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
comparison
equal deleted inserted replaced
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