Mercurial > repos > ifb-elixirfr > abromics_galaxy_json_extractor
comparison 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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| 5:e58c2cd8e624 | 6:089c8dda0782 |
|---|---|
| 128 #if str($tool.select_tool.seq_classification_file_path) != 'None' | 128 #if str($tool.select_tool.seq_classification_file_path) != 'None' |
| 129 --seq_classification_file_path "$tool.select_tool.seq_classification_file_path" | 129 --seq_classification_file_path "$tool.select_tool.seq_classification_file_path" |
| 130 --seq_classification_file_hid "$tool.select_tool.seq_classification_file_path.hid" | 130 --seq_classification_file_hid "$tool.select_tool.seq_classification_file_path.hid" |
| 131 #end if | 131 #end if |
| 132 #elif $tool.select_tool.tool_list == "plasmidfinder" | 132 #elif $tool.select_tool.tool_list == "plasmidfinder" |
| 133 #if str($tool.select_tool.plasmid_result_tabular_path) != 'None' | |
| 134 --plasmid_result_tabular_path "$tool.select_tool.plasmid_result_tabular_path" | |
| 135 --plasmid_result_tabular_hid "$tool.select_tool.plasmid_result_tabular_path.hid" | |
| 136 #end if | |
| 133 #if str($tool.select_tool.genome_hit_path) != 'None' | 137 #if str($tool.select_tool.genome_hit_path) != 'None' |
| 134 --genome_hit_path "$tool.select_tool.genome_hit_path" | 138 --genome_hit_path "$tool.select_tool.genome_hit_path" |
| 135 --genome_hit_hid "$tool.select_tool.genome_hit_path.hid" | 139 --genome_hit_hid "$tool.select_tool.genome_hit_path.hid" |
| 136 #end if | 140 #end if |
| 137 #if str($tool.select_tool.plasmid_hit_path) != 'None' | 141 #if str($tool.select_tool.plasmid_hit_path) != 'None' |
| 162 --bam_file_hid "$tool.select_tool.bam_file_path.hid" | 166 --bam_file_hid "$tool.select_tool.bam_file_path.hid" |
| 163 #end if | 167 #end if |
| 164 #elif $tool.select_tool.tool_list == "staramr" | 168 #elif $tool.select_tool.tool_list == "staramr" |
| 165 #if str($tool.select_tool.mlst_file_path) != 'None' | 169 #if str($tool.select_tool.mlst_file_path) != 'None' |
| 166 --mlst_file_path "$tool.select_tool.mlst_file_path" | 170 --mlst_file_path "$tool.select_tool.mlst_file_path" |
| 167 --mlst_hid "$tool.select_tool.mlst_file_path.hid" | 171 --mlst_file_hid "$tool.select_tool.mlst_file_path.hid" |
| 168 #end if | 172 #end if |
| 169 #if str($tool.select_tool.plasmidfinder_file_path) != 'None' | 173 #if str($tool.select_tool.plasmidfinder_file_path) != 'None' |
| 170 --plasmidfinder_file_path "$tool.select_tool.plasmidfinder_file_path" | 174 --plasmidfinder_file_path "$tool.select_tool.plasmidfinder_file_path" |
| 171 --plasmidfinder_hid "$tool.select_tool.plasmidfinder_file_path.hid" | 175 --plasmidfinder_file_hid "$tool.select_tool.plasmidfinder_file_path.hid" |
| 172 #end if | 176 #end if |
| 173 #if str($tool.select_tool.pointfinder_file_path) != 'None' | 177 #if str($tool.select_tool.pointfinder_file_path) != 'None' |
| 174 --pointfinder_file_path "$tool.select_tool.pointfinder_file_path" | 178 --pointfinder_file_path "$tool.select_tool.pointfinder_file_path" |
| 175 --pointfinder_hid "$tool.select_tool.pointfinder_file_path.hid" | 179 --pointfinder_file_hid "$tool.select_tool.pointfinder_file_path.hid" |
| 176 #end if | 180 #end if |
| 177 #if str($tool.select_tool.setting_file_path) != 'None' | 181 #if str($tool.select_tool.setting_file_path) != 'None' |
| 178 --setting_file_path "$tool.select_tool.setting_file_path" | 182 --setting_file_path "$tool.select_tool.setting_file_path" |
| 179 --setting_hid "$tool.select_tool.setting_file_path.hid" | 183 --setting_file_hid "$tool.select_tool.setting_file_path.hid" |
| 180 #end if | 184 #end if |
| 181 #elif $tool.select_tool.tool_list == "tabular_file" | 185 #elif $tool.select_tool.tool_list == "tabular_file" |
| 182 --analysis_software_name "$tool.select_tool.analysis_software_name" | 186 --analysis_software_name "$tool.select_tool.analysis_software_name" |
| 183 #end if | 187 #end if |
| 184 -o "abromics_extracted_folder/$($tool.select_tool.tool_list)_$(i)_output.json" | 188 -o "abromics_extracted_folder/$($tool.select_tool.tool_list)_$(i)_output.json" |
| 291 <expand macro="analysis_software_version"/> | 295 <expand macro="analysis_software_version"/> |
| 292 <expand macro="reference_database_version"/> | 296 <expand macro="reference_database_version"/> |
| 293 </when> | 297 </when> |
| 294 <when value="plasmidfinder"> | 298 <when value="plasmidfinder"> |
| 295 <param name="input" type="data" format="json" multiple="false" label="Json report" help="Plasmidfinder result from json file"/> | 299 <param name="input" type="data" format="json" multiple="false" label="Json report" help="Plasmidfinder result from json file"/> |
| 300 <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"/> | |
| 296 <param argument="--genome_hit_path" type="data" format="fasta" optional="true" multiple="false" label="Genome hits" help="Sequence hit in the analyzed genome"/> | 301 <param argument="--genome_hit_path" type="data" format="fasta" optional="true" multiple="false" label="Genome hits" help="Sequence hit in the analyzed genome"/> |
| 297 <param argument="--plasmid_hit_path" type="data" format="fasta" optional="true" multiple="false" label="Plasmid hits" help="Plasmid sequence identified"/> | 302 <param argument="--plasmid_hit_path" type="data" format="fasta" optional="true" multiple="false" label="Plasmid hits" help="Plasmid sequence identified"/> |
| 298 <expand macro="analysis_software_version"/> | 303 <expand macro="analysis_software_version"/> |
| 299 <expand macro="reference_database_version"/> | 304 <expand macro="reference_database_version"/> |
| 300 </when> | 305 </when> |
| 591 </tests> | 596 </tests> |
| 592 <help><![CDATA[**What it does** | 597 <help><![CDATA[**What it does** |
| 593 ** Tool input** | 598 ** Tool input** |
| 594 abromics_galaxy_json_extractor can use several input type from at least 14 different tools : | 599 abromics_galaxy_json_extractor can use several input type from at least 14 different tools : |
| 595 | 600 |
| 601 +----------------+----------------+-------------------+------------------------------------------------------------+ | |
| 596 | Tools | Version | Default input file| Optional files | | 602 | Tools | Version | Default input file| Optional files | |
| 597 | -: | :-: | :- | :- | | 603 +================+================+===================+============================================================+ |
| 598 | Abricate | 1.0.1 | output.tsv | | | 604 | Abricate | 1.0.1 | output.tsv | | |
| 605 +----------------+----------------+-------------------+------------------------------------------------------------+ | |
| 599 | Bakta | 1.7.0 | output.json | protein.faa, nucleotide.fna, annotation.gff3, summary.txt | | 606 | Bakta | 1.7.0 | output.json | protein.faa, nucleotide.fna, annotation.gff3, summary.txt | |
| 607 +----------------+----------------+-------------------+------------------------------------------------------------+ | |
| 600 | Bandage | 0.8.1 | info.txt | | | 608 | Bandage | 0.8.1 | info.txt | | |
| 609 +----------------+----------------+-------------------+------------------------------------------------------------+ | |
| 601 | Bracken | 2.8 | output.tsv | taxonomy.tsv | | 610 | Bracken | 2.8 | output.tsv | taxonomy.tsv | |
| 611 +----------------+----------------+-------------------+------------------------------------------------------------+ | |
| 602 | Fastp | 0.23.2 | output.json | | | 612 | Fastp | 0.23.2 | output.json | | |
| 613 +----------------+----------------+-------------------+------------------------------------------------------------+ | |
| 603 | Integronfinder2| 2.0.2 | output.integrons | output.summary | | 614 | Integronfinder2| 2.0.2 | output.integrons | output.summary | |
| 615 +----------------+----------------+-------------------+------------------------------------------------------------+ | |
| 604 | ISEScan | 1.7.2.3 | output.tsv | is.fna, orf.faa, orf.fna | | 616 | ISEScan | 1.7.2.3 | output.tsv | is.fna, orf.faa, orf.fna | |
| 617 +----------------+----------------+-------------------+------------------------------------------------------------+ | |
| 605 | Kraken2 | 2.1.2 | taxonomy.tsv | reads_assignation.txt | | 618 | Kraken2 | 2.1.2 | taxonomy.tsv | reads_assignation.txt | |
| 619 +----------------+----------------+-------------------+------------------------------------------------------------+ | |
| 606 | Plasmidfinder | 2.1.6 | output.json | genome_hits.fasta, plasmid_hits.fasta | | 620 | Plasmidfinder | 2.1.6 | output.json | genome_hits.fasta, plasmid_hits.fasta | |
| 621 +----------------+----------------+-------------------+------------------------------------------------------------+ | |
| 607 | Quast | 5.2.0 | output.tsv | | | 622 | Quast | 5.2.0 | output.tsv | | |
| 623 +----------------+----------------+-------------------+------------------------------------------------------------+ | |
| 608 | Recentrifuge | 1.10.0 | data.tsv | report.html, stat.tsv | | 624 | Recentrifuge | 1.10.0 | data.tsv | report.html, stat.tsv | |
| 625 +----------------+----------------+-------------------+------------------------------------------------------------+ | |
| 609 | Refseqmasher | 0.1.2 | output.tsv | | | 626 | Refseqmasher | 0.1.2 | output.tsv | | |
| 627 +----------------+----------------+-------------------+------------------------------------------------------------+ | |
| 610 | Shovill | 1.1.0 | contigs.fasta | alignment.bam, contigs.gfa | | 628 | Shovill | 1.1.0 | contigs.fasta | alignment.bam, contigs.gfa | |
| 629 +----------------+----------------+-------------------+------------------------------------------------------------+ | |
| 611 | Staramr | 0.9.1 | resfinder.tsv | mlst.tsv, pointfinder.tsv, plasmidfinder.tsv, settings.tsv | | 630 | Staramr | 0.9.1 | resfinder.tsv | mlst.tsv, pointfinder.tsv, plasmidfinder.tsv, settings.tsv | |
| 631 +----------------+----------------+-------------------+------------------------------------------------------------+ | |
| 612 | tabular_file | 0 | output.tsv | no optional files | | 632 | tabular_file | 0 | output.tsv | no optional files | |
| 633 +----------------+----------------+-------------------+------------------------------------------------------------+ | |
| 613 | 634 |
| 614 ** Options ** | 635 ** Options ** |
| 615 You can add a tool version and a database version for related tools. | 636 You can add a tool version and a database version for related tools. |
| 616 For some tools you can add optional files previously produced by the tool | 637 For some tools you can add optional files previously produced by the tool |
| 638 | |
| 617 ]]></help> | 639 ]]></help> |
| 618 <expand macro="citations"/> | 640 <expand macro="citations"/> |
| 619 </tool> | 641 </tool> |