Mercurial > repos > ifb-elixirfr > abromics_galaxy_json_extractor
diff abromics_galaxy_json_extractor.xml @ 6:089c8dda0782 draft
planemo upload for repository https://gitlab.com/ifb-elixirfr/abromics/galaxy-tools commit e7d9e8f7411e216a9e5277803854d23dba615504
author | ifb-elixirfr |
---|---|
date | Sun, 15 Oct 2023 08:34:08 +0000 |
parents | e58c2cd8e624 |
children | fe7c0554432c |
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--- a/abromics_galaxy_json_extractor.xml Fri Oct 06 13:42:25 2023 +0000 +++ b/abromics_galaxy_json_extractor.xml Sun Oct 15 08:34:08 2023 +0000 @@ -130,6 +130,10 @@ --seq_classification_file_hid "$tool.select_tool.seq_classification_file_path.hid" #end if #elif $tool.select_tool.tool_list == "plasmidfinder" + #if str($tool.select_tool.plasmid_result_tabular_path) != 'None' + --plasmid_result_tabular_path "$tool.select_tool.plasmid_result_tabular_path" + --plasmid_result_tabular_hid "$tool.select_tool.plasmid_result_tabular_path.hid" + #end if #if str($tool.select_tool.genome_hit_path) != 'None' --genome_hit_path "$tool.select_tool.genome_hit_path" --genome_hit_hid "$tool.select_tool.genome_hit_path.hid" @@ -164,19 +168,19 @@ #elif $tool.select_tool.tool_list == "staramr" #if str($tool.select_tool.mlst_file_path) != 'None' --mlst_file_path "$tool.select_tool.mlst_file_path" - --mlst_hid "$tool.select_tool.mlst_file_path.hid" + --mlst_file_hid "$tool.select_tool.mlst_file_path.hid" #end if #if str($tool.select_tool.plasmidfinder_file_path) != 'None' --plasmidfinder_file_path "$tool.select_tool.plasmidfinder_file_path" - --plasmidfinder_hid "$tool.select_tool.plasmidfinder_file_path.hid" + --plasmidfinder_file_hid "$tool.select_tool.plasmidfinder_file_path.hid" #end if #if str($tool.select_tool.pointfinder_file_path) != 'None' --pointfinder_file_path "$tool.select_tool.pointfinder_file_path" - --pointfinder_hid "$tool.select_tool.pointfinder_file_path.hid" + --pointfinder_file_hid "$tool.select_tool.pointfinder_file_path.hid" #end if #if str($tool.select_tool.setting_file_path) != 'None' --setting_file_path "$tool.select_tool.setting_file_path" - --setting_hid "$tool.select_tool.setting_file_path.hid" + --setting_file_hid "$tool.select_tool.setting_file_path.hid" #end if #elif $tool.select_tool.tool_list == "tabular_file" --analysis_software_name "$tool.select_tool.analysis_software_name" @@ -293,6 +297,7 @@ </when> <when value="plasmidfinder"> <param name="input" type="data" format="json" multiple="false" label="Json report" help="Plasmidfinder result from json file"/> + <param argument="--plasmid_result_tabular_path" type="data" format="tabular" optional="true" multiple="false" label="Result in tabular format" help="Plasmid result in tabular format"/> <param argument="--genome_hit_path" type="data" format="fasta" optional="true" multiple="false" label="Genome hits" help="Sequence hit in the analyzed genome"/> <param argument="--plasmid_hit_path" type="data" format="fasta" optional="true" multiple="false" label="Plasmid hits" help="Plasmid sequence identified"/> <expand macro="analysis_software_version"/> @@ -593,27 +598,44 @@ ** Tool input** abromics_galaxy_json_extractor can use several input type from at least 14 different tools : + +----------------+----------------+-------------------+------------------------------------------------------------+ | Tools | Version | Default input file| Optional files | - | -: | :-: | :- | :- | + +================+================+===================+============================================================+ | Abricate | 1.0.1 | output.tsv | | + +----------------+----------------+-------------------+------------------------------------------------------------+ | Bakta | 1.7.0 | output.json | protein.faa, nucleotide.fna, annotation.gff3, summary.txt | + +----------------+----------------+-------------------+------------------------------------------------------------+ | Bandage | 0.8.1 | info.txt | | + +----------------+----------------+-------------------+------------------------------------------------------------+ | Bracken | 2.8 | output.tsv | taxonomy.tsv | + +----------------+----------------+-------------------+------------------------------------------------------------+ | Fastp | 0.23.2 | output.json | | + +----------------+----------------+-------------------+------------------------------------------------------------+ | Integronfinder2| 2.0.2 | output.integrons | output.summary | + +----------------+----------------+-------------------+------------------------------------------------------------+ | ISEScan | 1.7.2.3 | output.tsv | is.fna, orf.faa, orf.fna | + +----------------+----------------+-------------------+------------------------------------------------------------+ | Kraken2 | 2.1.2 | taxonomy.tsv | reads_assignation.txt | + +----------------+----------------+-------------------+------------------------------------------------------------+ | Plasmidfinder | 2.1.6 | output.json | genome_hits.fasta, plasmid_hits.fasta | + +----------------+----------------+-------------------+------------------------------------------------------------+ | Quast | 5.2.0 | output.tsv | | + +----------------+----------------+-------------------+------------------------------------------------------------+ | Recentrifuge | 1.10.0 | data.tsv | report.html, stat.tsv | + +----------------+----------------+-------------------+------------------------------------------------------------+ | Refseqmasher | 0.1.2 | output.tsv | | + +----------------+----------------+-------------------+------------------------------------------------------------+ | Shovill | 1.1.0 | contigs.fasta | alignment.bam, contigs.gfa | + +----------------+----------------+-------------------+------------------------------------------------------------+ | Staramr | 0.9.1 | resfinder.tsv | mlst.tsv, pointfinder.tsv, plasmidfinder.tsv, settings.tsv | + +----------------+----------------+-------------------+------------------------------------------------------------+ | tabular_file | 0 | output.tsv | no optional files | + +----------------+----------------+-------------------+------------------------------------------------------------+ ** Options ** You can add a tool version and a database version for related tools. For some tools you can add optional files previously produced by the tool + ]]></help> <expand macro="citations"/> </tool>