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comparison staramr_search.xml @ 4:1e8ec0f861ff draft

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planemo upload for repository https://github.com/phac-nml/staramr commit fd6c4338e65d6a33900da6fe7ae6f507105d3446
author nml
date Thu, 22 Nov 2018 13:38:58 -0500
parents 9047a1d3d8ea
children 930893c83a1a
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3:9047a1d3d8ea 4:1e8ec0f861ff
1 <tool id="staramr_search" name="staramr" version="0.2.2"> 1 <tool id="staramr_search" name="staramr" version="0.3.0">
2 <description>Scans genome assemblies against the ResFinder and PointFinder databases searching for AMR genes.</description> 2 <description>Scans genome assemblies against the ResFinder and PointFinder databases searching for AMR genes.</description>
3 <requirements> 3 <requirements>
4 <requirement type="package" version="0.2.2">staramr</requirement> 4 <requirement type="package" version="0.3.0">staramr</requirement>
5 </requirements> 5 </requirements>
6 <command detect_errors="exit_code"><![CDATA[ 6 <command detect_errors="exit_code"><![CDATA[
7 #import re 7 #import re
8 8
9 #set $named_genomes = '' 9 #set $named_genomes = ''
25 --percent-length-overlap-pointfinder $advanced.plength_pointfinder 25 --percent-length-overlap-pointfinder $advanced.plength_pointfinder
26 26
27 $advanced.report_all_blast 27 $advanced.report_all_blast
28 $advanced.exclude_negatives 28 $advanced.exclude_negatives
29 $advanced.exclude_resistance_phenotypes 29 $advanced.exclude_resistance_phenotypes
30
31 #if str($advanced.exclude_genes.exclude_genes_condition) == 'custom'
32 --exclude-genes-file '${advanced.exclude_genes.exclude_genes_file}'
33 #elif str($advanced.exclude_genes.exclude_genes_condition) == 'none'
34 --no-exclude-genes
35 #end if
30 36
31 --output-summary $summary 37 --output-summary $summary
32 --output-resfinder $resfinder 38 --output-resfinder $resfinder
33 #if $use_pointfinder.enable 39 #if $use_pointfinder.enable
34 --output-pointfinder $pointfinder 40 --output-pointfinder $pointfinder
64 min="0" max="100" help="(--percent-length-overlap-pointfinder)" /> 70 min="0" max="100" help="(--percent-length-overlap-pointfinder)" />
65 <param name="report_all_blast" type="boolean" label="Report all BLAST results" truevalue="--report-all-blast" falsevalue="" 71 <param name="report_all_blast" type="boolean" label="Report all BLAST results" truevalue="--report-all-blast" falsevalue=""
66 help="Report all BLAST results (includes overlapping hits, mainly for debugging)" /> 72 help="Report all BLAST results (includes overlapping hits, mainly for debugging)" />
67 <param name="exclude_negatives" type="boolean" label="Exclude negative (non-resistant) results" truevalue="--exclude-negatives" falsevalue="" /> 73 <param name="exclude_negatives" type="boolean" label="Exclude negative (non-resistant) results" truevalue="--exclude-negatives" falsevalue="" />
68 <param name="exclude_resistance_phenotypes" type="boolean" label="Exclude resistance phenotypes" truevalue="--exclude-resistance-phenotypes" falsevalue="" /> 74 <param name="exclude_resistance_phenotypes" type="boolean" label="Exclude resistance phenotypes" truevalue="--exclude-resistance-phenotypes" falsevalue="" />
75 <conditional name="exclude_genes">
76 <param name="exclude_genes_condition" type="select" label="Exclude certain AMR genes from the results">
77 <option value="default" selected="true">Exclude default list of AMR genes</option>
78 <option value="custom">Provide a custom list of AMR genes to exclude</option>
79 <option value="none">Do not exclude any AMR genes</option>
80 </param>
81 <when value="default" />
82 <when value="custom">
83 <param type="data" name="exclude_genes_file" format="txt,tabular" label="Exclude genes file" help="Pass a file containing a list of genes to exclude from the ResFinder/PointFinder results" />
84 </when>
85 <when value="none" />
86 </conditional>
69 </section> 87 </section>
70 </inputs> 88 </inputs>
71 <outputs> 89 <outputs>
72 <data format="tabular" name="summary" label="${tool.name} on ${on_string}: summary.tsv" /> 90 <data format="tabular" name="summary" label="${tool.name} on ${on_string}: summary.tsv" />
73 <data format="tabular" name="resfinder" label="${tool.name} on ${on_string}: resfinder.tsv" /> 91 <data format="tabular" name="resfinder" label="${tool.name} on ${on_string}: resfinder.tsv" />
115 <param name="genomes" value="16S rc_gyrA rc_beta-lactam spaces (extra:characters).fsa" /> 133 <param name="genomes" value="16S rc_gyrA rc_beta-lactam spaces (extra:characters).fsa" />
116 <param name="pid_threshold" value="99.8" /> 134 <param name="pid_threshold" value="99.8" />
117 135
118 <output name="summary" file="test4-summary.tsv" ftype="tabular" /> 136 <output name="summary" file="test4-summary.tsv" ftype="tabular" />
119 </test> 137 </test>
138 <test>
139 <param name="genomes" value="test-aminoglycoside.fsa" />
140
141 <output name="summary" file="test5-summary.tsv" ftype="tabular" />
142 </test>
143 <test>
144 <param name="genomes" value="test-aminoglycoside.fsa" />
145 <param name="exclude_genes_condition" value="none" />
146
147 <output name="summary" file="test6-summary.tsv" ftype="tabular" />
148 </test>
149 <test>
150 <param name="genomes" value="test-aminoglycoside.fsa" />
151 <param name="exclude_genes_condition" value="custom" />
152 <param name="exclude_genes_file" value="genes_to_exclude.tsv" />
153
154 <output name="summary" file="test5-summary.tsv" ftype="tabular" />
155 </test>
120 </tests> 156 </tests>
121 <help><![CDATA[ 157 <help><![CDATA[
122 staramr 158 staramr
123 ======= 159 =======
124 160
128 ----- 164 -----
129 165
130 1. Select your genome contigs (in FASTA format). 166 1. Select your genome contigs (in FASTA format).
131 2. Select whether or not you wish to scan your genome for point mutations giving antimicrobial resistance using the PointFinder database. This requires you to specify the specific organism you are scanning (currently only *salmonella* is supported). 167 2. Select whether or not you wish to scan your genome for point mutations giving antimicrobial resistance using the PointFinder database. This requires you to specify the specific organism you are scanning (currently only *salmonella* is supported).
132 3. Run the tool. 168 3. Run the tool.
169
170 Input
171 -----
172
173 Genomes
174 ```````
175
176 staramr_ takes as input one or more assembled genomes (in FASTA format) to search for AMR genes.
177
178 Exclude genes file
179 ``````````````````
180
181 Setting **Provide a custom list of AMR genes to exclude** in the **Advanced options** allows you to pass a file containing a list of genes to exclude from the results. The file must start with a line **#gene_id** and the gene names must correspond to the sequence IDs in the ResFinder/PointFinder databases. For example:
182
183 ::
184
185 #gene_id
186 aac(6')-Iaa_1_NC_003197
133 187
134 Output 188 Output
135 ------ 189 ------
136 190
137 There are 5 different output files produced by `staramr` as well as a collection of additional files. 191 There are 5 different output files produced by `staramr` as well as a collection of additional files.