset	412 <repeat name="tools">
c49ec8c0b046 planemo upload commit bb69b191fe3ce756655bf90af4d69e4472f94ba9-dirty pimarin parents: diff changeset	413 <conditional name="select_tool">
c49ec8c0b046 planemo upload commit bb69b191fe3ce756655bf90af4d69e4472f94ba9-dirty pimarin parents: diff changeset	414 <param name="tool_list" value="abricate"/>
c49ec8c0b046 planemo upload commit bb69b191fe3ce756655bf90af4d69e4472f94ba9-dirty pimarin parents: diff changeset	415 <param name="input" value="abricate/report.tsv" ftype="tabular"/>
c49ec8c0b046 planemo upload commit bb69b191fe3ce756655bf90af4d69e4472f94ba9-dirty pimarin parents: diff changeset	416 <param name="analysis_software_version" value="1.0"/>
c49ec8c0b046 planemo upload commit bb69b191fe3ce756655bf90af4d69e4472f94ba9-dirty pimarin parents: diff changeset	417 <param name="reference_database_version" value="2.0" />
c49ec8c0b046 planemo upload commit bb69b191fe3ce756655bf90af4d69e4472f94ba9-dirty pimarin parents: diff changeset	418 </conditional>
c49ec8c0b046 planemo upload commit bb69b191fe3ce756655bf90af4d69e4472f94ba9-dirty pimarin parents: diff changeset	419 </repeat>
c49ec8c0b046 planemo upload commit bb69b191fe3ce756655bf90af4d69e4472f94ba9-dirty pimarin parents: diff changeset	420 <repeat name="tools">
c49ec8c0b046 planemo upload commit bb69b191fe3ce756655bf90af4d69e4472f94ba9-dirty pimarin parents: diff changeset	421 <conditional name="select_tool">
c49ec8c0b046 planemo upload commit bb69b191fe3ce756655bf90af4d69e4472f94ba9-dirty pimarin parents: diff changeset	422 <param name="tool_list" value="bakta"/>
c49ec8c0b046 planemo upload commit bb69b191fe3ce756655bf90af4d69e4472f94ba9-dirty pimarin parents: diff changeset	423 <param name="input" value="bakta/bakta.json" ftype="json"/>
1 421032d8dd5d planemo upload commit 0a5fc6ee1a42b0c1c413de143a01559cb491c2e5-dirty pimarin parents: 0 diff changeset	424 <param name="annotation_tabular_path" value="bakta/bakta_annotation.tsv" ftype="tabular"/>
421032d8dd5d planemo upload commit 0a5fc6ee1a42b0c1c413de143a01559cb491c2e5-dirty pimarin parents: 0 diff changeset	425 <param name="annotation_genbank_path" value="bakta/bakta_gbff.gbff"/>
421032d8dd5d planemo upload commit 0a5fc6ee1a42b0c1c413de143a01559cb491c2e5-dirty pimarin parents: 0 diff changeset	426 <param name="annotation_embl_path" value="bakta/bakta_embl.embl"/>
421032d8dd5d planemo upload commit 0a5fc6ee1a42b0c1c413de143a01559cb491c2e5-dirty pimarin parents: 0 diff changeset	427 <param name="contig_sequences_path" value="bakta/bakta_contigs_sequences.fna" ftype="fasta"/>
421032d8dd5d planemo upload commit 0a5fc6ee1a42b0c1c413de143a01559cb491c2e5-dirty pimarin parents: 0 diff changeset	428 <param name="hypothetical_protein_path" value="bakta/bakta_hypothetical.faa" ftype="fasta"/>
421032d8dd5d planemo upload commit 0a5fc6ee1a42b0c1c413de143a01559cb491c2e5-dirty pimarin parents: 0 diff changeset	429 <param name="hypothetical_tabular_path" value="bakta/bakta_hypothetical.tsv" ftype="tabular"/>
421032d8dd5d planemo upload commit 0a5fc6ee1a42b0c1c413de143a01559cb491c2e5-dirty pimarin parents: 0 diff changeset	430 <param name="plot_file_path" value="bakta/bakta_plot.svg"/>
421032d8dd5d planemo upload commit 0a5fc6ee1a42b0c1c413de143a01559cb491c2e5-dirty pimarin parents: 0 diff changeset	431 <param name="summary_result_path" value="bakta/bakta_summary.txt" ftype="txt"/>
421032d8dd5d planemo upload commit 0a5fc6ee1a42b0c1c413de143a01559cb491c2e5-dirty pimarin parents: 0 diff changeset	432 <param name="nucleotide_annotation_path" value="bakta/bakta_nucleotide_annotation.ffn" ftype="fasta"/>
421032d8dd5d planemo upload commit 0a5fc6ee1a42b0c1c413de143a01559cb491c2e5-dirty pimarin parents: 0 diff changeset	433 <param name="amino_acid_annotation_path" value="bakta/bakta_aminoacid.faa" ftype="fasta"/>
421032d8dd5d planemo upload commit 0a5fc6ee1a42b0c1c413de143a01559cb491c2e5-dirty pimarin parents: 0 diff changeset	434 <param name="gff_file_path" value="bakta/bakta_annotation.gff3" ftype="gff3"/>
421032d8dd5d planemo upload commit 0a5fc6ee1a42b0c1c413de143a01559cb491c2e5-dirty pimarin parents: 0 diff changeset	435 <param name="analysis_software_version" value="1.8.1"/>
421032d8dd5d planemo upload commit 0a5fc6ee1a42b0c1c413de143a01559cb491c2e5-dirty pimarin parents: 0 diff changeset	436 <param name="reference_database_version" value="5.0"/>
0 c49ec8c0b046 planemo upload commit bb69b191fe3ce756655bf90af4d69e4472f94ba9-dirty pimarin parents: diff changeset	437 </conditional>
c49ec8c0b046 planemo upload commit bb69b191fe3ce756655bf90af4d69e4472f94ba9-dirty pimarin parents: diff changeset	438 </repeat>
c49ec8c0b046 planemo upload commit bb69b191fe3ce756655bf90af4d69e4472f94ba9-dirty pimarin parents: diff changeset	439 <repeat name="tools">
c49ec8c0b046 planemo upload commit bb69b191fe3ce756655bf90af4d69e4472f94ba9-dirty pimarin parents: diff changeset	440 <conditional name="select_tool">
c49ec8c0b046 planemo upload commit bb69b191fe3ce756655bf90af4d69e4472f94ba9-dirty pimarin parents: diff changeset	441 <param name="tool_list" value="bandage"/>
c49ec8c0b046 planemo upload commit bb69b191fe3ce756655bf90af4d69e4472f94ba9-dirty pimarin parents: diff changeset	442 <param name="input" value="bandage/bandage_info.txt" ftype="txt"/>
1 421032d8dd5d planemo upload commit 0a5fc6ee1a42b0c1c413de143a01559cb491c2e5-dirty pimarin parents: 0 diff changeset	443 <param name="bandage_plot_path" value="bandage/bandage_plot.svg"/>
421032d8dd5d planemo upload commit 0a5fc6ee1a42b0c1c413de143a01559cb491c2e5-dirty pimarin parents: 0 diff changeset	444 <param name="analysis_software_version" value="1.0"/>
421032d8dd5d planemo upload commit 0a5fc6ee1a42b0c1c413de143a01559cb491c2e5-dirty pimarin parents: 0 diff changeset	445 <param name="reference_database_version" value="1.0"/>
0 c49ec8c0b046 planemo upload commit bb69b191fe3ce756655bf90af4d69e4472f94ba9-dirty pimarin parents: diff changeset	446 </conditional>
c49ec8c0b046 planemo upload commit bb69b191fe3ce756655bf90af4d69e4472f94ba9-dirty pimarin parents: diff changeset	447 </repeat>
c49ec8c0b046 planemo upload commit bb69b191fe3ce756655bf90af4d69e4472f94ba9-dirty pimarin parents: diff changeset	448 <repeat name="tools">
c49ec8c0b046 planemo upload commit bb69b191fe3ce756655bf90af4d69e4472f94ba9-dirty pimarin parents: diff changeset	449 <conditional name="select_tool">
c49ec8c0b046 planemo upload commit bb69b191fe3ce756655bf90af4d69e4472f94ba9-dirty pimarin parents: diff changeset	450 <param name="tool_list" value="bracken"/>
c49ec8c0b046 planemo upload commit bb69b191fe3ce756655bf90af4d69e4472f94ba9-dirty pimarin parents: diff changeset	451 <param name="input" value="bracken/bracken_report.tsv" ftype="tabular"/>
1 421032d8dd5d planemo upload commit 0a5fc6ee1a42b0c1c413de143a01559cb491c2e5-dirty pimarin parents: 0 diff changeset	452 <param name="kraken_report_path" value="bracken/bracken_kraken_report.tsv"/>
421032d8dd5d planemo upload commit 0a5fc6ee1a42b0c1c413de143a01559cb491c2e5-dirty pimarin parents: 0 diff changeset	453 <param name="read_len" value="100"/>
0 c49ec8c0b046 planemo upload commit bb69b191fe3ce756655bf90af4d69e4472f94ba9-dirty pimarin parents: diff changeset	454 <param name="level" value="S"/>
1 421032d8dd5d planemo upload commit 0a5fc6ee1a42b0c1c413de143a01559cb491c2e5-dirty pimarin parents: 0 diff changeset	455 <param name="threshold" value="1"/>
421032d8dd5d planemo upload commit 0a5fc6ee1a42b0c1c413de143a01559cb491c2e5-dirty pimarin parents: 0 diff changeset	456 <param name="analysis_software_version" value="1.0"/>
421032d8dd5d planemo upload commit 0a5fc6ee1a42b0c1c413de143a01559cb491c2e5-dirty pimarin parents: 0 diff changeset	457 <param name="reference_database_version" value="1.0"/>
0 c49ec8c0b046 planemo upload commit bb69b191fe3ce756655bf90af4d69e4472f94ba9-dirty pimarin parents: diff changeset	458 </conditional>
c49ec8c0b046 planemo upload commit bb69b191fe3ce756655bf90af4d69e4472f94ba9-dirty pimarin parents: diff changeset	459 </repeat>
c49ec8c0b046 planemo upload commit bb69b191fe3ce756655bf90af4d69e4472f94ba9-dirty pimarin parents: diff changeset	460 <repeat name="tools">
c49ec8c0b046 planemo upload commit bb69b191fe3ce756655bf90af4d69e4472f94ba9-dirty pimarin parents: diff changeset	461 <conditional name="select_tool">
c49ec8c0b046 planemo upload commit bb69b191fe3ce756655bf90af4d69e4472f94ba9-dirty pimarin parents: diff changeset	462 <param name="tool_list" value="fastp"/>
c49ec8c0b046 planemo upload commit bb69b191fe3ce756655bf90af4d69e4472f94ba9-dirty pimarin parents: diff changeset	463 <param name="input" value="fastp/fastp_report.json" ftype="json"/>
1 421032d8dd5d planemo upload commit 0a5fc6ee1a42b0c1c413de143a01559cb491c2e5-dirty pimarin parents: 0 diff changeset	464 <param name="trimmed_forward_R1_path" value="fastp/trimmed_R1.fastq.gz"/>
421032d8dd5d planemo upload commit 0a5fc6ee1a42b0c1c413de143a01559cb491c2e5-dirty pimarin parents: 0 diff changeset	465 <param name="trimmed_reverse_R2_path" value="fastp/trimmed_R2.fastq.gz"/>
421032d8dd5d planemo upload commit 0a5fc6ee1a42b0c1c413de143a01559cb491c2e5-dirty pimarin parents: 0 diff changeset	466 <param name="html_report_path" value="fastp/fastp_report.html"/>
421032d8dd5d planemo upload commit 0a5fc6ee1a42b0c1c413de143a01559cb491c2e5-dirty pimarin parents: 0 diff changeset	467 <param name="analysis_software_version" value="1.0"/>
421032d8dd5d planemo upload commit 0a5fc6ee1a42b0c1c413de143a01559cb491c2e5-dirty pimarin parents: 0 diff changeset	468 <param name="reference_database_version" value="1.0"/>
0 c49ec8c0b046 planemo upload commit bb69b191fe3ce756655bf90af4d69e4472f94ba9-dirty pimarin parents: diff changeset	469 </conditional>
c49ec8c0b046 planemo upload commit bb69b191fe3ce756655bf90af4d69e4472f94ba9-dirty pimarin parents: diff changeset	470 </repeat>
c49ec8c0b046 planemo upload commit bb69b191fe3ce756655bf90af4d69e4472f94ba9-dirty pimarin parents: diff changeset	471 <repeat name="tools">
c49ec8c0b046 planemo upload commit bb69b191fe3ce756655bf90af4d69e4472f94ba9-dirty pimarin parents: diff changeset	472 <conditional name="select_tool">
c49ec8c0b046 planemo upload commit bb69b191fe3ce756655bf90af4d69e4472f94ba9-dirty pimarin parents: diff changeset	473 <param name="tool_list" value="integronfinder2"/>
c49ec8c0b046 planemo upload commit bb69b191fe3ce756655bf90af4d69e4472f94ba9-dirty pimarin parents: diff changeset	474 <param name="input" value="integronfinder2/results.integrons" ftype="tabular"/>
c49ec8c0b046 planemo upload commit bb69b191fe3ce756655bf90af4d69e4472f94ba9-dirty pimarin parents: diff changeset	475 <param name="summary_file_path" value="integronfinder2/results.summary" ftype="tabular"/>
1 421032d8dd5d planemo upload commit 0a5fc6ee1a42b0c1c413de143a01559cb491c2e5-dirty pimarin parents: 0 diff changeset	476 <param name="analysis_software_version" value="1.0"/>
421032d8dd5d planemo upload commit 0a5fc6ee1a42b0c1c413de143a01559cb491c2e5-dirty pimarin parents: 0 diff changeset	477 <param name="reference_database_version" value="1.0"/>
421032d8dd5d planemo upload commit 0a5fc6ee1a42b0c1c413de143a01559cb491c2e5-dirty pimarin parents: 0 diff changeset	478
0 c49ec8c0b046 planemo upload commit bb69b191fe3ce756655bf90af4d69e4472f94ba9-dirty pimarin parents: diff changeset	479 </conditional>
c49ec8c0b046 planemo upload commit bb69b191fe3ce756655bf90af4d69e4472f94ba9-dirty pimarin parents: diff changeset	480 </repeat>
c49ec8c0b046 planemo upload commit bb69b191fe3ce756655bf90af4d69e4472f94ba9-dirty pimarin parents: diff changeset	481 <repeat name="tools">
c49ec8c0b046 planemo upload commit bb69b191fe3ce756655bf90af4d69e4472f94ba9-dirty pimarin parents: diff changeset	482 <conditional name="select_tool">
c49ec8c0b046 planemo upload commit bb69b191fe3ce756655bf90af4d69e4472f94ba9-dirty pimarin parents: diff changeset	483 <param name="tool_list" value="isescan"/>
c49ec8c0b046 planemo upload commit bb69b191fe3ce756655bf90af4d69e4472f94ba9-dirty pimarin parents: diff changeset	484 <param name="input" value="isescan/results.tsv" ftype="tabular"/>
1 421032d8dd5d planemo upload commit 0a5fc6ee1a42b0c1c413de143a01559cb491c2e5-dirty pimarin parents: 0 diff changeset	485 <param name="summary_path" value="isescan/summary.tsv"/>
421032d8dd5d planemo upload commit 0a5fc6ee1a42b0c1c413de143a01559cb491c2e5-dirty pimarin parents: 0 diff changeset	486 <param name="annotation_path" value="isescan/annotation.gff"/>
421032d8dd5d planemo upload commit 0a5fc6ee1a42b0c1c413de143a01559cb491c2e5-dirty pimarin parents: 0 diff changeset	487 <param name="orf_fna_path" value="isescan/orf.fna"/>
421032d8dd5d planemo upload commit 0a5fc6ee1a42b0c1c413de143a01559cb491c2e5-dirty pimarin parents: 0 diff changeset	488 <param name="orf_faa_path" value="isescan/orf.faa"/>
421032d8dd5d planemo upload commit 0a5fc6ee1a42b0c1c413de143a01559cb491c2e5-dirty pimarin parents: 0 diff changeset	489 <param name="is_fna_path" value="isescan/is.fna"/>
421032d8dd5d planemo upload commit 0a5fc6ee1a42b0c1c413de143a01559cb491c2e5-dirty pimarin parents: 0 diff changeset	490 <param name="analysis_software_version" value="1.0"/>
421032d8dd5d planemo upload commit 0a5fc6ee1a42b0c1c413de143a01559cb491c2e5-dirty pimarin parents: 0 diff changeset	491 <param name="reference_database_version" value="1.0"/>
0 c49ec8c0b046 planemo upload commit bb69b191fe3ce756655bf90af4d69e4472f94ba9-dirty pimarin parents: diff changeset	492 </conditional>
c49ec8c0b046 planemo upload commit bb69b191fe3ce756655bf90af4d69e4472f94ba9-dirty pimarin parents: diff changeset	493 </repeat>
c49ec8c0b046 planemo upload commit bb69b191fe3ce756655bf90af4d69e4472f94ba9-dirty pimarin parents: diff changeset	494 <repeat name="tools">
c49ec8c0b046 planemo upload commit bb69b191fe3ce756655bf90af4d69e4472f94ba9-dirty pimarin parents: diff changeset	495 <conditional name="select_tool">
c49ec8c0b046 planemo upload commit bb69b191fe3ce756655bf90af4d69e4472f94ba9-dirty pimarin parents: diff changeset	496 <param name="tool_list" value="kraken2"/>
c49ec8c0b046 planemo upload commit bb69b191fe3ce756655bf90af4d69e4472f94ba9-dirty pimarin parents: diff changeset	497 <param name="input" value="kraken2/taxonomy_report.tsv" ftype="tabular"/>
c49ec8c0b046 planemo upload commit bb69b191fe3ce756655bf90af4d69e4472f94ba9-dirty pimarin parents: diff changeset	498 <param name="seq_classification_file_path" value="kraken2/taxonomy_result.tsv" ftype="tabular"/>
1 421032d8dd5d planemo upload commit 0a5fc6ee1a42b0c1c413de143a01559cb491c2e5-dirty pimarin parents: 0 diff changeset	499 <param name="analysis_software_version" value="1.0"/>
421032d8dd5d planemo upload commit 0a5fc6ee1a42b0c1c413de143a01559cb491c2e5-dirty pimarin parents: 0 diff changeset	500 <param name="reference_database_version" value="1.0"/>
0 c49ec8c0b046 planemo upload commit bb69b191fe3ce756655bf90af4d69e4472f94ba9-dirty pimarin parents: diff changeset	501 </conditional>
c49ec8c0b046 planemo upload commit bb69b191fe3ce756655bf90af4d69e4472f94ba9-dirty pimarin parents: diff changeset	502 </repeat>
c49ec8c0b046 planemo upload commit bb69b191fe3ce756655bf90af4d69e4472f94ba9-dirty pimarin parents: diff changeset	503 <repeat name="tools">
c49ec8c0b046 planemo upload commit bb69b191fe3ce756655bf90af4d69e4472f94ba9-dirty pimarin parents: diff changeset	504 <conditional name="select_tool">
c49ec8c0b046 planemo upload commit bb69b191fe3ce756655bf90af4d69e4472f94ba9-dirty pimarin parents: diff changeset	505 <param name="tool_list" value="plasmidfinder"/>
c49ec8c0b046 planemo upload commit bb69b191fe3ce756655bf90af4d69e4472f94ba9-dirty pimarin parents: diff changeset	506 <param name="input" value="plasmidfinder/plasmidfinder_result.json" ftype="json"/>
1 421032d8dd5d planemo upload commit 0a5fc6ee1a42b0c1c413de143a01559cb491c2e5-dirty pimarin parents: 0 diff changeset	507 <param name="genome_hit_path" value="plasmidfinder/genome_hit.fasta" ftype="fasta"/>
421032d8dd5d planemo upload commit 0a5fc6ee1a42b0c1c413de143a01559cb491c2e5-dirty pimarin parents: 0 diff changeset	508 <param name="plasmid_hit_path" value="plasmidfinder/plasmid_hit.fasta" ftype="fasta"/>
421032d8dd5d planemo upload commit 0a5fc6ee1a42b0c1c413de143a01559cb491c2e5-dirty pimarin parents: 0 diff changeset	509 <param name="analysis_software_version" value="1.0"/>
421032d8dd5d planemo upload commit 0a5fc6ee1a42b0c1c413de143a01559cb491c2e5-dirty pimarin parents: 0 diff changeset	510 <param name="reference_database_version" value="1.0"/>
0 c49ec8c0b046 planemo upload commit bb69b191fe3ce756655bf90af4d69e4472f94ba9-dirty pimarin parents: diff changeset	511 </conditional>
c49ec8c0b046 planemo upload commit bb69b191fe3ce756655bf90af4d69e4472f94ba9-dirty pimarin parents: diff changeset	512 </repeat>
c49ec8c0b046 planemo upload commit bb69b191fe3ce756655bf90af4d69e4472f94ba9-dirty pimarin parents: diff changeset	513 <repeat name="tools">
c49ec8c0b046 planemo upload commit bb69b191fe3ce756655bf90af4d69e4472f94ba9-dirty pimarin parents: diff changeset	514 <conditional name="select_tool">
c49ec8c0b046 planemo upload commit bb69b191fe3ce756655bf90af4d69e4472f94ba9-dirty pimarin parents: diff changeset	515 <param name="tool_list" value="quast"/>
c49ec8c0b046 planemo upload commit bb69b191fe3ce756655bf90af4d69e4472f94ba9-dirty pimarin parents: diff changeset	516 <param name="input" value="quast/quast_result.tsv" ftype="tabular"/>
1 421032d8dd5d planemo upload commit 0a5fc6ee1a42b0c1c413de143a01559cb491c2e5-dirty pimarin parents: 0 diff changeset	517 <param name="quast_html_path" value="quast/quast_report.html"/>
421032d8dd5d planemo upload commit 0a5fc6ee1a42b0c1c413de143a01559cb491c2e5-dirty pimarin parents: 0 diff changeset	518 <param name="analysis_software_version" value="1.0"/>
421032d8dd5d planemo upload commit 0a5fc6ee1a42b0c1c413de143a01559cb491c2e5-dirty pimarin parents: 0 diff changeset	519 <param name="reference_database_version" value="1.0"/>
0 c49ec8c0b046 planemo upload commit bb69b191fe3ce756655bf90af4d69e4472f94ba9-dirty pimarin parents: diff changeset	520 </conditional>
c49ec8c0b046 planemo upload commit bb69b191fe3ce756655bf90af4d69e4472f94ba9-dirty pimarin parents: diff changeset	521 </repeat>
c49ec8c0b046 planemo upload commit bb69b191fe3ce756655bf90af4d69e4472f94ba9-dirty pimarin parents: diff changeset	522 <repeat name="tools">
c49ec8c0b046 planemo upload commit bb69b191fe3ce756655bf90af4d69e4472f94ba9-dirty pimarin parents: diff changeset	523 <conditional name="select_tool">
c49ec8c0b046 planemo upload commit bb69b191fe3ce756655bf90af4d69e4472f94ba9-dirty pimarin parents: diff changeset	524 <param name="tool_list" value="recentrifuge"/>
c49ec8c0b046 planemo upload commit bb69b191fe3ce756655bf90af4d69e4472f94ba9-dirty pimarin parents: diff changeset	525 <param name="input" value="recentrifuge/rcf_data.tsv" ftype="tabular"/>
1 421032d8dd5d planemo upload commit 0a5fc6ee1a42b0c1c413de143a01559cb491c2e5-dirty pimarin parents: 0 diff changeset	526 <param name="rcf_stat_path" value="recentrifuge/rcf_stat.tsv" ftype="tabular"/>
0 c49ec8c0b046 planemo upload commit bb69b191fe3ce756655bf90af4d69e4472f94ba9-dirty pimarin parents: diff changeset	527 <param name="rcf_html_path" value="recentrifuge/rcf_report.html"/>
1 421032d8dd5d planemo upload commit 0a5fc6ee1a42b0c1c413de143a01559cb491c2e5-dirty pimarin parents: 0 diff changeset	528 <param name="analysis_software_version" value="1.0"/>
421032d8dd5d planemo upload commit 0a5fc6ee1a42b0c1c413de143a01559cb491c2e5-dirty pimarin parents: 0 diff changeset	529 <param name="reference_database_version" value="1.0"/>
0 c49ec8c0b046 planemo upload commit bb69b191fe3ce756655bf90af4d69e4472f94ba9-dirty pimarin parents: diff changeset	530 </conditional>
c49ec8c0b046 planemo upload commit bb69b191fe3ce756655bf90af4d69e4472f94ba9-dirty pimarin parents: diff changeset	531 </repeat>
c49ec8c0b046 planemo upload commit bb69b191fe3ce756655bf90af4d69e4472f94ba9-dirty pimarin parents: diff changeset	532 <repeat name="tools">
c49ec8c0b046 planemo upload commit bb69b191fe3ce756655bf90af4d69e4472f94ba9-dirty pimarin parents: diff changeset	533 <conditional name="select_tool">
c49ec8c0b046 planemo upload commit bb69b191fe3ce756655bf90af4d69e4472f94ba9-dirty pimarin parents: diff changeset	534 <param name="tool_list" value="refseqmasher"/>
c49ec8c0b046 planemo upload commit bb69b191fe3ce756655bf90af4d69e4472f94ba9-dirty pimarin parents: diff changeset	535 <param name="input" value="refseqmasher/refsesqmasher.tsv" ftype="tabular"/>
1 421032d8dd5d planemo upload commit 0a5fc6ee1a42b0c1c413de143a01559cb491c2e5-dirty pimarin parents: 0 diff changeset	536 <param name="analysis_software_version" value="1.0"/>
421032d8dd5d planemo upload commit 0a5fc6ee1a42b0c1c413de143a01559cb491c2e5-dirty pimarin parents: 0 diff changeset	537 <param name="reference_database_version" value="1.0"/>
0 c49ec8c0b046 planemo upload commit bb69b191fe3ce756655bf90af4d69e4472f94ba9-dirty pimarin parents: diff changeset	538 </conditional>
c49ec8c0b046 planemo upload commit bb69b191fe3ce756655bf90af4d69e4472f94ba9-dirty pimarin parents: diff changeset	539 </repeat>
c49ec8c0b046 planemo upload commit bb69b191fe3ce756655bf90af4d69e4472f94ba9-dirty pimarin parents: diff changeset	540 <repeat name="tools">
c49ec8c0b046 planemo upload commit bb69b191fe3ce756655bf90af4d69e4472f94ba9-dirty pimarin parents: diff changeset	541 <conditional name="select_tool">
c49ec8c0b046 planemo upload commit bb69b191fe3ce756655bf90af4d69e4472f94ba9-dirty pimarin parents: diff changeset	542 <param name="tool_list" value="shovill"/>
c49ec8c0b046 planemo upload commit bb69b191fe3ce756655bf90af4d69e4472f94ba9-dirty pimarin parents: diff changeset	543 <param name="input" value="shovill/contigs.fa" ftype="fasta"/>
c49ec8c0b046 planemo upload commit bb69b191fe3ce756655bf90af4d69e4472f94ba9-dirty pimarin parents: diff changeset	544 <param name="contig_graph_path" value="shovill/contigs.gfa" ftype="txt"/>
c49ec8c0b046 planemo upload commit bb69b191fe3ce756655bf90af4d69e4472f94ba9-dirty pimarin parents: diff changeset	545 <param name="bam_file_path" value="shovill/alignment.bam" ftype="bam"/>
1 421032d8dd5d planemo upload commit 0a5fc6ee1a42b0c1c413de143a01559cb491c2e5-dirty pimarin parents: 0 diff changeset	546 <param name="analysis_software_version" value="1.0"/>
421032d8dd5d planemo upload commit 0a5fc6ee1a42b0c1c413de143a01559cb491c2e5-dirty pimarin parents: 0 diff changeset	547 <param name="reference_database_version" value="1.0"/>
0 c49ec8c0b046 planemo upload commit bb69b191fe3ce756655bf90af4d69e4472f94ba9-dirty pimarin parents: diff changeset	548 </conditional>
c49ec8c0b046 planemo upload commit bb69b191fe3ce756655bf90af4d69e4472f94ba9-dirty pimarin parents: diff changeset	549 </repeat>
c49ec8c0b046 planemo upload commit bb69b191fe3ce756655bf90af4d69e4472f94ba9-dirty pimarin parents: diff changeset	550 <repeat name="tools">
c49ec8c0b046 planemo upload commit bb69b191fe3ce756655bf90af4d69e4472f94ba9-dirty pimarin parents: diff changeset	551 <conditional name="select_tool">
c49ec8c0b046 planemo upload commit bb69b191fe3ce756655bf90af4d69e4472f94ba9-dirty pimarin parents: diff changeset	552 <param name="tool_list" value="staramr"/>
c49ec8c0b046 planemo upload commit bb69b191fe3ce756655bf90af4d69e4472f94ba9-dirty pimarin parents: diff changeset	553 <param name="input" value="staramr/resfinder.tsv" ftype="tabular"/>
c49ec8c0b046 planemo upload commit bb69b191fe3ce756655bf90af4d69e4472f94ba9-dirty pimarin parents: diff changeset	554 <param name="mlst_file_path" value="staramr/mlst.tsv" ftype="tabular"/>
c49ec8c0b046 planemo upload commit bb69b191fe3ce756655bf90af4d69e4472f94ba9-dirty pimarin parents: diff changeset	555 <param name="plasmidfinder_file_path" value="staramr/plasmidfinder.tsv" ftype="tabular"/>
c49ec8c0b046 planemo upload commit bb69b191fe3ce756655bf90af4d69e4472f94ba9-dirty pimarin parents: diff changeset	556 <param name="pointfinder_file_path" value="staramr/pointfinder.tsv" ftype="tabular"/>
c49ec8c0b046 planemo upload commit bb69b191fe3ce756655bf90af4d69e4472f94ba9-dirty pimarin parents: diff changeset	557 <param name="setting_file_path" value="staramr/settings.txt" ftype="tabular"/>
1 421032d8dd5d planemo upload commit 0a5fc6ee1a42b0c1c413de143a01559cb491c2e5-dirty pimarin parents: 0 diff changeset	558 <param name="analysis_software_version" value="1.0"/>
421032d8dd5d planemo upload commit 0a5fc6ee1a42b0c1c413de143a01559cb491c2e5-dirty pimarin parents: 0 diff changeset	559 <param name="reference_database_version" value="1.0"/>
0 c49ec8c0b046 planemo upload commit bb69b191fe3ce756655bf90af4d69e4472f94ba9-dirty pimarin parents: diff changeset	560 </conditional>
c49ec8c0b046 planemo upload commit bb69b191fe3ce756655bf90af4d69e4472f94ba9-dirty pimarin parents: diff changeset	561 </repeat>
c49ec8c0b046 planemo upload commit bb69b191fe3ce756655bf90af4d69e4472f94ba9-dirty pimarin parents: diff changeset	562 <repeat name="tools">
c49ec8c0b046 planemo upload commit bb69b191fe3ce756655bf90af4d69e4472f94ba9-dirty pimarin parents: diff changeset	563 <conditional name="select_tool">
c49ec8c0b046 planemo upload commit bb69b191fe3ce756655bf90af4d69e4472f94ba9-dirty pimarin parents: diff changeset	564 <param name="tool_list" value="tabular_file"/>
c49ec8c0b046 planemo upload commit bb69b191fe3ce756655bf90af4d69e4472f94ba9-dirty pimarin parents: diff changeset	565 <param name="input" value="tabular_file/report.tsv" ftype="tabular"/>
1 421032d8dd5d planemo upload commit 0a5fc6ee1a42b0c1c413de143a01559cb491c2e5-dirty pimarin parents: 0 diff changeset	566 <param name="analysis_software_name" value="test_galaxy"/>
421032d8dd5d planemo upload commit 0a5fc6ee1a42b0c1c413de143a01559cb491c2e5-dirty pimarin parents: 0 diff changeset	567 <param name="analysis_software_version" value="1.0"/>
421032d8dd5d planemo upload commit 0a5fc6ee1a42b0c1c413de143a01559cb491c2e5-dirty pimarin parents: 0 diff changeset	568 <param name="reference_database_version" value="1.0"/>
0 c49ec8c0b046 planemo upload commit bb69b191fe3ce756655bf90af4d69e4472f94ba9-dirty pimarin parents: diff changeset	569 </conditional>
c49ec8c0b046 planemo upload commit bb69b191fe3ce756655bf90af4d69e4472f94ba9-dirty pimarin parents: diff changeset	570 </repeat>
c49ec8c0b046 planemo upload commit bb69b191fe3ce756655bf90af4d69e4472f94ba9-dirty pimarin parents: diff changeset	571 </section>
c49ec8c0b046 planemo upload commit bb69b191fe3ce756655bf90af4d69e4472f94ba9-dirty pimarin parents: diff changeset	572 <output_collection name="output_json" type="list" count="15">
c49ec8c0b046 planemo upload commit bb69b191fe3ce756655bf90af4d69e4472f94ba9-dirty pimarin parents: diff changeset	573 <expand macro="element_assert" name="abricate_0_output" text="Enterococcus faecalis V583"/>
c49ec8c0b046 planemo upload commit bb69b191fe3ce756655bf90af4d69e4472f94ba9-dirty pimarin parents: diff changeset	574 <expand macro="element_assert" name="bakta_1_output" text="UniRef50_A0A0H2ZNL3"/>
c49ec8c0b046 planemo upload commit bb69b191fe3ce756655bf90af4d69e4472f94ba9-dirty pimarin parents: diff changeset	575 <expand macro="element_assert" name="bandage_2_output" text="3042326"/>
c49ec8c0b046 planemo upload commit bb69b191fe3ce756655bf90af4d69e4472f94ba9-dirty pimarin parents: diff changeset	576 <expand macro="element_assert" name="bracken_3_output" text="Staphylococcus_aureus"/>
c49ec8c0b046 planemo upload commit bb69b191fe3ce756655bf90af4d69e4472f94ba9-dirty pimarin parents: diff changeset	577 <expand macro="element_assert" name="fastp_4_output" text="705053822"/>
c49ec8c0b046 planemo upload commit bb69b191fe3ce756655bf90af4d69e4472f94ba9-dirty pimarin parents: diff changeset	578 <expand macro="element_assert" name="integronfinder2_5_output" text="2353.0"/>
c49ec8c0b046 planemo upload commit bb69b191fe3ce756655bf90af4d69e4472f94ba9-dirty pimarin parents: diff changeset	579 <expand macro="element_assert" name="isescan_6_output" text="IS200/IS605"/>
c49ec8c0b046 planemo upload commit bb69b191fe3ce756655bf90af4d69e4472f94ba9-dirty pimarin parents: diff changeset	580 <expand macro="element_assert" name="kraken2_7_output" text="Enterococcus_faecalis_ATCC_29212"/>
c49ec8c0b046 planemo upload commit bb69b191fe3ce756655bf90af4d69e4472f94ba9-dirty pimarin parents: diff changeset	581 <expand macro="element_assert" name="plasmidfinder_8_output" text="repUS40_1_repB"/>
c49ec8c0b046 planemo upload commit bb69b191fe3ce756655bf90af4d69e4472f94ba9-dirty pimarin parents: diff changeset	582 <expand macro="element_assert" name="quast_9_output" text="2944723"/>
c49ec8c0b046 planemo upload commit bb69b191fe3ce756655bf90af4d69e4472f94ba9-dirty pimarin parents: diff changeset	583 <expand macro="element_assert" name="recentrifuge_10_output" text="6.4917947578"/>
c49ec8c0b046 planemo upload commit bb69b191fe3ce756655bf90af4d69e4472f94ba9-dirty pimarin parents: diff changeset	584 <expand macro="element_assert" name="refseqmasher_11_output" text="GCF_000519925.1"/>
c49ec8c0b046 planemo upload commit bb69b191fe3ce756655bf90af4d69e4472f94ba9-dirty pimarin parents: diff changeset	585 <expand macro="element_assert" name="shovill_12_output" text="436224"/>
c49ec8c0b046 planemo upload commit bb69b191fe3ce756655bf90af4d69e4472f94ba9-dirty pimarin parents: diff changeset	586 <expand macro="element_assert" name="staramr_13_output" text="10_Enterococcus_faecalis_S17_L001"/>
c49ec8c0b046 planemo upload commit bb69b191fe3ce756655bf90af4d69e4472f94ba9-dirty pimarin parents: diff changeset	587 <expand macro="element_assert" name="tabular_file_14_output" text="NP_814691"/>
c49ec8c0b046 planemo upload commit bb69b191fe3ce756655bf90af4d69e4472f94ba9-dirty pimarin parents: diff changeset	588 </output_collection>
c49ec8c0b046 planemo upload commit bb69b191fe3ce756655bf90af4d69e4472f94ba9-dirty pimarin parents: diff changeset	589 </test>
1 421032d8dd5d planemo upload commit 0a5fc6ee1a42b0c1c413de143a01559cb491c2e5-dirty pimarin parents: 0 diff changeset	590
0 c49ec8c0b046 planemo upload commit bb69b191fe3ce756655bf90af4d69e4472f94ba9-dirty pimarin parents: diff changeset	591 </tests>
c49ec8c0b046 planemo upload commit bb69b191fe3ce756655bf90af4d69e4472f94ba9-dirty pimarin parents: diff changeset	592 <help><![CDATA[What it does
c49ec8c0b046 planemo upload commit bb69b191fe3ce756655bf90af4d69e4472f94ba9-dirty pimarin parents: diff changeset	593 Tool input
c49ec8c0b046 planemo upload commit bb69b191fe3ce756655bf90af4d69e4472f94ba9-dirty pimarin parents: diff changeset	594 abromics_galaxy_json_extractor can use several input type from at least 14 different tools :
1 421032d8dd5d planemo upload commit 0a5fc6ee1a42b0c1c413de143a01559cb491c2e5-dirty pimarin parents: 0 diff changeset	595
0 c49ec8c0b046 planemo upload commit bb69b191fe3ce756655bf90af4d69e4472f94ba9-dirty pimarin parents: diff changeset	596 \| Tools \| Version \| Default input file\| Optional files \|
c49ec8c0b046 planemo upload commit bb69b191fe3ce756655bf90af4d69e4472f94ba9-dirty pimarin parents: diff changeset	597 \| -: \| :-: \| :- \| :- \|
c49ec8c0b046 planemo upload commit bb69b191fe3ce756655bf90af4d69e4472f94ba9-dirty pimarin parents: diff changeset	598 \| Abricate \| 1.0.1 \| output.tsv \| \|
c49ec8c0b046 planemo upload commit bb69b191fe3ce756655bf90af4d69e4472f94ba9-dirty pimarin parents: diff changeset	599 \| Bakta \| 1.7.0 \| output.json \| protein.faa, nucleotide.fna, annotation.gff3, summary.txt \|
c49ec8c0b046 planemo upload commit bb69b191fe3ce756655bf90af4d69e4472f94ba9-dirty pimarin parents: diff changeset	600 \| Bandage \| 0.8.1 \| info.txt \| \|
c49ec8c0b046 planemo upload commit bb69b191fe3ce756655bf90af4d69e4472f94ba9-dirty pimarin parents: diff changeset	601 \| Bracken \| 2.8 \| output.tsv \| taxonomy.tsv \|
c49ec8c0b046 planemo upload commit bb69b191fe3ce756655bf90af4d69e4472f94ba9-dirty pimarin parents: diff changeset	602 \| Fastp \| 0.23.2 \| output.json \| \|
c49ec8c0b046 planemo upload commit bb69b191fe3ce756655bf90af4d69e4472f94ba9-dirty pimarin parents: diff changeset	603 \| Integronfinder2\| 2.0.2 \| output.integrons \| output.summary \|
c49ec8c0b046 planemo upload commit bb69b191fe3ce756655bf90af4d69e4472f94ba9-dirty pimarin parents: diff changeset	604 \| ISEScan \| 1.7.2.3 \| output.tsv \| is.fna, orf.faa, orf.fna \|
c49ec8c0b046 planemo upload commit bb69b191fe3ce756655bf90af4d69e4472f94ba9-dirty pimarin parents: diff changeset	605 \| Kraken2 \| 2.1.2 \| taxonomy.tsv \| reads_assignation.txt \|
c49ec8c0b046 planemo upload commit bb69b191fe3ce756655bf90af4d69e4472f94ba9-dirty pimarin parents: diff changeset	606 \| Plasmidfinder \| 2.1.6 \| output.json \| genome_hits.fasta, plasmid_hits.fasta \|
c49ec8c0b046 planemo upload commit bb69b191fe3ce756655bf90af4d69e4472f94ba9-dirty pimarin parents: diff changeset	607 \| Quast \| 5.2.0 \| output.tsv \| \|
c49ec8c0b046 planemo upload commit bb69b191fe3ce756655bf90af4d69e4472f94ba9-dirty pimarin parents: diff changeset	608 \| Recentrifuge \| 1.10.0 \| data.tsv \| report.html, stat.tsv \|
c49ec8c0b046 planemo upload commit bb69b191fe3ce756655bf90af4d69e4472f94ba9-dirty pimarin parents: diff changeset	609 \| Refseqmasher \| 0.1.2 \| output.tsv \| \|
c49ec8c0b046 planemo upload commit bb69b191fe3ce756655bf90af4d69e4472f94ba9-dirty pimarin parents: diff changeset	610 \| Shovill \| 1.1.0 \| contigs.fasta \| alignment.bam, contigs.gfa \|
c49ec8c0b046 planemo upload commit bb69b191fe3ce756655bf90af4d69e4472f94ba9-dirty pimarin parents: diff changeset	611 \| Staramr \| 0.9.1 \| resfinder.tsv \| mlst.tsv, pointfinder.tsv, plasmidfinder.tsv, settings.tsv \|
c49ec8c0b046 planemo upload commit bb69b191fe3ce756655bf90af4d69e4472f94ba9-dirty pimarin parents: diff changeset	612 \| tabular_file \| 0 \| output.tsv \| no optional files \|
c49ec8c0b046 planemo upload commit bb69b191fe3ce756655bf90af4d69e4472f94ba9-dirty pimarin parents: diff changeset	613
c49ec8c0b046 planemo upload commit bb69b191fe3ce756655bf90af4d69e4472f94ba9-dirty pimarin parents: diff changeset	614 Options
c49ec8c0b046 planemo upload commit bb69b191fe3ce756655bf90af4d69e4472f94ba9-dirty pimarin parents: diff changeset	615 You can add a tool version and a database version for related tools.
c49ec8c0b046 planemo upload commit bb69b191fe3ce756655bf90af4d69e4472f94ba9-dirty pimarin parents: diff changeset	616 For some tools you can add optional files previously produced by the tool
c49ec8c0b046 planemo upload commit bb69b191fe3ce756655bf90af4d69e4472f94ba9-dirty pimarin parents: diff changeset	617 ]]></help>
c49ec8c0b046 planemo upload commit bb69b191fe3ce756655bf90af4d69e4472f94ba9-dirty pimarin parents: diff changeset	618 <expand macro="citations"/>
c49ec8c0b046 planemo upload commit bb69b191fe3ce756655bf90af4d69e4472f94ba9-dirty pimarin parents: diff changeset	619 </tool>

Mercurial > repos > pimarin > abromics_galaxy_json_extractor

annotate abromics_galaxy_json_extractor.xml @ 3:73aea20004ff draft default tip