Mercurial > repos > nml > staramr
comparison staramr_search.xml @ 10:7573a6c11c4d draft
"planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit 69b939934ff9f503c7314cdbe6e3cb08e5f84db5"
| author | nml |
|---|---|
| date | Wed, 27 Nov 2019 08:59:23 -0500 |
| parents | 61a3e97aa865 |
| children | 5f43703968cf |
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| 9:61a3e97aa865 | 10:7573a6c11c4d |
|---|---|
| 1 <tool id="staramr_search" name="staramr" version="@VERSION@"> | 1 <tool id="staramr_search" name="staramr" version="@VERSION@"> |
| 2 <description>Scans genome assemblies against the ResFinder, PlasmidFinder, and PointFinder databases searching for AMR genes.</description> | 2 <description>Scans genome assemblies against the ResFinder, PlasmidFinder, and PointFinder databases searching for AMR genes.</description> |
| 3 <macros> | 3 <macros> |
| 4 <token name="@VERSION@">0.6.1</token> | 4 <token name="@VERSION@">0.7.0</token> |
| 5 </macros> | 5 </macros> |
| 6 <requirements> | 6 <requirements> |
| 7 <requirement type="package" version="@VERSION@">staramr</requirement> | 7 <requirement type="package" version="@VERSION@">staramr</requirement> |
| 8 </requirements> | 8 </requirements> |
| 9 <version_command>staramr --version</version_command> | 9 <version_command>staramr --version</version_command> |
| 21 ln -s "$excel" $excel_proper_extension && | 21 ln -s "$excel" $excel_proper_extension && |
| 22 | 22 |
| 23 staramr search | 23 staramr search |
| 24 | 24 |
| 25 --nprocs "\${GALAXY_SLOTS:-1}" | 25 --nprocs "\${GALAXY_SLOTS:-1}" |
| 26 | |
| 27 --genome-size-lower-bound $advanced.genome_size_lower_bound | |
| 28 --genome-size-upper-bound $advanced.genome_size_upper_bound | |
| 29 --minimum-N50-value $advanced.minimum_N50_value | |
| 30 --minimum-contig-length $advanced.minimum_contig_length | |
| 31 --unacceptable-number-contigs $advanced.unacceptable_number_contigs | |
| 26 | 32 |
| 27 --pid-threshold $advanced.pid_threshold | 33 --pid-threshold $advanced.pid_threshold |
| 28 --percent-length-overlap-resfinder $advanced.plength_resfinder | 34 --percent-length-overlap-resfinder $advanced.plength_resfinder |
| 29 --percent-length-overlap-plasmidfinder $advanced.plength_plasmidfinder | 35 --percent-length-overlap-plasmidfinder $advanced.plength_plasmidfinder |
| 30 --percent-length-overlap-pointfinder $advanced.plength_pointfinder | 36 --percent-length-overlap-pointfinder $advanced.plength_pointfinder |
| 75 min="0" max="100" help="(--percent-length-overlap-resfinder)" /> | 81 min="0" max="100" help="(--percent-length-overlap-resfinder)" /> |
| 76 <param name="plength_pointfinder" type="float" label="Percent length overlap of BLAST hit for PointFinder database" value="95.0" | 82 <param name="plength_pointfinder" type="float" label="Percent length overlap of BLAST hit for PointFinder database" value="95.0" |
| 77 min="0" max="100" help="(--percent-length-overlap-pointfinder)" /> | 83 min="0" max="100" help="(--percent-length-overlap-pointfinder)" /> |
| 78 <param name="plength_plasmidfinder" type="float" label="Percent length overlap of BLAST hit for PlasmidFinder database" value="60.0" | 84 <param name="plength_plasmidfinder" type="float" label="Percent length overlap of BLAST hit for PlasmidFinder database" value="60.0" |
| 79 min="0" max="100" help="(--percent-length-overlap-plasmidfinder)" /> | 85 min="0" max="100" help="(--percent-length-overlap-plasmidfinder)" /> |
| 86 <param name="genome_size_lower_bound" type="integer" label="The lower bound for our genome size for the quality metrics" value="4000000" | |
| 87 help="(--genome-size-lower-bound)" /> | |
| 88 <param name="genome_size_upper_bound" type="integer" label="The upper bound for our genome size for the quality metrics" value="6000000" | |
| 89 help="(--genome-size-upper-bound)" /> | |
| 90 <param name="minimum_N50_value" type="integer" label="The minimum N50 value for the quality metrics" value="10000" | |
| 91 help="(--minimum-N50-value)" /> | |
| 92 <param name="minimum_contig_length" type="integer" label="The minimum contig length for the quality metrics" value="300" | |
| 93 help="(--minimum-contig-length)" /> | |
| 94 <param name="unacceptable_number_contigs" type="integer" label="The number of contigs, under the minimum contig length which is unacceptable for the quality metrics" value="1000" | |
| 95 help="(--unacceptable-number-contigs)" /> | |
| 80 <param name="report_all_blast" type="boolean" label="Report all BLAST results" truevalue="--report-all-blast" falsevalue="" | 96 <param name="report_all_blast" type="boolean" label="Report all BLAST results" truevalue="--report-all-blast" falsevalue="" |
| 81 help="Report all BLAST results (includes overlapping hits, mainly for debugging)" /> | 97 help="Report all BLAST results (includes overlapping hits, mainly for debugging)" /> |
| 82 <param name="exclude_negatives" type="boolean" label="Exclude negative (non-resistant) results" truevalue="--exclude-negatives" falsevalue="" /> | 98 <param name="exclude_negatives" type="boolean" label="Exclude negative (non-resistant) results" truevalue="--exclude-negatives" falsevalue="" /> |
| 83 <param name="exclude_resistance_phenotypes" type="boolean" label="Exclude resistance phenotypes" truevalue="--exclude-resistance-phenotypes" falsevalue="" /> | 99 <param name="exclude_resistance_phenotypes" type="boolean" label="Exclude resistance phenotypes" truevalue="--exclude-resistance-phenotypes" falsevalue="" /> |
| 84 <conditional name="exclude_genes"> | 100 <conditional name="exclude_genes"> |
| 167 <param name="exclude_genes_condition" value="custom" /> | 183 <param name="exclude_genes_condition" value="custom" /> |
| 168 <param name="exclude_genes_file" value="genes_to_exclude.tsv" /> | 184 <param name="exclude_genes_file" value="genes_to_exclude.tsv" /> |
| 169 | 185 |
| 170 <output name="summary" file="test5-summary.tsv" ftype="tabular" /> | 186 <output name="summary" file="test5-summary.tsv" ftype="tabular" /> |
| 171 </test> | 187 </test> |
| 188 <test> | |
| 189 <param name="genomes" value="test-aminoglycoside.fsa" /> | |
| 190 <param name="genome_size_lower_bound" value="1" /> | |
| 191 <param name="genome_size_upper_bound" value="10" /> | |
| 192 | |
| 193 <output name="summary" file="test8-summary.tsv" ftype="tabular"/> | |
| 194 </test> | |
| 172 </tests> | 195 </tests> |
| 173 <help><![CDATA[ | 196 <help><![CDATA[ |
| 174 staramr | 197 staramr |
| 175 ======= | 198 ======= |
| 176 | 199 |