Mercurial > repos > pimarin > abromicsextractor

annotate abromics_galaxy_json_extractor.xml @ 0:a157d29ef11d draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
author pimarin
date Mon, 15 May 2023 14:20:18 +0000
parents
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
1 <tool id="abromicsextractor" name="abromicsextractor" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
2 <description>
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
3 Result extractor to json format
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
4 </description>
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
5 <macros>
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
6 <import>macro.xml</import>
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
7 </macros>
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
8 <expand macro='edam'/>
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
9 <expand macro="requirements"/>
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
10 <expand macro="version_command"/>
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
11
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
12 <command detect_errors="aggressive"><![CDATA[
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
13
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
14 mkdir "abromics_extracted_folder" &&
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
15 #*=================================================================
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
16 Paramaters to add Database and tool version if available
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
17 =================================================================*#
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
18 #set $software_with_database = str("abricate,bakta,bracken,kraken2,plasmidfinder,recentrifuge").split(",")
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
19
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
20 #*======================================================
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
21 Loop to include some different tool in one time
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
22 ======================================================*#
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
23 #for $i, $tool in enumerate( $tool_section.tools )
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
24 abromics
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
25 "$tool.select_tool.tool_list"
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
26 --hid $tool.select_tool.input.hid
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
27 "$tool.select_tool.input"
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
28 --analysis_software_version "$tool.select_tool.analysis_software_version"
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
29 #if str($tool.select_tool.tool_list) in str($software_with_database)
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
30 --reference_database_version "$tool.select_tool.reference_database_version"
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
31 #end if
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
32 #if "$tool.select_tool.tool_list" == "bakta"
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
33 --summary_result_path "$tool.select_tool.summary_result_path"
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
34 --nucleotide_annotation_path "$tool.select_tool.nucleotide_annotation_path"
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
35 --amino_acid_annotation_path "$tool.select_tool.amino_acid_annotation_path"
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
36 --gff_file_path "$tool.select_tool.gff_file_path"
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
37 #elif "$tool.select_tool.tool_list" == "bracken"
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
38 --kraken_report_path "tool.select_tool.kraken_report_path"
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
39 --threshold "tool.select_tool.threshold"
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
40 --read_length "tool.select_tool.read_length"
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
41 --level "tool.select_tool.level"
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
42 #elif"$tool.select_tool.tool_list" == "integronfinder2"
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
43 --summary_file_path "tool.select_tool.summary_file_path"
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
44 #elif "$tool.select_tool.tool_list" == "isescan"
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
45 --orf_fna_file "tool.select_tool.orf_fna_file"
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
46 --orf_faa_file "tool.select_tool.orf_faa_file"
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
47 --is_fna_file "tool.select_tool.is_fna_file"
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
48 #elif "$tool.select_tool.tool_list" == "kraken2"
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
49 --seq_classification_file_path "tool.select_tool.seq_classification_file_path"
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
50 #elif "$tool.select_tool.tool_list" == "plasmidfinder"
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
51 --genome_hit_file_path "tool.select_tool.genome_hit_file_path"
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
52 --plasmid_sequence_file_path "tool.select_tool.plasmid_sequence_file_path"
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
53 #elif "$tool.select_tool.tool_list" == "recentrifuge"
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
54 --rcf_stat_file_path "tool.select_tool.rcf_stat_file_path"
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
55 --rcf_html_path "tool.select_tool.rcf_html_path"
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
56 #elif "$tool.select_tool.tool_list" == "shovill"
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
57 --contig_graph_path "tool.select_tool.contig_graph_path"
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
58 --bam_file_path "tool.select_tool.bam_file_path"
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
59 #elif "$tool.select_tool.tool_list" == "staramr"
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
60 --mlst_file_path "tool.select_tool.mlst_file_path"
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
61 --plasmidfinder_file_path "tool.select_tool.plasmidfinder_file_path"
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
62 --pointfinder_file_path "tool.select_tool.pointfinder_file_path"
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
63 --setting_file_path "tool.select_tool.setting_file_path"
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
64 #elif "$tool.select_tool.tool_list" == "tabular_file"
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
65 --analysis_software_name "tool.select_tool.analysis_software_name"
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
66 #end if
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
67 -o "abromics_extracted_folder/$($tool.select_tool.tool_list)_$(i)_output.json"
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
68 | tee "$logfile" ;
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
69 #end for
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
70 #if $summarize == "true"
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
71 abromics summarize abromics_extracted_folder/* -o abromics_summary.json &&
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
72 rm -r abromics_extracted_folder
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
73 #end if
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
74 ]]>
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
75 </command>
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
76 <inputs>
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
77 <section name="tool_section" title="Available tool screen" expanded="false">
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
78 <repeat name="tools" title="Tools" min="1">
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
79 <conditional name="select_tool">
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
80 <param name="tool_list" type="select" label="Available tools">
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
81 <option value="abricate">abricate</option>
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
82 <option value="bakta">bakta</option>
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
83 <option value="bandage">bandage</option>
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
84 <option value="bracken">bracken</option>
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
85 <option value="fastp">fastp</option>
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
86 <option value="integronfinder2">integronfinder2</option>
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
87 <option value="isescan">isescan</option>
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
88 <option value="kraken2">kraken2</option>
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
89 <option value="plasmidfinder">plasmidfinder</option>
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
90 <option value="quast">quast</option>
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
91 <option value="recentrifuge">recentrifuge</option>
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
92 <option value="refseqmasher">refseqmasher</option>
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
93 <option value="shovill">shovill</option>
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
94 <option value="staramr">staramr</option>
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
95 <option value="tabular_file">tabular_generic_file</option>
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
96 </param>
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
97 <when value="abricate">
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
98 <param name="input" type="data" format="txt,tabular" multiple="false" label="Abricate report file" help="Tabular file from abricate output"/>
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
99 <expand macro="analysis_software_version"/>
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
100 <expand macro="reference_database_version"/>
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
101 </when>
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
102 <when value="bakta">
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
103 <param name="input" type="data" format="json" multiple="false" label="Bakta report file" help="Json file from bakta output"/>
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
104 <param argument="--summary_result_path" type="data" format="txt" multiple="false" optional="true" label="Bakta summary file" help="Summary file from bakta output"/>
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
105 <param argument="--nucleotide_annotation_path" type="data" format="fasta" multiple="false" optional="true" label="Bakta nucleotide file" help="Nucleotide sequence annotation file"/>
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
106 <param argument="--amino_acid_annotation_path" type="data" format="fasta" multiple="false" optional="true" label="Bakta amino acide file" help="Amino acid sequence annotation file"/>
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
107 <param argument="--gff_file_path" type="data" format="gff3" multiple="false" optional="true" label="Bakta annotation file" help="Annotation file"/>
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
108 <expand macro="analysis_software_version"/>
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
109 <expand macro="reference_database_version"/>
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
110 </when>
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
111 <when value="bandage">
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
112 <param name="input" type="data" format="txt,tabular" multiple="false" label="Bandage report file" help="Tabular file from bandage output"/>
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
113 <expand macro="analysis_software_version"/>
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
114 </when>
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
115 <when value="bracken">
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
116 <param name="input" type="data" format="txt,tabular" multiple="false" label="Bracken report file" help="Tabular file from bracken output"/>
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
117 <expand macro="analysis_software_version"/>
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
118 <expand macro="reference_database_version"/>
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
119 <param argument="--kraken_report_path" type="data" format="txt,tabular" multiple="false" label="Kraken re-estimated report" help="New kraken report from bracken tool"/>
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
120 <param argument="--threshold" type="integer" min="0" optional="true" label="PRIOR on read numbers" help="Prior of read for estimation, default is 0"/>
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
121 <param argument="--read_length" type="integer" min="0" optional="true" label="Read length"/>
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
122 <param argument="--level" type="select" label="Taxonomic level estimation" help="Level of final abundance (from Domain to subspecies, default on species)">
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
123 <option value="D">Domain</option>
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
124 <option value="P">Phylum</option>
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
125 <option value="C">Class</option>
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
126 <option value="O">Order</option>
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
127 <option value="F">Family</option>
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
128 <option value="G">Genus</option>
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
129 <option value="S">Species</option>
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
130 <option value="S+">Subspecies</option>
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
131 </param>
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
132 </when>
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
133 <when value="fastp">
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
134 <param name="input" type="data" format="json" multiple="false" label="Fastp report file" help="Fastp result in json format"/>
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
135 <expand macro="analysis_software_version"/>
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
136 </when>
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
137 <when value="integronfinder2">
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
138 <param name="input" type="data" format="txt,tabular" multiple="false" label="Integronfinder report" help="Integron file from integronfinder2"/>
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
139 <param argument="--summary_file_path" type="data" format="txt,tabular" multiple="false" label="Summary report" help="Summary file from integronfinder2"/>
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
140 <expand macro="analysis_software_version"/>
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
141 </when>
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
142 <when value="isescan">
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
143 <param name="input" type="data" format="txt,tabular" multiple="false" label="Isescan report" help="IseScan file from integronfinder2"/>
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
144 <param argument="--orf_fna_file" type="data" format="fasta" optional="true" multiple="false" label="ORF fna file" help="Nuleotide sequence to the ORFs"/>
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
145 <param argument="--orf_faa_file" type="data" format="fasta" optional="true" multiple="false" label="ORF faa file" help="Amino acid sequence to the ORFs"/>
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
146 <param argument="--is_fna_file" type="data" format="fasta" optional="true" multiple="false" label="IS fna file" help="Nuleotide sequence to the inserted elements"/>
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
147 <expand macro="analysis_software_version"/>
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
148 </when>
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
149 <when value="kraken2">
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
150 <param name="input" type="data" format="txt,tabular" multiple="false" label="kraken report" help="Taxonomic assignation file from kraken2"/>
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
151 <param argument="--seq_classification_file_path" type="data" format="txt,tabular" optional="true" multiple="false" label="Sequence assignation" help="Reads assignation file"/>
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
152 <expand macro="analysis_software_version"/>
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
153 <expand macro="reference_database_version"/>
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
154 </when>
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
155 <when value="plasmidfinder">
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
156 <param name="input" type="data" format="json" multiple="false" label="Json report" help="Plasmidfinder result from json file"/>
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
157 <param argument="--genome_hit_file_path" type="data" format="fasta" optional="true" multiple="false" label="Genome hits" help="Sequence hit in the analyzed genome"/>
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
158 <param argument="--plasmid_sequence_file_path" type="data" format="fasta" optional="true" multiple="false" label="Plasmid hits" help="Plasmid sequence identified"/>
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
159 <expand macro="analysis_software_version"/>
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
160 <expand macro="reference_database_version"/>
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
161 </when>
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
162 <when value="quast">
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
163 <param name="input" type="data" format="txt,tabular" multiple="false" label="Quast report" help="Tabular Quast report"/>
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
164 <expand macro="analysis_software_version"/>
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
165 </when>
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
166 <when value="recentrifuge">
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
167 <param name="input" type="data" format="txt,tabular" multiple="false" label="Recentrifuge data file"/>
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
168 <param argument="--rcf_stat_file_path" type="data" format="txt,tabular" optional="true" multiple="false" label="Recentrifuge stat file"/>
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
169 <param argument="--rcf_html_path" type="data" format="html" optional="true" multiple="false" label="Recentrifuge html report file"/>
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
170 <expand macro="analysis_software_version"/>
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
171 <expand macro="reference_database_version"/>
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
172 </when>
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
173 <when value="refseqmasher">
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
174 <param name="input" type="data" format="txt,tabular" multiple="false" label="RefsesMasher results"/>
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
175 <expand macro="analysis_software_version"/>
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
176 </when>
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
177 <when value="shovill">
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
178 <param name="input" type="data" format="fasta" multiple="false" label="Contigs file" help="Contig fasta file from assembly"/>
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
179 <param argument="--contig_graph_path" type="data" format="txt" optional="true" multiple="false" label="Contig graph file" help="Graphic file assembly"/>
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
180 <param argument="--bam_file_path" type="data" format="bam" optional="true" multiple="false" label="Bam file" help="Alignemnt file in bam format"/>
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
181 <expand macro="analysis_software_version"/>
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
182
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
183 </when>
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
184 <when value="staramr">
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
185 <param name="input" type="data" format="txt,tabular" multiple="false" label="Resfinder report" help="Resfinder result from starAMR"/>
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
186 <param argument="--mlst_file_path" type="data" format="txt,tabular" optional="true" multiple="false" label="MLST results" help="mlst scheme file result from starAMR"/>
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
187 <param argument="--plasmidfinder_file_path" type="data" optional="true" format="txt,tabular" multiple="false" label="Plasmid results" help="Plasmidfinder result from starAMR"/>
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
188 <param argument="--pointfinder_file_path" type="data" optional="true" format="txt,tabular" multiple="false" label="Pointfinder results" help="PointFinder result from starAMR"/>
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
189 <param argument="--setting_file_path" type="data" optional="true" format="txt,tabular" multiple="false" label="Setting informations" help="Settings file from starAMR"/>
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
190 <expand macro="analysis_software_version"/>
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
191 </when>
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
192 <when value="tabular_file">
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
193 <param name="input" type="data" format="txt,tabular" multiple="false" label="Tabular file type" help="Generic result file in tabular format with header"/>
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
194 <param argument="--analysis_software_name" type="text" multiple="false" label="Tool name" help="Tool name which generated the result file"/>
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
195 <expand macro="analysis_software_version"/>
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
196 </when>
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
197 </conditional>
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
198 </repeat>
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
199 </section>
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
200 <param argument="summarize" type="boolean" truevalue="true" falsevalue="" label="Summarize results" help="Summarize all outputs in only one file"/>
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
201 <param name="log" type="boolean" truevalue="true" falsevalue="" label="Add log" help="Activate/Deactivate the log"/>
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
202 </inputs>
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
203 <outputs>
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
204 <collection name="output_json" type="list" label="${tool.name} on ${on_string}: abromics formated json results">
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
205 <discover_datasets pattern="(?P&lt;designation&gt;.+)\.json" format="json" directory="abromics_extracted_folder" />
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
206 </collection>
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
207 <data name="summary_json" format="json" from_work_dir="abromics_summary.json" label="${tool.name} on ${on_string}: Summarized file">
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
208 <filter> summarize == True </filter>
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
209 </data>
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
210 <data name="logfile" format="txt" label="${tool.name} on ${on_string}: log file">
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
211 <filter> log == True </filter>
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
212 </data>
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
213 </outputs>
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
214 <tests>
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
215 <test expect_num_outputs="2"> <!-- TEST_1 abricate with logfile -->
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
216 <section name="tool_section">
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
217 <repeat name="tools">
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
218 <conditional name="select_tool">
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
219 <param name="tool_list" value="abricate"/>
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
220 <param name="input" value="abricate/report.tsv" ftype="tabular"/>
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
221 <param name="analysis_software_version" value="1.0"/>
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
222 <param name="reference_database_version" value="2.0" />
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
223 </conditional>
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
224 </repeat>
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
225 </section>
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
226 <param name="log" value="true"/>
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
227 <output name="logfile" value="abricate/abricate_logfile.txt" lines_diff="1"/>
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
228 <output_collection name="output_json" type="list">
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
229 <expand macro="element_assert" name="abricate_0_output" text="Enterococcus faecalis V583"/>
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
230 </output_collection>
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
231 </test>
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
232 <test expect_num_outputs="1"> <!-- TEST_2 bakta all files -->
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
233 <section name="tool_section">
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
234 <repeat name="tools">
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
235 <conditional name="select_tool">
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
236 <param name="tool_list" value="bakta"/>
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
237 <param name="input" value="bakta/bakta.json" ftype="json"/>
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
238 <param name="summary_result_path" value="bakta/bakta_summary.txt" ftype="txt"/>
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
239 <param name="nucleotide_annotation_path" value="bakta/bakta_nucleotide.fasta" ftype="fasta"/>
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
240 <param name="amino_acid_annotation_path" value="bakta/bakta_aminoacid.faa" ftype="fasta"/>
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
241 <param name="gff_file_path" value="bakta/bakta_annotation.gff3" ftype="gff3"/>
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
242 <param name="reference_database_version" value="1.6.1"/>
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
243 </conditional>
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
244 </repeat>
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
245 </section>
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
246 <output_collection name="output_json" type="list" count="1">
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
247 <expand macro="element_assert" name="bakta_0_output" text="UniRef50_A0A0H2ZNL3"/>
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
248 </output_collection>
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
249 </test>
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
250 <test expect_num_outputs="1"> <!-- TEST_3 All tool in repeat -->
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
251 <section name="tool_section">
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
252 <repeat name="tools">
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
253 <conditional name="select_tool">
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
254 <param name="tool_list" value="abricate"/>
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
255 <param name="input" value="abricate/report.tsv" ftype="tabular"/>
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
256 <param name="analysis_software_version" value="1.0"/>
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
257 <param name="reference_database_version" value="2.0" />
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
258 </conditional>
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
259 </repeat>
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
260 <repeat name="tools">
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
261 <conditional name="select_tool">
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
262 <param name="tool_list" value="bakta"/>
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
263 <param name="input" value="bakta/bakta.json" ftype="json"/>
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
264 </conditional>
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
265 </repeat>
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
266 <repeat name="tools">
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
267 <conditional name="select_tool">
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
268 <param name="tool_list" value="bandage"/>
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
269 <param name="input" value="bandage/bandage_info.txt" ftype="txt"/>
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
270 </conditional>
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
271 </repeat>
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
272 <repeat name="tools">
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
273 <conditional name="select_tool">
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
274 <param name="tool_list" value="bracken"/>
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
275 <param name="input" value="bracken/bracken_report.tsv" ftype="tabular"/>
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
276 <param name="bracken/bracken_kraken_report" ftype="tabular" />
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
277 <param name="threshold" value="0" />
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
278 <param name="read_length" value="100"/>
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
279 <param name="level" value="S"/>
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
280 </conditional>
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
281 </repeat>
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
282 <repeat name="tools">
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
283 <conditional name="select_tool">
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
284 <param name="tool_list" value="fastp"/>
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
285 <param name="input" value="fastp/fastp_report.json" ftype="json"/>
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
286 </conditional>
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
287 </repeat>
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
288 <repeat name="tools">
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
289 <conditional name="select_tool">
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
290 <param name="tool_list" value="integronfinder2"/>
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
291 <param name="input" value="integronfinder2/results.integrons" ftype="tabular"/>
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
292 <param name="summary_file_path" value="integronfinder2/results.summary" ftype="tabular"/>
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
293 </conditional>
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
294 </repeat>
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
295 <repeat name="tools">
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
296 <conditional name="select_tool">
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
297 <param name="tool_list" value="isescan"/>
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
298 <param name="input" value="isescan/results.tsv" ftype="tabular"/>
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
299 <param name="orf_fna_file" value="isescan/orf.fna" ftype="fasta"/>
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
300 <param name="orf_faa_file" value="isescan/orf.faa" ftype="fasta"/>
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
301 <param name="is_fna_file" value="isescan/is.fna" ftype="fasta"/>
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
302 </conditional>
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
303 </repeat>
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
304 <repeat name="tools">
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
305 <conditional name="select_tool">
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
306 <param name="tool_list" value="kraken2"/>
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
307 <param name="input" value="kraken2/taxonomy_report.tsv" ftype="tabular"/>
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
308 <param name="seq_classification_file_path" value="kraken2/taxonomy_result.tsv" ftype="tabular"/>
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
309 </conditional>
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
310 </repeat>
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
311 <repeat name="tools">
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
312 <conditional name="select_tool">
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
313 <param name="tool_list" value="plasmidfinder"/>
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
314 <param name="input" value="plasmidfinder/plasmidfinder_result.json" ftype="json"/>
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
315 <param name="genome_hit_file_path" value="plasmidfinder/genome_hit.fasta" ftype="fasta"/>
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
316 <param name="plasmid_sequence_file_path" value="plasmidfinder/plasmid_hit.fasta" ftype="fasta"/>
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
317 </conditional>
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
318 </repeat>
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
319 <repeat name="tools">
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
320 <conditional name="select_tool">
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
321 <param name="tool_list" value="quast"/>
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
322 <param name="input" value="quast/quast_result.tsv" ftype="tabular"/>
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
323 </conditional>
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
324 </repeat>
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
325 <repeat name="tools">
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
326 <conditional name="select_tool">
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
327 <param name="tool_list" value="recentrifuge"/>
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
328 <param name="input" value="recentrifuge/rcf_data.tsv" ftype="tabular"/>
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
329 <param name="rcf_stat_file_path" value="recentrifuge/rcf_stat.tsv" ftype="tabular"/>
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
330 <param name="rcf_html_path" value="recentrifuge/rcf_report.html"/>
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
331 </conditional>
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
332 </repeat>
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
333 <repeat name="tools">
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
334 <conditional name="select_tool">
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
335 <param name="tool_list" value="refseqmasher"/>
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
336 <param name="input" value="refseqmasher/refsesqmasher.tsv" ftype="tabular"/>
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
337 </conditional>
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
338 </repeat>
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
339 <repeat name="tools">
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
340 <conditional name="select_tool">
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
341 <param name="tool_list" value="shovill"/>
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
342 <param name="input" value="shovill/contigs.fa" ftype="fasta"/>
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
343 <param name="contig_graph_path" value="shovill/contigs.gfa" ftype="txt"/>
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
344 <param name="bam_file_path" value="shovill/alignment.bam" ftype="bam"/>
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
345 </conditional>
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
346 </repeat>
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
347 <repeat name="tools">
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
348 <conditional name="select_tool">
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
349 <param name="tool_list" value="staramr"/>
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
350 <param name="input" value="staramr/resfinder.tsv" ftype="tabular"/>
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
351 <param name="mlst_file_path" value="staramr/mlst.tsv" ftype="tabular"/>
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
352 <param name="plasmidfinder_file_path" value="staramr/plasmidfinder.tsv" ftype="tabular"/>
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
353 <param name="pointfinder_file_path" value="staramr/pointfinder.tsv" ftype="tabular"/>
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
354 <param name="setting_file_path" value="staramr/settings.txt" ftype="tabular"/>
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
355 </conditional>
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
356 </repeat>
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
357 <repeat name="tools">
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
358 <conditional name="select_tool">
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
359 <param name="tool_list" value="tabular_file"/>
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
360 <param name="input" value="tabular_file/report.tsv" ftype="tabular"/>
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
361 </conditional>
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
362 </repeat>
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
363 </section>
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
364 <output_collection name="output_json" type="list" count="15">
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
365 <expand macro="element_assert" name="abricate_0_output" text="Enterococcus faecalis V583"/>
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
366 <expand macro="element_assert" name="bakta_1_output" text="UniRef50_A0A0H2ZNL3"/>
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
367 <expand macro="element_assert" name="bandage_2_output" text="3042326"/>
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
368 <expand macro="element_assert" name="bracken_3_output" text="Staphylococcus_aureus"/>
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
369 <expand macro="element_assert" name="fastp_4_output" text="705053822"/>
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
370 <expand macro="element_assert" name="integronfinder2_5_output" text="2353.0"/>
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
371 <expand macro="element_assert" name="isescan_6_output" text="IS200/IS605"/>
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
372 <expand macro="element_assert" name="kraken2_7_output" text="Enterococcus_faecalis_ATCC_29212"/>
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
373 <expand macro="element_assert" name="plasmidfinder_8_output" text="repUS40_1_repB"/>
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
374 <expand macro="element_assert" name="quast_9_output" text="2944723"/>
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
375 <expand macro="element_assert" name="recentrifuge_10_output" text="6.4917947578"/>
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
376 <expand macro="element_assert" name="refseqmasher_11_output" text="GCF_000519925.1"/>
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
377 <expand macro="element_assert" name="shovill_12_output" text="436224"/>
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
378 <expand macro="element_assert" name="staramr_13_output" text="10_Enterococcus_faecalis_S17_L001"/>
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
379 <expand macro="element_assert" name="tabular_file_14_output" text="NP_814691"/>
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
380 </output_collection>
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
381 </test>
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
382 <test expect_num_outputs="2"> <!-- TEST_4 repeat with summary option -->
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
383 <section name="tool_section">
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
384 <repeat name="tools">
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
385 <conditional name="select_tool">
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
386 <param name="tool_list" value="abricate"/>
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
387 <param name="input" value="abricate/report.tsv" ftype="tabular"/>
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
388 <param name="analysis_software_version" value="1.0"/>
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
389 <param name="reference_database_version" value="2.0" />
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
390 </conditional>
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
391 </repeat>
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
392 <repeat name="tools">
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
393 <conditional name="select_tool">
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
394 <param name="tool_list" value="bakta"/>
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
395 <param name="input" value="bakta/bakta.json" ftype="json"/>
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
396 </conditional>
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
397 </repeat>
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
398 <repeat name="tools">
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
399 <conditional name="select_tool">
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
400 <param name="tool_list" value="bandage"/>
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
401 <param name="input" value="bandage/bandage_info.txt" ftype="txt"/>
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
402 </conditional>
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
403 </repeat>
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
404 <repeat name="tools">
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
405 <conditional name="select_tool">
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
406 <param name="tool_list" value="bracken"/>
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
407 <param name="input" value="bracken/bracken_report.tsv" ftype="tabular"/>
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
408 <param name="bracken/bracken_kraken_report" ftype="tabular" />
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
409 <param name="threshold" value="0" />
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
410 <param name="read_length" value="100"/>
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
411 <param name="level" value="S"/>
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
412 </conditional>
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
413 </repeat>
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
414 <repeat name="tools">
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
415 <conditional name="select_tool">
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
416 <param name="tool_list" value="fastp"/>
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
417 <param name="input" value="fastp/fastp_report.json" ftype="json"/>
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
418 </conditional>
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
419 </repeat>
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
420 <repeat name="tools">
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
421 <conditional name="select_tool">
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
422 <param name="tool_list" value="integronfinder2"/>
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
423 <param name="input" value="integronfinder2/results.integrons" ftype="tabular"/>
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
424 <param name="summary_file_path" value="integronfinder2/results.summary" ftype="tabular"/>
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
425 </conditional>
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
426 </repeat>
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
427 <repeat name="tools">
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
428 <conditional name="select_tool">
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
429 <param name="tool_list" value="isescan"/>
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
430 <param name="input" value="isescan/results.tsv" ftype="tabular"/>
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
431 <param name="orf_fna_file" value="isescan/orf.fna" ftype="fasta"/>
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
432 <param name="orf_faa_file" value="isescan/orf.faa" ftype="fasta"/>
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
433 <param name="is_fna_file" value="isescan/is.fna" ftype="fasta"/>
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
434 </conditional>
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
435 </repeat>
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
436 <repeat name="tools">
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
437 <conditional name="select_tool">
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
438 <param name="tool_list" value="kraken2"/>
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
439 <param name="input" value="kraken2/taxonomy_report.tsv" ftype="tabular"/>
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
440 <param name="seq_classification_file_path" value="kraken2/taxonomy_result.tsv" ftype="tabular"/>
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
441 </conditional>
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
442 </repeat>
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
443 <repeat name="tools">
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
444 <conditional name="select_tool">
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
445 <param name="tool_list" value="plasmidfinder"/>
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
446 <param name="input" value="plasmidfinder/plasmidfinder_result.json" ftype="json"/>
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
447 <param name="genome_hit_file_path" value="plasmidfinder/genome_hit.fasta" ftype="fasta"/>
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
448 <param name="plasmid_sequence_file_path" value="plasmidfinder/plasmid_hit.fasta" ftype="fasta"/>
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
449 </conditional>
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
450 </repeat>
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
451 <repeat name="tools">
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
452 <conditional name="select_tool">
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
453 <param name="tool_list" value="quast"/>
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
454 <param name="input" value="quast/quast_result.tsv" ftype="tabular"/>
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
455 </conditional>
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
456 </repeat>
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
457 <repeat name="tools">
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
458 <conditional name="select_tool">
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
459 <param name="tool_list" value="recentrifuge"/>
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
460 <param name="input" value="recentrifuge/rcf_data.tsv" ftype="tabular"/>
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
461 <param name="rcf_stat_file_path" value="recentrifuge/rcf_stat.tsv" ftype="tabular"/>
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
462 <param name="rcf_html_path" value="recentrifuge/rcf_report.html"/>
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
463 </conditional>
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
464 </repeat>
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
465 <repeat name="tools">
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
466 <conditional name="select_tool">
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
467 <param name="tool_list" value="refseqmasher"/>
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
468 <param name="input" value="refseqmasher/refsesqmasher.tsv" ftype="tabular"/>
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
469 </conditional>
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
470 </repeat>
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
471 <repeat name="tools">
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
472 <conditional name="select_tool">
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
473 <param name="tool_list" value="shovill"/>
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
474 <param name="input" value="shovill/contigs.fa" ftype="fasta"/>
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
475 <param name="contig_graph_path" value="shovill/contigs.gfa" ftype="txt"/>
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
476 <param name="bam_file_path" value="shovill/alignment.bam" ftype="bam"/>
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
477 </conditional>
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
478 </repeat>
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
479 <repeat name="tools">
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
480 <conditional name="select_tool">
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
481 <param name="tool_list" value="staramr"/>
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
482 <param name="input" value="staramr/resfinder.tsv" ftype="tabular"/>
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
483 <param name="mlst_file_path" value="staramr/mlst.tsv" ftype="tabular"/>
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
484 <param name="plasmidfinder_file_path" value="staramr/plasmidfinder.tsv" ftype="tabular"/>
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
485 <param name="pointfinder_file_path" value="staramr/pointfinder.tsv" ftype="tabular"/>
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
486 <param name="setting_file_path" value="staramr/settings.txt" ftype="tabular"/>
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
487 </conditional>
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
488 </repeat>
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
489 <repeat name="tools">
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
490 <conditional name="select_tool">
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
491 <param name="tool_list" value="tabular_file"/>
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
492 <param name="input" value="tabular_file/report.tsv" ftype="tabular"/>
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
493 </conditional>
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
494 </repeat>
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
495 </section>
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
496 <param name="summarize" value="true"/>
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
497 <output name="summary_json" value="summarize/summarize.json" lines_diff="6"/>
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
498 </test>
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
499 </tests>
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
500 <help><![CDATA[**What it does**
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
501 efljvl
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
502 zvlzhv
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
503 ]]></help>
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
504 <expand macro="citations"/>
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
parents:
diff changeset
505 </tool>