Mercurial > repos > dcouvin > catchsequenceinfo
comparison catchsequence/catchsequence.xml @ 0:37d48392bf22 draft default tip
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| author | dcouvin |
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| date | Tue, 21 Sep 2021 16:44:26 +0000 |
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| -1:000000000000 | 0:37d48392bf22 |
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| 1 <tool id="catchsequence" name="catchSequenceInfo" version="1.0.0"> | |
| 2 <description>catchSequenceInfo allows to get resistance/virulence/plasmids/mlst information from DNA sequences</description> | |
| 3 <requirements> | |
| 4 <requirement type="package" version="1.0.1">abricate</requirement> | |
| 5 <requirement type="package" version="2.19.0">mlst</requirement> | |
| 6 <!--<requirement type="package" version="6.6.0">emboss</requirement> | |
| 7 <requirement type="package" version="1.3.2">pandas</requirement>--> | |
| 8 </requirements> | |
| 9 | |
| 10 | |
| 11 <command detect_errors="aggressive"><![CDATA[ | |
| 12 | |
| 13 #import re | |
| 14 ## Creates symlinks for each input file based on the Galaxy 'element_identifier' | |
| 15 ## Used so that a human-readable name appears in the output table (instead of 'dataset_xyz.dat') | |
| 16 #set $named_input_files = '' | |
| 17 #for $input_file in $input_files | |
| 18 ## Add single quotes around each input file identifier | |
| 19 #set $_input_file = "'{}'".format($input_file.element_identifier) | |
| 20 ln -s '${input_file}' ${_input_file} && | |
| 21 #set $named_input_files = $named_input_files + ',' + $_input_file | |
| 22 #end for | |
| 23 | |
| 24 | |
| 25 perl '$__tool_directory__/catchsequence.pl' $named_input_files -perc $percent -res $res -plas $plas -vf $vf > "$output" | |
| 26 | |
| 27 | |
| 28 | |
| 29 ]]></command> | |
| 30 <!-- perl '$__tool_directory__/nucleScore.pl' $_input_file > "$output" --> | |
| 31 <!-- ./nuclescore.sh ${named_input_files} > "$output" --> | |
| 32 | |
| 33 <inputs> | |
| 34 <param type="data" name="input_files" format="fasta,fasta.gz,fasta.bz2,gbk,gbk.gz,gbk.bz2" multiple="true" label="Genome fasta files"/> | |
| 35 | |
| 36 <param name="percent" type="select" label="Percentage type:"> | |
| 37 <option value="ident">Identity</option> | |
| 38 <option value="cov">Coverage</option> | |
| 39 </param> | |
| 40 | |
| 41 <param name="res" type="text" area="false" value="90.00" label="ResFinder %: " /> | |
| 42 <param name="plas" type="text" area="false" value="90.00" label="PlasmidFinder %: " /> | |
| 43 <param name="vf" type="text" area="false" value="80.00" label="VFDB %: " /> | |
| 44 | |
| 45 </inputs> | |
| 46 | |
| 47 <outputs> | |
| 48 <data format="tabular" name="output" /> | |
| 49 </outputs> | |
| 50 | |
| 51 <help> | |
| 52 catchSequenceInfo allows to get resistance/virulence/plasmids/mlst information from DNA sequences. | |
| 53 | |
| 54 This tool uses ABRicate (https://github.com/tseemann/abricate) and MLST (https://github.com/tseemann/mlst) programs to get dedicated information from DNA sequences (such as resistance genes, plasmid genes, virulence genes, allele IDs and MLST number). | |
| 55 | |
| 56 | |
| 57 </help> | |
| 58 | |
| 59 <citations> | |
| 60 <citation type="doi">10.1186/1471-2105-11-595</citation> | |
| 61 <citation type="doi">10.1093/jac/dks261</citation> | |
| 62 <citation type="doi">10.1128/AAC.02412-14</citation> | |
| 63 <citation type="doi">10.1093/nar/gkv1239</citation> | |
| 64 </citations> | |
| 65 | |
| 66 </tool> |