Mercurial > repos > iuc > plasmidfinder
comparison plasmidfinder.xml @ 1:eccc7495c3d9 draft
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/plasmidfinder commit 69aab27f0210af0f0986d63575f9bfdb3f9d1f6a
| author | iuc |
|---|---|
| date | Fri, 14 Oct 2022 11:54:49 +0000 |
| parents | 2b6e795b22a9 |
| children | 7075b7a5441b |
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| 0:2b6e795b22a9 | 1:eccc7495c3d9 |
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| 15 -p '$input.database_name.fields.path' | 15 -p '$input.database_name.fields.path' |
| 16 -l '$options.min_cov' | 16 -l '$options.min_cov' |
| 17 -t '$options.threshold' | 17 -t '$options.threshold' |
| 18 #if $input.input_file.ext == 'fasta' or $input.input_file.ext == 'fasta.gz' | 18 #if $input.input_file.ext == 'fasta' or $input.input_file.ext == 'fasta.gz' |
| 19 -mp blastn | 19 -mp blastn |
| 20 #else if $input.input_file.ext == 'fastqsanger.gz' or $input.input_file.ext == 'fastqsanger' | 20 #elif $input.input_file.ext == 'fastqsanger' or $input.input_file.ext == 'fastqsanger.gz' |
| 21 -mp kma | 21 -mp kma |
| 22 #end if | 22 #end if |
| 23 -x | 23 -x |
| 24 -o output_dir | 24 -o output_dir |
| 25 -tmp temp_dir | 25 -tmp temp_dir |
| 29 | tee '$log_file' | 29 | tee '$log_file' |
| 30 ]]> | 30 ]]> |
| 31 </command> | 31 </command> |
| 32 <inputs> | 32 <inputs> |
| 33 <section name="input" title="Input parameters" expanded="true"> | 33 <section name="input" title="Input parameters" expanded="true"> |
| 34 <param name="input_file" type="data" format="fasta,fastq,fasta.gz,fastq.gz" label="Choose a fasta or fastq file" help="File to be analyzed"/> | 34 <param name="input_file" type="data" format="fasta,fasta.gz,fastqsanger,fastqsanger.gz" label="Choose a fasta or fastq file" help="File to be analyzed"/> |
| 35 <param name="database_name" type="select" label="PlasmidFinder database"> | 35 <param name="database_name" type="select" label="PlasmidFinder database"> |
| 36 <options from_data_table="plasmidfinder_db"> | 36 <options from_data_table="plasmidfinder_db"> |
| 37 <validator message="No PlasmidFinder database is available" type="no_options"/> | 37 <validator message="No PlasmidFinder database is available" type="no_options"/> |
| 38 </options> | 38 </options> |
| 39 </param> | 39 </param> |
| 40 </section> | 40 </section> |
| 41 <section name="options" title="Options"> | 41 <section name="options" title="Options"> |
| 42 <param name="min_cov" type="float" min="0" max="1" value="0.6" label="Minimal coverage" help="Choose a minimum coverage value (default: 0.6)"/> | 42 <param name="min_cov" type="float" min="0" max="1" value="0.6" label="Minimal coverage" help=" Fraction of matching sequence on the total target sequence(default: 0.6)"/> |
| 43 <param name="threshold" type="float" min="0" max="1" value="0.95" label="Minimal identity" help="Choose a minimum identity value (default: 0.95)"/> | 43 <param name="threshold" type="float" min="0" max="1" value="0.95" label="Minimal identity" help=" Fraction of shared nucleotide on the match (default: 0.95)"/> |
| 44 </section> | 44 </section> |
| 45 <section name="output_files" title="Output file selection"> | 45 <section name="output_files" title="Output file selection"> |
| 46 <param name="output_selection" type="select" display="checkboxes" multiple="true" label="Output files selection"> | 46 <param name="output_selection" type="select" display="checkboxes" multiple="true" label="Output files selection"> |
| 47 <option value="data_json">JSON file result</option> | 47 <option value="data_json">JSON file result</option> |
| 48 <option value="hit_fasta" selected="true">Hits in genome</option> | 48 <option value="hit_fasta" selected="true">Matching sequences in the genome for plasmid</option> |
| 49 <option value="plasmid_fasta" selected="true">Plasmid hits</option> | 49 <option value="plasmid_fasta" selected="true">Plasmid sequences discovered in the genome</option> |
| 50 <option value="result_tsv" selected="true">Plasmid results</option> | 50 <option value="result_tsv" selected="true">Plasmid match list</option> |
| 51 <option value="result_txt" selected="true">Raw results</option> | 51 <option value="result_txt" selected="true">Plasmid match list in raw format</option> |
| 52 <option value="logfile">Log file</option> | 52 <option value="logfile">Log file</option> |
| 53 </param> | 53 </param> |
| 54 </section> | 54 </section> |
| 55 </inputs> | 55 </inputs> |
| 56 <outputs> | 56 <outputs> |
| 126 </test> | 126 </test> |
| 127 </tests> | 127 </tests> |
| 128 <help>< with hundreds sequences. | 131 It is based on the [plasmidfinder database](https://bitbucket.org/genomicepidemiology/plasmidfinder_db/) with hundreds sequences. |
| 132 **Input** | 132 **Input** |
| 133 It can analyse raw data using a k-mer approach based on KMA or a blastn for genome assembly. | 133 PlasmidFinder takes raw data (with a k-mer analysisi) as reads or genome assembly (blastn analysis) to search plasmids. |
| 134 A database is need obtained from the plasmidfinder database. | |
| 135 **Options** | |
| 136 You can modify the coverage value (% of matching sequence on the total target sequence) | |
| 137 You can modify the identity threshold (% of shared nucleotide on the match) | |
| 138 **Output** | 134 **Output** |
| 139 Some output files are availables | 135 Some output files are availables |
| 140 - A fasta file with all available hits detected in the genome | 136 - A fasta file with all available sequences detected in the genome |
| 141 - A fasta file with all plasmid sequences from the database | 137 - A fasta file with all plasmid sequences from the database |
| 142 - A summary of the analysis in tabular format | 138 - A summary of the analysis in tabular format |
| 143 - A Raw result file in text format | 139 - A Raw result file in text format |
| 144 - A JSON file could be use for other boinformatic analaysis | 140 - A JSON file could be use for other boinformatic analysis |
| 145 - A log file with analysis parameters | 141 - A log file with analysis parameters |
| 146 | 142 |
| 147 ]]></help> | 143 ]]></help> |
| 148 <expand macro="citations"/> | 144 <expand macro="citations"/> |
| 149 </tool> | 145 </tool> |