Mercurial > repos > thanhlv > amrfinderplus
annotate amrfinderplus.xml @ 2:a9e5d593228e draft default tip
planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/ncbi-armfinderplus commit 2c3091cc8850849ac99884f92f195e4de9774f99
author | thanhlv |
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date | Wed, 11 Sep 2019 09:51:28 -0400 |
parents | f92ab7729a35 |
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rev | line source |
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23454c5b9812
planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/ncbi-armfinderplus commit fe4ac04b9d5bef519eba3d041f495cd73e71bfdf
thanhlv
parents:
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1 <tool id="amrfinder" name="amrfinder" version="@VERSION@+galaxy1"> |
23454c5b9812
planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/ncbi-armfinderplus commit fe4ac04b9d5bef519eba3d041f495cd73e71bfdf
thanhlv
parents:
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2 <description> |
23454c5b9812
planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/ncbi-armfinderplus commit fe4ac04b9d5bef519eba3d041f495cd73e71bfdf
thanhlv
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3 identifies AMR genes using either protein annotations or nucleotide sequence. |
23454c5b9812
planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/ncbi-armfinderplus commit fe4ac04b9d5bef519eba3d041f495cd73e71bfdf
thanhlv
parents:
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4 </description> |
23454c5b9812
planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/ncbi-armfinderplus commit fe4ac04b9d5bef519eba3d041f495cd73e71bfdf
thanhlv
parents:
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5 <macros> |
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planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/ncbi-armfinderplus commit fe4ac04b9d5bef519eba3d041f495cd73e71bfdf
thanhlv
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6 <token name="@VERSION@">3.1.1b</token> |
23454c5b9812
planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/ncbi-armfinderplus commit fe4ac04b9d5bef519eba3d041f495cd73e71bfdf
thanhlv
parents:
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7 </macros> |
23454c5b9812
planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/ncbi-armfinderplus commit fe4ac04b9d5bef519eba3d041f495cd73e71bfdf
thanhlv
parents:
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8 <requirements> |
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planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/ncbi-armfinderplus commit fe4ac04b9d5bef519eba3d041f495cd73e71bfdf
thanhlv
parents:
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9 <requirement type="package" version="@VERSION@">ncbi-amrfinderplus</requirement> |
23454c5b9812
planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/ncbi-armfinderplus commit fe4ac04b9d5bef519eba3d041f495cd73e71bfdf
thanhlv
parents:
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10 </requirements> |
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planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/ncbi-armfinderplus commit fe4ac04b9d5bef519eba3d041f495cd73e71bfdf
thanhlv
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11 <version_command><![CDATA[amrfinder --version]]></version_command> |
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planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/ncbi-armfinderplus commit fe4ac04b9d5bef519eba3d041f495cd73e71bfdf
thanhlv
parents:
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12 |
23454c5b9812
planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/ncbi-armfinderplus commit fe4ac04b9d5bef519eba3d041f495cd73e71bfdf
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13 <command detect_errors="exit_code"><![CDATA[ |
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planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/ncbi-armfinderplus commit fe4ac04b9d5bef519eba3d041f495cd73e71bfdf
thanhlv
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14 amrfinder |
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planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/ncbi-armfinderplus commit fe4ac04b9d5bef519eba3d041f495cd73e71bfdf
thanhlv
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15 $plus |
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planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/ncbi-armfinderplus commit fe4ac04b9d5bef519eba3d041f495cd73e71bfdf
thanhlv
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16 --threads \${GALAXY_SLOTS:-1} |
23454c5b9812
planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/ncbi-armfinderplus commit fe4ac04b9d5bef519eba3d041f495cd73e71bfdf
thanhlv
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17 --database '$amrfinder_databases.fields.path' |
23454c5b9812
planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/ncbi-armfinderplus commit fe4ac04b9d5bef519eba3d041f495cd73e71bfdf
thanhlv
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18 #if $input_selection.input_source_selector == 'nuc' |
23454c5b9812
planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/ncbi-armfinderplus commit fe4ac04b9d5bef519eba3d041f495cd73e71bfdf
thanhlv
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19 -n '$input_selection.fasta_file' |
23454c5b9812
planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/ncbi-armfinderplus commit fe4ac04b9d5bef519eba3d041f495cd73e71bfdf
thanhlv
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20 #elif $input_selection.input_source_selector == 'pro' |
23454c5b9812
planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/ncbi-armfinderplus commit fe4ac04b9d5bef519eba3d041f495cd73e71bfdf
thanhlv
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21 -p '$input_selection.fasta_file' |
23454c5b9812
planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/ncbi-armfinderplus commit fe4ac04b9d5bef519eba3d041f495cd73e71bfdf
thanhlv
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22 #if $input_selection.gff.use == 'gff_yes' |
23454c5b9812
planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/ncbi-armfinderplus commit fe4ac04b9d5bef519eba3d041f495cd73e71bfdf
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23 -g '$input_selection.gff.gff_file' |
23454c5b9812
planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/ncbi-armfinderplus commit fe4ac04b9d5bef519eba3d041f495cd73e71bfdf
thanhlv
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24 #end if |
23454c5b9812
planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/ncbi-armfinderplus commit fe4ac04b9d5bef519eba3d041f495cd73e71bfdf
thanhlv
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25 #elif $input_selection.input_source_selector == 'both' |
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planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/ncbi-armfinderplus commit fe4ac04b9d5bef519eba3d041f495cd73e71bfdf
thanhlv
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26 -n '$input_selection.nuc_file' |
23454c5b9812
planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/ncbi-armfinderplus commit fe4ac04b9d5bef519eba3d041f495cd73e71bfdf
thanhlv
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27 -p '$input_selection.pro_file' |
23454c5b9812
planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/ncbi-armfinderplus commit fe4ac04b9d5bef519eba3d041f495cd73e71bfdf
thanhlv
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28 #if $input_selection.gff.use == 'gff_yes' |
23454c5b9812
planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/ncbi-armfinderplus commit fe4ac04b9d5bef519eba3d041f495cd73e71bfdf
thanhlv
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29 -g '$input_selection.gff.gff_file' |
23454c5b9812
planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/ncbi-armfinderplus commit fe4ac04b9d5bef519eba3d041f495cd73e71bfdf
thanhlv
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30 #end if |
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planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/ncbi-armfinderplus commit fe4ac04b9d5bef519eba3d041f495cd73e71bfdf
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31 #end if |
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planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/ncbi-armfinderplus commit 2c3091cc8850849ac99884f92f195e4de9774f99
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32 #if str($organism) != 'None' |
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planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/ncbi-armfinderplus commit fe4ac04b9d5bef519eba3d041f495cd73e71bfdf
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33 -O $organism |
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planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/ncbi-armfinderplus commit fe4ac04b9d5bef519eba3d041f495cd73e71bfdf
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34 #end if |
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planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/ncbi-armfinderplus commit fe4ac04b9d5bef519eba3d041f495cd73e71bfdf
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35 -o results.tsv |
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planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/ncbi-armfinderplus commit fe4ac04b9d5bef519eba3d041f495cd73e71bfdf
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36 $report_common |
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planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/ncbi-armfinderplus commit fe4ac04b9d5bef519eba3d041f495cd73e71bfdf
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37 #if $point_mut_all |
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planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/ncbi-armfinderplus commit fe4ac04b9d5bef519eba3d041f495cd73e71bfdf
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38 --point_mut_all point_mutate.tsv |
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planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/ncbi-armfinderplus commit fe4ac04b9d5bef519eba3d041f495cd73e71bfdf
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39 #end if |
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planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/ncbi-armfinderplus commit fe4ac04b9d5bef519eba3d041f495cd73e71bfdf
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40 $gpipe |
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planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/ncbi-armfinderplus commit fe4ac04b9d5bef519eba3d041f495cd73e71bfdf
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41 ]]> </command> |
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planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/ncbi-armfinderplus commit fe4ac04b9d5bef519eba3d041f495cd73e71bfdf
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42 |
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planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/ncbi-armfinderplus commit fe4ac04b9d5bef519eba3d041f495cd73e71bfdf
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43 <inputs> |
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planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/ncbi-armfinderplus commit fe4ac04b9d5bef519eba3d041f495cd73e71bfdf
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44 <conditional name="input_selection"> |
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planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/ncbi-armfinderplus commit fe4ac04b9d5bef519eba3d041f495cd73e71bfdf
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45 <param name="input_source_selector" type="select" label="Input data type"> |
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planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/ncbi-armfinderplus commit fe4ac04b9d5bef519eba3d041f495cd73e71bfdf
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46 <option value="nuc">Nucleotide</option> |
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planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/ncbi-armfinderplus commit fe4ac04b9d5bef519eba3d041f495cd73e71bfdf
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47 <option value="pro">Protein</option> |
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planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/ncbi-armfinderplus commit fe4ac04b9d5bef519eba3d041f495cd73e71bfdf
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48 <option value="both">Nucleotide and Protein</option> |
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planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/ncbi-armfinderplus commit fe4ac04b9d5bef519eba3d041f495cd73e71bfdf
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49 </param> |
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planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/ncbi-armfinderplus commit fe4ac04b9d5bef519eba3d041f495cd73e71bfdf
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50 <when value="nuc"> |
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planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/ncbi-armfinderplus commit fe4ac04b9d5bef519eba3d041f495cd73e71bfdf
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51 <param name="fasta_file" type="data" format="fasta" label="Select nucleotide fasta file"/> |
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planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/ncbi-armfinderplus commit fe4ac04b9d5bef519eba3d041f495cd73e71bfdf
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52 </when> |
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planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/ncbi-armfinderplus commit fe4ac04b9d5bef519eba3d041f495cd73e71bfdf
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53 <when value="pro"> |
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planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/ncbi-armfinderplus commit fe4ac04b9d5bef519eba3d041f495cd73e71bfdf
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54 <param name="fasta_file" type="data" format="fasta" label="Select protein fasta file"/> |
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planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/ncbi-armfinderplus commit fe4ac04b9d5bef519eba3d041f495cd73e71bfdf
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55 <conditional name="gff"> |
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planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/ncbi-armfinderplus commit fe4ac04b9d5bef519eba3d041f495cd73e71bfdf
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56 <param name="use" type="select" label="Using GFF to get genomic coordinates"> |
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planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/ncbi-armfinderplus commit fe4ac04b9d5bef519eba3d041f495cd73e71bfdf
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57 <option value="gff_yes">Yes</option> |
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planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/ncbi-armfinderplus commit fe4ac04b9d5bef519eba3d041f495cd73e71bfdf
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58 <option value="gff_no" selected="true">No</option> |
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planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/ncbi-armfinderplus commit fe4ac04b9d5bef519eba3d041f495cd73e71bfdf
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59 </param> |
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planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/ncbi-armfinderplus commit fe4ac04b9d5bef519eba3d041f495cd73e71bfdf
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60 <when value="gff_yes"> |
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planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/ncbi-armfinderplus commit fe4ac04b9d5bef519eba3d041f495cd73e71bfdf
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61 <param name="gff_file" type="data" format="gff,gff3" label="Select GFF file" help="Protein id should be in the attribute 'Name=id' (9th field) of the rows with type 'CDS' or 'gene' (3rd field)."/> |
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planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/ncbi-armfinderplus commit fe4ac04b9d5bef519eba3d041f495cd73e71bfdf
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62 </when> |
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planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/ncbi-armfinderplus commit fe4ac04b9d5bef519eba3d041f495cd73e71bfdf
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63 <when value="gff_no"> |
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64 </when> |
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65 </conditional> |
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66 </when> |
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planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/ncbi-armfinderplus commit fe4ac04b9d5bef519eba3d041f495cd73e71bfdf
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67 <when value="both"> |
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planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/ncbi-armfinderplus commit fe4ac04b9d5bef519eba3d041f495cd73e71bfdf
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68 <param name="nuc_file" type="data" format="fasta" label="Select a nucleotide fasta file"/> |
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planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/ncbi-armfinderplus commit fe4ac04b9d5bef519eba3d041f495cd73e71bfdf
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69 <param name="pro_file" type="data" format="fasta" label="Select a protein fasta file"/> |
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planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/ncbi-armfinderplus commit fe4ac04b9d5bef519eba3d041f495cd73e71bfdf
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70 <conditional name="gff"> |
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planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/ncbi-armfinderplus commit fe4ac04b9d5bef519eba3d041f495cd73e71bfdf
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71 <param name="use" type="select" label="Using GFF to get genomic coordinates"> |
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planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/ncbi-armfinderplus commit fe4ac04b9d5bef519eba3d041f495cd73e71bfdf
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72 <option value="gff_yes">Yes</option> |
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73 <option value="gff_no" selected="true">No</option> |
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planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/ncbi-armfinderplus commit fe4ac04b9d5bef519eba3d041f495cd73e71bfdf
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74 </param> |
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planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/ncbi-armfinderplus commit fe4ac04b9d5bef519eba3d041f495cd73e71bfdf
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75 <when value="gff_yes"> |
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76 <param name="gff_file" type="data" format="gff,gff3" label="Select GFF file" help="Protein id should be in the attribute 'Name=id' (9th field) of the rows with type 'CDS' or 'gene' (3rd field)."/> |
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77 </when> |
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78 <when value="gff_no"> |
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79 </when> |
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80 </conditional> |
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81 </when> |
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82 </conditional> |
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83 <!-- DATABASE INPUT--> |
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84 <param name="amrfinder_databases" label="Select a database" type="select"> |
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85 <options from_data_table="amrfinder_databases"> |
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86 <validator message="No database is available" type="no_options" /> |
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87 </options> |
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88 </param> |
1
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89 <param name="organism" type="select" optional="true" label="Get organism-specific results"> |
0
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90 <option value="Campylobacter">Campylobacter</option> |
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91 <option value="Escherichia">Escherichia</option> |
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92 <option value="Klebsiella">Klebsiella</option> |
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93 <option value="Salmonella">Salmonella</option> |
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94 <option value="Staphylococcus">Staphylococcus</option> |
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95 <option value="Vibrio">Vibrio</option> |
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96 </param> |
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97 <param name="min_iden" argument="--ident_min" type="float" value="-1" label="Minimum identity for a blast-based hit" help="(Methods BLAST or PARTIAL). -1 means use a curated threshold if it exists and 0.9 otherwise. Setting this value to something other than -1 will override any curated similarity cutoffs" /> |
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98 <param name="min_cov" argument="--coverage_min" type="float" min="0" max="1" value="0.5" label="Minimum coverage of the reference protein" /> |
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99 <param name="plus" type="boolean" truevalue="--plus" falsevalue="" label="Add the plus genes to the report" /> |
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100 <param name="report_common" type="boolean" truevalue="--report_common" falsevalue="" label="Suppress proteins common to a taxonomy group" /> |
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101 <param name="point_mut_all" type="boolean" truevalue="true" falsevalue="false" label="Report all target positions of reference point mutations" /> |
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102 <param name="gpipe" type="boolean" truevalue="--gpipe" falsevalue="" label="Protein identifiers in the protein FASTA file have format gnl-project-accession" /> |
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103 </inputs> |
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104 |
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105 <outputs> |
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106 <data name="result" format="tabular" from_work_dir="results.tsv" label="${tool.name} on ${on_string}: Result"/> |
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107 <data name="point_mutate" format="tabular" from_work_dir="point_mutate.tsv" label="${tool.name} on ${on_string}: Point mutate all"> |
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108 <filter>point_mut_all</filter> |
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109 </data> |
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110 </outputs> |
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111 |
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112 <tests> |
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113 <test> <!-- dna input--> |
2
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114 <param name="input_source_selector" value="nuc"/> |
0
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115 <param name="fasta_file" value="test_dna.fa" ftype="fasta"/> |
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116 <param name="amrfinder_databases" value="2019-08-27.1" /> |
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117 <output name="result" file="test_dna.expected" lines_diff="1"/> |
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118 </test> |
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119 <test> <!-- dna input and organism, plus gene--> |
2
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120 <param name="input_source_selector" value="nuc"/> |
0
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121 <param name="fasta_file" value="test_dna.fa" ftype="fasta"/> |
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122 <param name="organism" value="Escherichia" /> |
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123 <param name="plus" value="true" /> |
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124 <param name="amrfinder_databases" value="2019-08-27.1" /> |
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125 <output name="result" file="test_dna_Escherichia.expected" lines_diff="1"/> |
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126 </test> |
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127 <test> <!-- AA input--> |
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128 <param name="input_source_selector" value="pro"/> |
0
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129 <param name="fasta_file" value="test_prot.fa" ftype="fasta"/> |
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130 <param name="amrfinder_databases" value="2019-08-27.1" /> |
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131 <output name="result" file="test_prot.expected" lines_diff="1"/> |
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132 </test> |
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133 <test> <!-- DNA and AA input--> |
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134 <param name="input_source_selector" value="both"/> |
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135 <param name="use" value="gff_yes"/> |
0
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136 <param name="nuc_file" value="test_dna.fa" ftype="fasta"/> |
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137 <param name="pro_file" value="test_prot.fa" ftype="fasta"/> |
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138 <param name="use" value="gff_yes"/> |
0
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139 <param name="gff_file" value="test_prot.gff" ftype="gff3"/> |
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140 <param name="amrfinder_databases" value="2019-08-27.1" /> |
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141 <output name="result" file="test_both.expected" lines_diff="1"/> |
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142 </test> |
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143 </tests> |
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144 |
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145 |
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146 <help><![CDATA[ |
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147 This software and the accompanying database are designed to find acquired |
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148 antimicrobial resistance genes in bacterial protein or assembled nucleotide |
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149 sequences as well as known point mutations for several taxa. With |
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150 AMRFinderPlus we have added select members of additional classes of genes |
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151 such as virulence factors, biocide, heat, acid, and metal resistance genes. |
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152 More details: https://github.com/ncbi/amr/wiki |
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153 ]]> </help> |
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154 <citations> |
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155 <citation type="doi">10.1101/550707</citation> |
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156 </citations> |
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157 |
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158 </tool> |