Mercurial > repos > nml > staramr
annotate staramr_search.xml @ 9:61a3e97aa865 draft
"planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit 07b1134fbf48f0f94e6060b861651e1ab48cde71"
author | nml |
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date | Mon, 30 Sep 2019 12:45:02 -0400 |
parents | da787fc8b740 |
children | 7573a6c11c4d |
rev | line source |
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930893c83a1a
planemo upload for repository https://github.com/phac-nml/staramr commit 0794053d021c92d4dd7459abca46d4bf823d7203
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1 <tool id="staramr_search" name="staramr" version="@VERSION@"> |
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3c09557ac425
planemo upload for repository https://github.com/phac-nml/staramr commit 52535d98ad1e03c83c93f230abf966613b4b8fa2
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2 <description>Scans genome assemblies against the ResFinder, PlasmidFinder, and PointFinder databases searching for AMR genes.</description> |
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930893c83a1a
planemo upload for repository https://github.com/phac-nml/staramr commit 0794053d021c92d4dd7459abca46d4bf823d7203
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3 <macros> |
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61a3e97aa865
"planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit 07b1134fbf48f0f94e6060b861651e1ab48cde71"
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4 <token name="@VERSION@">0.6.1</token> |
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930893c83a1a
planemo upload for repository https://github.com/phac-nml/staramr commit 0794053d021c92d4dd7459abca46d4bf823d7203
nml
parents:
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5 </macros> |
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fef5aff062c7
planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
nml
parents:
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6 <requirements> |
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930893c83a1a
planemo upload for repository https://github.com/phac-nml/staramr commit 0794053d021c92d4dd7459abca46d4bf823d7203
nml
parents:
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7 <requirement type="package" version="@VERSION@">staramr</requirement> |
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fef5aff062c7
planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
nml
parents:
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8 </requirements> |
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930893c83a1a
planemo upload for repository https://github.com/phac-nml/staramr commit 0794053d021c92d4dd7459abca46d4bf823d7203
nml
parents:
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9 <version_command>staramr --version</version_command> |
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fef5aff062c7
planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
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10 <command detect_errors="exit_code"><![CDATA[ |
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3801ea82c888
planemo upload for repository https://github.com/phac-nml/staramr commit 1b3cd6d32c357a59fa437e29ede4a6c1e78427f8
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11 #import re |
3801ea82c888
planemo upload for repository https://github.com/phac-nml/staramr commit 1b3cd6d32c357a59fa437e29ede4a6c1e78427f8
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12 |
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fef5aff062c7
planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
nml
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13 #set $named_genomes = '' |
fef5aff062c7
planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
nml
parents:
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14 #for $genome in $genomes |
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da787fc8b740
planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit f1641993d71fc04fadf20753a63cc72a412f4af5
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15 #set $_named_genome = re.sub(r'(\s|\(|\)|\/)', '_', '"{}.fasta"'.format($genome.element_identifier)) |
da787fc8b740
planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit f1641993d71fc04fadf20753a63cc72a412f4af5
nml
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16 ln -s '$genome' $_named_genome && |
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fef5aff062c7
planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
nml
parents:
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17 #set $named_genomes = $named_genomes + ' ' + $_named_genome |
fef5aff062c7
planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
nml
parents:
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18 #end for |
fef5aff062c7
planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
nml
parents:
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19 |
fef5aff062c7
planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
nml
parents:
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20 #set $excel_proper_extension = '"{}.xlsx"'.format($excel) |
fef5aff062c7
planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
nml
parents:
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21 ln -s "$excel" $excel_proper_extension && |
fef5aff062c7
planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
nml
parents:
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22 |
fef5aff062c7
planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
nml
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23 staramr search |
fef5aff062c7
planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
nml
parents:
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24 |
fef5aff062c7
planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
nml
parents:
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25 --nprocs "\${GALAXY_SLOTS:-1}" |
fef5aff062c7
planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
nml
parents:
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26 |
fef5aff062c7
planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
nml
parents:
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27 --pid-threshold $advanced.pid_threshold |
fef5aff062c7
planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
nml
parents:
diff
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28 --percent-length-overlap-resfinder $advanced.plength_resfinder |
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3c09557ac425
planemo upload for repository https://github.com/phac-nml/staramr commit 52535d98ad1e03c83c93f230abf966613b4b8fa2
nml
parents:
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29 --percent-length-overlap-plasmidfinder $advanced.plength_plasmidfinder |
0
fef5aff062c7
planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
nml
parents:
diff
changeset
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30 --percent-length-overlap-pointfinder $advanced.plength_pointfinder |
fef5aff062c7
planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
nml
parents:
diff
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31 |
fef5aff062c7
planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
nml
parents:
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32 $advanced.report_all_blast |
fef5aff062c7
planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
nml
parents:
diff
changeset
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33 $advanced.exclude_negatives |
fef5aff062c7
planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
nml
parents:
diff
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34 $advanced.exclude_resistance_phenotypes |
fef5aff062c7
planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
nml
parents:
diff
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35 |
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1e8ec0f861ff
planemo upload for repository https://github.com/phac-nml/staramr commit fd6c4338e65d6a33900da6fe7ae6f507105d3446
nml
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36 #if str($advanced.exclude_genes.exclude_genes_condition) == 'custom' |
1e8ec0f861ff
planemo upload for repository https://github.com/phac-nml/staramr commit fd6c4338e65d6a33900da6fe7ae6f507105d3446
nml
parents:
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37 --exclude-genes-file '${advanced.exclude_genes.exclude_genes_file}' |
1e8ec0f861ff
planemo upload for repository https://github.com/phac-nml/staramr commit fd6c4338e65d6a33900da6fe7ae6f507105d3446
nml
parents:
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38 #elif str($advanced.exclude_genes.exclude_genes_condition) == 'none' |
1e8ec0f861ff
planemo upload for repository https://github.com/phac-nml/staramr commit fd6c4338e65d6a33900da6fe7ae6f507105d3446
nml
parents:
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39 --no-exclude-genes |
1e8ec0f861ff
planemo upload for repository https://github.com/phac-nml/staramr commit fd6c4338e65d6a33900da6fe7ae6f507105d3446
nml
parents:
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40 #end if |
1e8ec0f861ff
planemo upload for repository https://github.com/phac-nml/staramr commit fd6c4338e65d6a33900da6fe7ae6f507105d3446
nml
parents:
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41 |
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3c09557ac425
planemo upload for repository https://github.com/phac-nml/staramr commit 52535d98ad1e03c83c93f230abf966613b4b8fa2
nml
parents:
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42 #if str($advanced.plasmidfinder_type) != 'include_all' |
3c09557ac425
planemo upload for repository https://github.com/phac-nml/staramr commit 52535d98ad1e03c83c93f230abf966613b4b8fa2
nml
parents:
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43 --plasmidfinder-database-type '${advanced.plasmidfinder_type}' |
3c09557ac425
planemo upload for repository https://github.com/phac-nml/staramr commit 52535d98ad1e03c83c93f230abf966613b4b8fa2
nml
parents:
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44 #end if |
3c09557ac425
planemo upload for repository https://github.com/phac-nml/staramr commit 52535d98ad1e03c83c93f230abf966613b4b8fa2
nml
parents:
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45 |
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fef5aff062c7
planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
nml
parents:
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46 --output-summary $summary |
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3c09557ac425
planemo upload for repository https://github.com/phac-nml/staramr commit 52535d98ad1e03c83c93f230abf966613b4b8fa2
nml
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47 --output-detailed-summary $detailed_summary |
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fef5aff062c7
planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
nml
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48 --output-resfinder $resfinder |
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3c09557ac425
planemo upload for repository https://github.com/phac-nml/staramr commit 52535d98ad1e03c83c93f230abf966613b4b8fa2
nml
parents:
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49 --output-plasmidfinder $plasmidfinder |
3c09557ac425
planemo upload for repository https://github.com/phac-nml/staramr commit 52535d98ad1e03c83c93f230abf966613b4b8fa2
nml
parents:
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50 #if str($use_pointfinder) != 'disabled' |
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fef5aff062c7
planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
nml
parents:
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51 --output-pointfinder $pointfinder |
fef5aff062c7
planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
nml
parents:
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52 #end if |
fef5aff062c7
planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
nml
parents:
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53 --output-settings $settings |
fef5aff062c7
planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
nml
parents:
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54 --output-excel $excel_proper_extension |
fef5aff062c7
planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
nml
parents:
diff
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55 |
fef5aff062c7
planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
nml
parents:
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56 --output-hits-dir staramr_hits |
fef5aff062c7
planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
nml
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57 |
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3c09557ac425
planemo upload for repository https://github.com/phac-nml/staramr commit 52535d98ad1e03c83c93f230abf966613b4b8fa2
nml
parents:
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58 #if str($use_pointfinder) != 'disabled' |
3c09557ac425
planemo upload for repository https://github.com/phac-nml/staramr commit 52535d98ad1e03c83c93f230abf966613b4b8fa2
nml
parents:
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59 --pointfinder-organism '${use_pointfinder}' |
0
fef5aff062c7
planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
nml
parents:
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60 #end if |
fef5aff062c7
planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
nml
parents:
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61 |
fef5aff062c7
planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
nml
parents:
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62 $named_genomes |
fef5aff062c7
planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
nml
parents:
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63 ]]></command> |
fef5aff062c7
planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
nml
parents:
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64 <inputs> |
fef5aff062c7
planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
nml
parents:
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65 <param type="data" name="genomes" format="fasta" multiple="true"/> |
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3c09557ac425
planemo upload for repository https://github.com/phac-nml/staramr commit 52535d98ad1e03c83c93f230abf966613b4b8fa2
nml
parents:
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66 <param name="use_pointfinder" type="select" label="Enable scanning for point mutations using the PointFinder database"> |
3c09557ac425
planemo upload for repository https://github.com/phac-nml/staramr commit 52535d98ad1e03c83c93f230abf966613b4b8fa2
nml
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67 <option value="disabled" selected="true">Disable PointFinder</option> |
3c09557ac425
planemo upload for repository https://github.com/phac-nml/staramr commit 52535d98ad1e03c83c93f230abf966613b4b8fa2
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68 <option value="salmonella">Salmonella</option> |
3c09557ac425
planemo upload for repository https://github.com/phac-nml/staramr commit 52535d98ad1e03c83c93f230abf966613b4b8fa2
nml
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69 <option value="campylobacter">Campylobacter</option> |
3c09557ac425
planemo upload for repository https://github.com/phac-nml/staramr commit 52535d98ad1e03c83c93f230abf966613b4b8fa2
nml
parents:
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70 </param> |
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fef5aff062c7
planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
nml
parents:
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71 <section name="advanced" title="Advanced options" expanded="false"> |
fef5aff062c7
planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
nml
parents:
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72 <param name="pid_threshold" type="float" label="Percent identity threshold for BLAST" value="98.0" |
fef5aff062c7
planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
nml
parents:
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73 min="0" max="100" help="(--pid-threshold)" /> |
fef5aff062c7
planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
nml
parents:
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74 <param name="plength_resfinder" type="float" label="Percent length overlap of BLAST hit for ResFinder database" value="60.0" |
fef5aff062c7
planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
nml
parents:
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75 min="0" max="100" help="(--percent-length-overlap-resfinder)" /> |
fef5aff062c7
planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
nml
parents:
diff
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76 <param name="plength_pointfinder" type="float" label="Percent length overlap of BLAST hit for PointFinder database" value="95.0" |
fef5aff062c7
planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
nml
parents:
diff
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77 min="0" max="100" help="(--percent-length-overlap-pointfinder)" /> |
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3c09557ac425
planemo upload for repository https://github.com/phac-nml/staramr commit 52535d98ad1e03c83c93f230abf966613b4b8fa2
nml
parents:
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78 <param name="plength_plasmidfinder" type="float" label="Percent length overlap of BLAST hit for PlasmidFinder database" value="60.0" |
3c09557ac425
planemo upload for repository https://github.com/phac-nml/staramr commit 52535d98ad1e03c83c93f230abf966613b4b8fa2
nml
parents:
5
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79 min="0" max="100" help="(--percent-length-overlap-plasmidfinder)" /> |
0
fef5aff062c7
planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
nml
parents:
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80 <param name="report_all_blast" type="boolean" label="Report all BLAST results" truevalue="--report-all-blast" falsevalue="" |
fef5aff062c7
planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
nml
parents:
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81 help="Report all BLAST results (includes overlapping hits, mainly for debugging)" /> |
fef5aff062c7
planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
nml
parents:
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82 <param name="exclude_negatives" type="boolean" label="Exclude negative (non-resistant) results" truevalue="--exclude-negatives" falsevalue="" /> |
fef5aff062c7
planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
nml
parents:
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83 <param name="exclude_resistance_phenotypes" type="boolean" label="Exclude resistance phenotypes" truevalue="--exclude-resistance-phenotypes" falsevalue="" /> |
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1e8ec0f861ff
planemo upload for repository https://github.com/phac-nml/staramr commit fd6c4338e65d6a33900da6fe7ae6f507105d3446
nml
parents:
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diff
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84 <conditional name="exclude_genes"> |
1e8ec0f861ff
planemo upload for repository https://github.com/phac-nml/staramr commit fd6c4338e65d6a33900da6fe7ae6f507105d3446
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85 <param name="exclude_genes_condition" type="select" label="Exclude certain AMR genes from the results"> |
1e8ec0f861ff
planemo upload for repository https://github.com/phac-nml/staramr commit fd6c4338e65d6a33900da6fe7ae6f507105d3446
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86 <option value="default" selected="true">Exclude default list of AMR genes</option> |
1e8ec0f861ff
planemo upload for repository https://github.com/phac-nml/staramr commit fd6c4338e65d6a33900da6fe7ae6f507105d3446
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87 <option value="custom">Provide a custom list of AMR genes to exclude</option> |
1e8ec0f861ff
planemo upload for repository https://github.com/phac-nml/staramr commit fd6c4338e65d6a33900da6fe7ae6f507105d3446
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88 <option value="none">Do not exclude any AMR genes</option> |
1e8ec0f861ff
planemo upload for repository https://github.com/phac-nml/staramr commit fd6c4338e65d6a33900da6fe7ae6f507105d3446
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89 </param> |
1e8ec0f861ff
planemo upload for repository https://github.com/phac-nml/staramr commit fd6c4338e65d6a33900da6fe7ae6f507105d3446
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90 <when value="default" /> |
1e8ec0f861ff
planemo upload for repository https://github.com/phac-nml/staramr commit fd6c4338e65d6a33900da6fe7ae6f507105d3446
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91 <when value="custom"> |
1e8ec0f861ff
planemo upload for repository https://github.com/phac-nml/staramr commit fd6c4338e65d6a33900da6fe7ae6f507105d3446
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92 <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" /> |
1e8ec0f861ff
planemo upload for repository https://github.com/phac-nml/staramr commit fd6c4338e65d6a33900da6fe7ae6f507105d3446
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93 </when> |
1e8ec0f861ff
planemo upload for repository https://github.com/phac-nml/staramr commit fd6c4338e65d6a33900da6fe7ae6f507105d3446
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94 <when value="none" /> |
1e8ec0f861ff
planemo upload for repository https://github.com/phac-nml/staramr commit fd6c4338e65d6a33900da6fe7ae6f507105d3446
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95 </conditional> |
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3c09557ac425
planemo upload for repository https://github.com/phac-nml/staramr commit 52535d98ad1e03c83c93f230abf966613b4b8fa2
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96 <param name="plasmidfinder_type" type="select" label="Specify PlasmidFinder Database type"> |
3c09557ac425
planemo upload for repository https://github.com/phac-nml/staramr commit 52535d98ad1e03c83c93f230abf966613b4b8fa2
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97 <option value="include_all" selected="true">Include all available database types</option> |
3c09557ac425
planemo upload for repository https://github.com/phac-nml/staramr commit 52535d98ad1e03c83c93f230abf966613b4b8fa2
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98 <option value="gram_positive">Gram Positive</option> |
3c09557ac425
planemo upload for repository https://github.com/phac-nml/staramr commit 52535d98ad1e03c83c93f230abf966613b4b8fa2
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99 <option value="enterobacteriaceae">Enterobacteriaceae</option> |
3c09557ac425
planemo upload for repository https://github.com/phac-nml/staramr commit 52535d98ad1e03c83c93f230abf966613b4b8fa2
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100 </param> |
0
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planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
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101 </section> |
fef5aff062c7
planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
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102 </inputs> |
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planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
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103 <outputs> |
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61a3e97aa865
"planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit 07b1134fbf48f0f94e6060b861651e1ab48cde71"
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104 <data format="tabular" name="mlst" label="${tool.name} on ${on_string}: mlst.tsv" /> |
0
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planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
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105 <data format="tabular" name="summary" label="${tool.name} on ${on_string}: summary.tsv" /> |
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planemo upload for repository https://github.com/phac-nml/staramr commit 52535d98ad1e03c83c93f230abf966613b4b8fa2
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106 <data format="tabular" name="detailed_summary" label="${tool.name} on ${on_string}: detailed_summary.tsv" /> |
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planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
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107 <data format="tabular" name="resfinder" label="${tool.name} on ${on_string}: resfinder.tsv" /> |
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108 <data format="tabular" name="plasmidfinder" label="${tool.name} on ${on_string}: plasmidfinder.tsv" /> |
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planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
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109 <data format="tabular" name="pointfinder" label="${tool.name} on ${on_string}: pointfinder.tsv"> |
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110 <filter>use_pointfinder != "disabled"</filter> |
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fef5aff062c7
planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
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111 </data> |
fef5aff062c7
planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
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112 <data format="txt" name="settings" label="${tool.name} on ${on_string}: settings.txt" /> |
fef5aff062c7
planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
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113 <data format="xlsx" name="excel" label="${tool.name} on ${on_string}: results.xlsx" /> |
fef5aff062c7
planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
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114 <collection name="blast_hits" type="list" label="${tool.name} on ${on_string}: hits"> |
fef5aff062c7
planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
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115 <discover_datasets pattern="__name_and_ext__" directory="staramr_hits" /> |
fef5aff062c7
planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
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116 </collection> |
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planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
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117 </outputs> |
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planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
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118 <tests> |
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119 <test> |
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planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
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120 <param name="genomes" value="16S-rc_gyrA-rc_beta-lactam.fsa" /> |
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61a3e97aa865
"planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit 07b1134fbf48f0f94e6060b861651e1ab48cde71"
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121 <param name="use_pointfinder" value="salmonella" /> |
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planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
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122 |
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planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
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123 <output name="summary" file="test1-summary.tsv" ftype="tabular" /> |
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124 <output name="detailed_summary" file="test1-detailed-summary.tsv" ftype="tabular" /> |
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planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
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125 <output name="resfinder" file="test1-resfinder.tsv" ftype="tabular" /> |
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3c09557ac425
planemo upload for repository https://github.com/phac-nml/staramr commit 52535d98ad1e03c83c93f230abf966613b4b8fa2
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126 <output name="plasmidfinder" file="test1-plasmidfinder.tsv" ftype="tabular" /> |
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planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
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127 <output name="pointfinder" file="test1-pointfinder.tsv" ftype="tabular" /> |
fef5aff062c7
planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
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128 <output_collection name="blast_hits" type="list"> |
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planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
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129 <element name="resfinder_16S-rc_gyrA-rc_beta-lactam.fsa" file="test1-hits/resfinder_16S-rc_gyrA-rc_beta-lactam.fsa" /> |
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planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
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130 <element name="pointfinder_16S-rc_gyrA-rc_beta-lactam.fsa" file="test1-hits/pointfinder_16S-rc_gyrA-rc_beta-lactam.fsa" /> |
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planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
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131 </output_collection> |
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planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
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132 </test> |
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planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
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133 <test> |
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134 <param name="genomes" value="16S-rc_gyrA-rc_beta-lactam.fsa" /> |
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planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
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135 |
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planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
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136 <output name="summary" file="test2-summary.tsv" ftype="tabular" /> |
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planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
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137 <output name="resfinder" file="test2-resfinder.tsv" ftype="tabular" /> |
fef5aff062c7
planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
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138 <output_collection name="blast_hits" type="list"> |
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planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
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139 <element name="resfinder_16S-rc_gyrA-rc_beta-lactam.fsa" file="test2-hits/resfinder_16S-rc_gyrA-rc_beta-lactam.fsa" /> |
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planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
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140 </output_collection> |
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141 </test> |
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142 <test> |
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planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
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143 <param name="genomes" value="16S-rc_gyrA-rc_beta-lactam.fsa" /> |
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planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
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144 <param name="pid_threshold" value="99.8" /> |
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planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
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145 |
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planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
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146 <output name="summary" file="test3-summary.tsv" ftype="tabular" /> |
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planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
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147 </test> |
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148 <test> |
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149 <param name="genomes" value="16S rc_gyrA rc_beta-lactam spaces (extra:characters).fsa" /> |
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planemo upload for repository https://github.com/phac-nml/staramr commit 1b3cd6d32c357a59fa437e29ede4a6c1e78427f8
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150 <param name="pid_threshold" value="99.8" /> |
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planemo upload for repository https://github.com/phac-nml/staramr commit 1b3cd6d32c357a59fa437e29ede4a6c1e78427f8
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151 |
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planemo upload for repository https://github.com/phac-nml/staramr commit 1b3cd6d32c357a59fa437e29ede4a6c1e78427f8
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152 <output name="summary" file="test4-summary.tsv" ftype="tabular" /> |
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153 </test> |
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154 <test> |
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155 <param name="genomes" value="test-aminoglycoside.fsa" /> |
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156 |
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planemo upload for repository https://github.com/phac-nml/staramr commit fd6c4338e65d6a33900da6fe7ae6f507105d3446
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157 <output name="summary" file="test5-summary.tsv" ftype="tabular" /> |
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planemo upload for repository https://github.com/phac-nml/staramr commit fd6c4338e65d6a33900da6fe7ae6f507105d3446
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158 </test> |
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planemo upload for repository https://github.com/phac-nml/staramr commit fd6c4338e65d6a33900da6fe7ae6f507105d3446
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159 <test> |
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160 <param name="genomes" value="test-aminoglycoside.fsa" /> |
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planemo upload for repository https://github.com/phac-nml/staramr commit fd6c4338e65d6a33900da6fe7ae6f507105d3446
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161 <param name="exclude_genes_condition" value="none" /> |
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planemo upload for repository https://github.com/phac-nml/staramr commit fd6c4338e65d6a33900da6fe7ae6f507105d3446
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162 |
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planemo upload for repository https://github.com/phac-nml/staramr commit fd6c4338e65d6a33900da6fe7ae6f507105d3446
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163 <output name="summary" file="test6-summary.tsv" ftype="tabular" /> |
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164 </test> |
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planemo upload for repository https://github.com/phac-nml/staramr commit fd6c4338e65d6a33900da6fe7ae6f507105d3446
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165 <test> |
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planemo upload for repository https://github.com/phac-nml/staramr commit fd6c4338e65d6a33900da6fe7ae6f507105d3446
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166 <param name="genomes" value="test-aminoglycoside.fsa" /> |
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planemo upload for repository https://github.com/phac-nml/staramr commit fd6c4338e65d6a33900da6fe7ae6f507105d3446
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167 <param name="exclude_genes_condition" value="custom" /> |
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168 <param name="exclude_genes_file" value="genes_to_exclude.tsv" /> |
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169 |
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170 <output name="summary" file="test5-summary.tsv" ftype="tabular" /> |
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171 </test> |
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172 </tests> |
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173 <help><![CDATA[ |
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174 staramr |
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175 ======= |
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176 |
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177 staramr_ scans bacterial genome contigs against both the ResFinder_, PlasmidFinder_ and PointFinder_ databases (used by the ResFinder webservice_) and compiles a summary report of detected antimicrobial resistance genes. |
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178 |
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179 Usage |
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180 ----- |
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181 |
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182 1. Select your genome contigs (in FASTA format). |
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183 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* and *campylobacter* is supported). |
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184 3. Run the tool. |
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185 |
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186 Input |
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187 ----- |
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188 |
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189 Genomes |
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190 ``````` |
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191 |
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192 staramr_ takes as input one or more assembled genomes (in FASTA format) to search for AMR genes. |
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193 |
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194 Exclude genes file |
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195 `````````````````` |
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196 |
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197 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: |
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198 |
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199 :: |
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200 |
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201 #gene_id |
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202 aac(6')-Iaa_1_NC_003197 |
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203 ColpVC_1__JX133088 |
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204 |
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205 Output |
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206 ------ |
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207 |
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"planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit 07b1134fbf48f0f94e6060b861651e1ab48cde71"
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208 There are 6 different output files produced by `staramr` as well as a collection of additional files. |
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209 |
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"planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit 07b1134fbf48f0f94e6060b861651e1ab48cde71"
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210 mlst.tsv |
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211 ```````````````````` |
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212 |
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"planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit 07b1134fbf48f0f94e6060b861651e1ab48cde71"
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213 A tabular file of each multi-locus sequence type (MLST) and it's corresponding locus/alleles, one genome per line. |
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214 |
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215 +------------+--------------+-----------------------------------+------------+------------+------------+------------+------------+------------+------------+ |
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"planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit 07b1134fbf48f0f94e6060b861651e1ab48cde71"
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216 | Isolate ID | Scheme | Sequence Type | Locus 1 | Locus 2 | Locus 3 | Locus 4 | Locus 5 | Locus 6 | Locus 7 | |
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217 +============+==============+===================================+============+============+============+============+============+============+============+ |
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"planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit 07b1134fbf48f0f94e6060b861651e1ab48cde71"
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218 | SRR1952908 | senterica | 11 | aroC(5) | dnaN(2) | hemD(3) | hisD(7) | purE(6) | sucA(6) | thrA(11) | |
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"planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit 07b1134fbf48f0f94e6060b861651e1ab48cde71"
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219 +------------+--------------+-----------------------------------+------------+------------+------------+------------+------------+------------+---+--------+ |
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"planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit 07b1134fbf48f0f94e6060b861651e1ab48cde71"
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220 | SRR1952926 | senterica | 11 | aroC(5) | dnaN(2) | hemD(3) | hisD(7) | purE(6) | sucA(6) | thrA(11) | |
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"planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit 07b1134fbf48f0f94e6060b861651e1ab48cde71"
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221 +------------+--------------+-----------------------------------+------------+------------+------------+------------+------------+------------+------------+ |
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"planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit 07b1134fbf48f0f94e6060b861651e1ab48cde71"
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222 |
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223 |
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224 summary.tsv |
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225 ``````````` |
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226 |
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227 A summary of all detected AMR genes/mutations in each genome, one genome per line. |
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228 |
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229 +------------+-----------------------------------------------------------+-----------------------------------------------------------------------------------------------------------+-------------------------------------+ |
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230 | Isolate ID | Genotype | Predicted Phenotype | Plasmid | |
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231 +============+===========================================================+===========================================================================================================+=====================================+ |
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232 | SRR1952908 | aadA1, aadA2, blaTEM-57, cmlA1, gyrA (S83Y), sul3, tet(A) | streptomycin, ampicillin, chloramphenicol, ciprofloxacin I/R, nalidixic acid, sulfisoxazole, tetracycline | ColpVC, IncFIB(S), IncFII(S), IncI1 | |
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233 +------------+-----------------------------------------------------------+-----------------------------------------------------------------------------------------------------------+-------------------------------------+ |
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234 | SRR1952926 | blaTEM-57, gyrA (S83Y), tet(A) | ampicillin, ciprofloxacin I/R, nalidixic acid, tetracycline | ColpVC, IncFIB(S), IncFII(S), IncI1 | |
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235 +------------+-----------------------------------------------------------+-----------------------------------------------------------------------------------------------------------+-------------------------------------+ |
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236 |
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237 detailed_summary.tsv |
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238 ```````````````````` |
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239 |
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240 A detailed summary of all detected AMR genes/mutations/plasmids in each genome/type, one gene/type per line. |
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241 |
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242 +------------+--------------+-----------------------------------+-----------+----------+-------------------------+-------------+--------+--------+-----------+------------+ |
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243 | Isolate ID | Gene/Plasmid | Predicted Phenotype | %Identity | %Overlap | HSP Length/Total Length | Contig | Start | End | Accession | Data Type | |
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244 +============+==============+===================================+===========+==========+=========================+=============+========+========+===========+============+ |
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245 | SRR1952908 | ColpVC | | 98.96 | 100 | 193/193 | contig00038 | 1618 | 1426 | JX133088 | Plasmid | |
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246 +------------+--------------+-----------------------------------+-----------+----------+-------------------------+-------------+--------+--------+-----------+------------+ |
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247 | SRR1952908 | IncFIB(S) | | 98.91 | 100 | 643/643 | contig00024 | 10302 | 9660 | FN432031 | Plasmid | |
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248 +------------+--------------+-----------------------------------+-----------+----------+-------------------------+-------------+--------+--------+-----------+------------+ |
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249 | SRR1952908 | IncFII(S) | | 100 | 100 | 262/262 | contig00024 | 54294 | 54555 | CP000858 | Plasmid | |
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planemo upload for repository https://github.com/phac-nml/staramr commit dad82f0ddadb5e106a54d5aa6609918325e49d23
nml
parents:
6
diff
changeset
|
250 +------------+--------------+-----------------------------------+-----------+----------+-------------------------+-------------+--------+--------+-----------+------------+ |
f1adc47e017a
planemo upload for repository https://github.com/phac-nml/staramr commit dad82f0ddadb5e106a54d5aa6609918325e49d23
nml
parents:
6
diff
changeset
|
251 | SRR1952908 | IncI1 | | 100 | 100 | 142/142 | contig00020 | 3907 | 3766 | AP005147 | Plasmid | |
f1adc47e017a
planemo upload for repository https://github.com/phac-nml/staramr commit dad82f0ddadb5e106a54d5aa6609918325e49d23
nml
parents:
6
diff
changeset
|
252 +------------+--------------+-----------------------------------+-----------+----------+-------------------------+-------------+--------+--------+-----------+------------+ |
f1adc47e017a
planemo upload for repository https://github.com/phac-nml/staramr commit dad82f0ddadb5e106a54d5aa6609918325e49d23
nml
parents:
6
diff
changeset
|
253 | SRR1952908 | aadA1 | streptomycin | 100 | 100 | 792/792 | contig00030 | 5355 | 4564 | JQ414041 | Resistance | |
f1adc47e017a
planemo upload for repository https://github.com/phac-nml/staramr commit dad82f0ddadb5e106a54d5aa6609918325e49d23
nml
parents:
6
diff
changeset
|
254 +------------+--------------+-----------------------------------+-----------+----------+-------------------------+-------------+--------+--------+-----------+------------+ |
f1adc47e017a
planemo upload for repository https://github.com/phac-nml/staramr commit dad82f0ddadb5e106a54d5aa6609918325e49d23
nml
parents:
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diff
changeset
|
255 | SRR1952908 | aadA2 | streptomycin | 100 | 100 | 780/780 | contig00030 | 7748 | 6969 | X68227 | Resistance | |
f1adc47e017a
planemo upload for repository https://github.com/phac-nml/staramr commit dad82f0ddadb5e106a54d5aa6609918325e49d23
nml
parents:
6
diff
changeset
|
256 +------------+--------------+-----------------------------------+-----------+----------+-------------------------+-------------+--------+--------+-----------+------------+ |
f1adc47e017a
planemo upload for repository https://github.com/phac-nml/staramr commit dad82f0ddadb5e106a54d5aa6609918325e49d23
nml
parents:
6
diff
changeset
|
257 | SRR1952908 | blaTEM-57 | ampicillin | 99.88 | 100 | 861/861 | contig00032 | 6247 | 5387 | FJ405211 | Resistance | |
f1adc47e017a
planemo upload for repository https://github.com/phac-nml/staramr commit dad82f0ddadb5e106a54d5aa6609918325e49d23
nml
parents:
6
diff
changeset
|
258 +------------+--------------+-----------------------------------+-----------+----------+-------------------------+-------------+--------+--------+-----------+------------+ |
f1adc47e017a
planemo upload for repository https://github.com/phac-nml/staramr commit dad82f0ddadb5e106a54d5aa6609918325e49d23
nml
parents:
6
diff
changeset
|
259 | SRR1952908 | cmlA1 | chloramphenicol | 99.92 | 100 | 1260/1260 | contig00030 | 6707 | 5448 | M64556 | Resistance | |
f1adc47e017a
planemo upload for repository https://github.com/phac-nml/staramr commit dad82f0ddadb5e106a54d5aa6609918325e49d23
nml
parents:
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diff
changeset
|
260 +------------+--------------+-----------------------------------+-----------+----------+-------------------------+-------------+--------+--------+-----------+------------+ |
f1adc47e017a
planemo upload for repository https://github.com/phac-nml/staramr commit dad82f0ddadb5e106a54d5aa6609918325e49d23
nml
parents:
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diff
changeset
|
261 | SRR1952908 | gyrA (S83Y) | ciprofloxacin I/R, nalidixic acid | 99.96 | 100 | 2637/2637 | contig00008 | 22801 | 20165 | | Resistance | |
f1adc47e017a
planemo upload for repository https://github.com/phac-nml/staramr commit dad82f0ddadb5e106a54d5aa6609918325e49d23
nml
parents:
6
diff
changeset
|
262 +------------+--------------+-----------------------------------+-----------+----------+-------------------------+-------------+--------+--------+-----------+------------+ |
f1adc47e017a
planemo upload for repository https://github.com/phac-nml/staramr commit dad82f0ddadb5e106a54d5aa6609918325e49d23
nml
parents:
6
diff
changeset
|
263 | SRR1952908 | sul3 | sulfisoxazole | 100 | 100 | 792/792 | contig00030 | 2091 | 2882 | AJ459418 | Resistance | |
f1adc47e017a
planemo upload for repository https://github.com/phac-nml/staramr commit dad82f0ddadb5e106a54d5aa6609918325e49d23
nml
parents:
6
diff
changeset
|
264 +------------+--------------+-----------------------------------+-----------+----------+-------------------------+-------------+--------+--------+-----------+------------+ |
f1adc47e017a
planemo upload for repository https://github.com/phac-nml/staramr commit dad82f0ddadb5e106a54d5aa6609918325e49d23
nml
parents:
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diff
changeset
|
265 | SRR1952908 | tet(A) | tetracycline | 99.92 | 97.8 | 1247/1275 | contig00032 | 1476 | 2722 | AF534183 | Resistance | |
f1adc47e017a
planemo upload for repository https://github.com/phac-nml/staramr commit dad82f0ddadb5e106a54d5aa6609918325e49d23
nml
parents:
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diff
changeset
|
266 +------------+--------------+-----------------------------------+-----------+----------+-------------------------+-------------+--------+--------+-----------+------------+ |
f1adc47e017a
planemo upload for repository https://github.com/phac-nml/staramr commit dad82f0ddadb5e106a54d5aa6609918325e49d23
nml
parents:
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diff
changeset
|
267 | SRR1952926 | ColpVC | | 98.96 | 100 | 193/193 | contig00037 | 657 | 849 | JX133088 | Plasmid | |
f1adc47e017a
planemo upload for repository https://github.com/phac-nml/staramr commit dad82f0ddadb5e106a54d5aa6609918325e49d23
nml
parents:
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diff
changeset
|
268 +------------+--------------+-----------------------------------+-----------+----------+-------------------------+-------------+--------+--------+-----------+------------+ |
f1adc47e017a
planemo upload for repository https://github.com/phac-nml/staramr commit dad82f0ddadb5e106a54d5aa6609918325e49d23
nml
parents:
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diff
changeset
|
269 | SRR1952926 | IncFIB(S) | | 98.91 | 100 | 643/643 | contig00021 | 10302 | 9660 | FN432031 | Plasmid | |
f1adc47e017a
planemo upload for repository https://github.com/phac-nml/staramr commit dad82f0ddadb5e106a54d5aa6609918325e49d23
nml
parents:
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diff
changeset
|
270 +------------+--------------+-----------------------------------+-----------+----------+-------------------------+-------------+--------+--------+-----------+------------+ |
f1adc47e017a
planemo upload for repository https://github.com/phac-nml/staramr commit dad82f0ddadb5e106a54d5aa6609918325e49d23
nml
parents:
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diff
changeset
|
271 | SRR1952926 | IncFII(S) | | 100 | 100 | 262/262 | contig00021 | 54294 | 54555 | CP000858 | Plasmid | |
f1adc47e017a
planemo upload for repository https://github.com/phac-nml/staramr commit dad82f0ddadb5e106a54d5aa6609918325e49d23
nml
parents:
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diff
changeset
|
272 +------------+--------------+-----------------------------------+-----------+----------+-------------------------+-------------+--------+--------+-----------+------------+ |
f1adc47e017a
planemo upload for repository https://github.com/phac-nml/staramr commit dad82f0ddadb5e106a54d5aa6609918325e49d23
nml
parents:
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diff
changeset
|
273 | SRR1952926 | IncI1 | | 100 | 100 | 142/142 | contig00017 | 3907 | 3766 | AP005147 | Plasmid | |
f1adc47e017a
planemo upload for repository https://github.com/phac-nml/staramr commit dad82f0ddadb5e106a54d5aa6609918325e49d23
nml
parents:
6
diff
changeset
|
274 +------------+--------------+-----------------------------------+-----------+----------+-------------------------+-------------+--------+--------+-----------+------------+ |
f1adc47e017a
planemo upload for repository https://github.com/phac-nml/staramr commit dad82f0ddadb5e106a54d5aa6609918325e49d23
nml
parents:
6
diff
changeset
|
275 | SRR1952926 | blaTEM-57 | ampicillin | 99.88 | 100 | 861/861 | contig00027 | 6176 | 5316 | FJ405211 | Resistance | |
f1adc47e017a
planemo upload for repository https://github.com/phac-nml/staramr commit dad82f0ddadb5e106a54d5aa6609918325e49d23
nml
parents:
6
diff
changeset
|
276 +------------+--------------+-----------------------------------+-----------+----------+-------------------------+-------------+--------+--------+-----------+------------+ |
f1adc47e017a
planemo upload for repository https://github.com/phac-nml/staramr commit dad82f0ddadb5e106a54d5aa6609918325e49d23
nml
parents:
6
diff
changeset
|
277 | SRR1952926 | gyrA (S83Y) | ciprofloxacin I/R, nalidixic acid | 99.96 | 100 | 2637/2637 | contig00011 | 157768 | 160404 | | Resistance | |
f1adc47e017a
planemo upload for repository https://github.com/phac-nml/staramr commit dad82f0ddadb5e106a54d5aa6609918325e49d23
nml
parents:
6
diff
changeset
|
278 +------------+--------------+-----------------------------------+-----------+----------+-------------------------+-------------+--------+--------+-----------+------------+ |
f1adc47e017a
planemo upload for repository https://github.com/phac-nml/staramr commit dad82f0ddadb5e106a54d5aa6609918325e49d23
nml
parents:
6
diff
changeset
|
279 | SRR1952926 | tet(A) | tetracycline | 99.92 | 97.8 | 1247/1275 | contig00027 | 1405 | 2651 | AF534183 | Resistance | |
f1adc47e017a
planemo upload for repository https://github.com/phac-nml/staramr commit dad82f0ddadb5e106a54d5aa6609918325e49d23
nml
parents:
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diff
changeset
|
280 +------------+--------------+-----------------------------------+-----------+----------+-------------------------+-------------+--------+--------+-----------+------------+ |
6
3c09557ac425
planemo upload for repository https://github.com/phac-nml/staramr commit 52535d98ad1e03c83c93f230abf966613b4b8fa2
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|
281 |
0
fef5aff062c7
planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
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282 |
fef5aff062c7
planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
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|
283 resfinder.tsv |
fef5aff062c7
planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
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|
284 ````````````` |
fef5aff062c7
planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
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parents:
diff
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285 |
fef5aff062c7
planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
nml
parents:
diff
changeset
|
286 A tabular file of each AMR gene and additional BLAST information from the **ResFinder** database, one gene per line. |
fef5aff062c7
planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
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parents:
diff
changeset
|
287 |
fef5aff062c7
planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
nml
parents:
diff
changeset
|
288 +------------+------------+----------------------+------------+-----------+--------------------------+--------------+--------+-------+-----------+ |
fef5aff062c7
planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
nml
parents:
diff
changeset
|
289 | Isolate ID | Gene | Predicted Phenotype | %Identity | %Overlap | HSP Length/Total Length | Contig | Start | End | Accession | |
fef5aff062c7
planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
nml
parents:
diff
changeset
|
290 +============+============+======================+============+===========+==========================+==============+========+=======+===========+ |
fef5aff062c7
planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
nml
parents:
diff
changeset
|
291 | SRR1952908 | sul3 | sulfisoxazole | 100.00 | 100.00 | 792/792 | contig00030 | 2091 | 2882 | AJ459418 | |
fef5aff062c7
planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
nml
parents:
diff
changeset
|
292 +------------+------------+----------------------+------------+-----------+--------------------------+--------------+--------+-------+-----------+ |
fef5aff062c7
planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
nml
parents:
diff
changeset
|
293 | SRR1952908 | tet(A) | tetracycline | 99.92 | 100.00 | 1200/1200 | contig00032 | 1551 | 2750 | AJ517790 | |
fef5aff062c7
planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
nml
parents:
diff
changeset
|
294 +------------+------------+----------------------+------------+-----------+--------------------------+--------------+--------+-------+-----------+ |
fef5aff062c7
planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
nml
parents:
diff
changeset
|
295 | SRR1952908 | cmlA1 | chloramphenicol | 99.92 | 100.00 | 1260/1260 | contig00030 | 6707 | 5448 | M64556 | |
fef5aff062c7
planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
nml
parents:
diff
changeset
|
296 +------------+------------+----------------------+------------+-----------+--------------------------+--------------+--------+-------+-----------+ |
fef5aff062c7
planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
nml
parents:
diff
changeset
|
297 | SRR1952908 | aadA1 | streptomycin | 100.00 | 100.00 | 792/792 | contig00030 | 5355 | 4564 | JQ414041 | |
fef5aff062c7
planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
nml
parents:
diff
changeset
|
298 +------------+------------+----------------------+------------+-----------+--------------------------+--------------+--------+-------+-----------+ |
fef5aff062c7
planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
nml
parents:
diff
changeset
|
299 | SRR1952908 | aadA2 | streptomycin | 99.75 | 100.00 | 792/792 | contig00030 | 7760 | 6969 | JQ364967 | |
fef5aff062c7
planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
nml
parents:
diff
changeset
|
300 +------------+------------+----------------------+------------+-----------+--------------------------+--------------+--------+-------+-----------+ |
fef5aff062c7
planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
nml
parents:
diff
changeset
|
301 | SRR1952908 | blaTEM-57 | ampicillin | 99.88 | 100.00 | 861/861 | contig00032 | 6247 | 5387 | FJ405211 | |
fef5aff062c7
planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
nml
parents:
diff
changeset
|
302 +------------+------------+----------------------+------------+-----------+--------------------------+--------------+--------+-------+-----------+ |
fef5aff062c7
planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
nml
parents:
diff
changeset
|
303 | SRR1952926 | tet(A) | tetracycline | 99.92 | 100.00 | 1200/1200 | contig00027 | 1480 | 2679 | AJ517790 | |
fef5aff062c7
planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
nml
parents:
diff
changeset
|
304 +------------+------------+----------------------+------------+-----------+--------------------------+--------------+--------+-------+-----------+ |
fef5aff062c7
planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
nml
parents:
diff
changeset
|
305 | SRR1952926 | blaTEM-57 | ampicillin | 99.88 | 100.00 | 861/861 | contig00027 | 6176 | 5316 | FJ405211 | |
fef5aff062c7
planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
nml
parents:
diff
changeset
|
306 +------------+------------+----------------------+------------+-----------+--------------------------+--------------+--------+-------+-----------+ |
fef5aff062c7
planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
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parents:
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changeset
|
307 |
6
3c09557ac425
planemo upload for repository https://github.com/phac-nml/staramr commit 52535d98ad1e03c83c93f230abf966613b4b8fa2
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parents:
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diff
changeset
|
308 plasmidfinder.tsv |
3c09557ac425
planemo upload for repository https://github.com/phac-nml/staramr commit 52535d98ad1e03c83c93f230abf966613b4b8fa2
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309 ````````````````` |
3c09557ac425
planemo upload for repository https://github.com/phac-nml/staramr commit 52535d98ad1e03c83c93f230abf966613b4b8fa2
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310 |
7
f1adc47e017a
planemo upload for repository https://github.com/phac-nml/staramr commit dad82f0ddadb5e106a54d5aa6609918325e49d23
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parents:
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diff
changeset
|
311 A tabular file of each AMR plasmid type and additional BLAST information from the **PlasmidFinder** database, one plasmid type per line. |
6
3c09557ac425
planemo upload for repository https://github.com/phac-nml/staramr commit 52535d98ad1e03c83c93f230abf966613b4b8fa2
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parents:
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312 |
3c09557ac425
planemo upload for repository https://github.com/phac-nml/staramr commit 52535d98ad1e03c83c93f230abf966613b4b8fa2
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parents:
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diff
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|
313 +------------+-----------+-----------+----------+-------------------------+-------------+-------+-------+-----------+ |
7
f1adc47e017a
planemo upload for repository https://github.com/phac-nml/staramr commit dad82f0ddadb5e106a54d5aa6609918325e49d23
nml
parents:
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diff
changeset
|
314 | Isolate ID | Plasmid | %Identity | %Overlap | HSP Length/Total Length | Contig | Start | End | Accession | |
6
3c09557ac425
planemo upload for repository https://github.com/phac-nml/staramr commit 52535d98ad1e03c83c93f230abf966613b4b8fa2
nml
parents:
5
diff
changeset
|
315 +============+===========+===========+==========+=========================+=============+=======+=======+===========+ |
3c09557ac425
planemo upload for repository https://github.com/phac-nml/staramr commit 52535d98ad1e03c83c93f230abf966613b4b8fa2
nml
parents:
5
diff
changeset
|
316 | SRR1952908 | ColpVC | 98.96 | 100 | 193/193 | contig00038 | 1618 | 1426 | JX133088 | |
3c09557ac425
planemo upload for repository https://github.com/phac-nml/staramr commit 52535d98ad1e03c83c93f230abf966613b4b8fa2
nml
parents:
5
diff
changeset
|
317 +------------+-----------+-----------+----------+-------------------------+-------------+-------+-------+-----------+ |
3c09557ac425
planemo upload for repository https://github.com/phac-nml/staramr commit 52535d98ad1e03c83c93f230abf966613b4b8fa2
nml
parents:
5
diff
changeset
|
318 | SRR1952908 | IncFIB(S) | 98.91 | 100 | 643/643 | contig00024 | 10302 | 9660 | FN432031 | |
3c09557ac425
planemo upload for repository https://github.com/phac-nml/staramr commit 52535d98ad1e03c83c93f230abf966613b4b8fa2
nml
parents:
5
diff
changeset
|
319 +------------+-----------+-----------+----------+-------------------------+-------------+-------+-------+-----------+ |
3c09557ac425
planemo upload for repository https://github.com/phac-nml/staramr commit 52535d98ad1e03c83c93f230abf966613b4b8fa2
nml
parents:
5
diff
changeset
|
320 | SRR1952908 | IncFII(S) | 100 | 100 | 262/262 | contig00024 | 54294 | 54555 | CP000858 | |
3c09557ac425
planemo upload for repository https://github.com/phac-nml/staramr commit 52535d98ad1e03c83c93f230abf966613b4b8fa2
nml
parents:
5
diff
changeset
|
321 +------------+-----------+-----------+----------+-------------------------+-------------+-------+-------+-----------+ |
3c09557ac425
planemo upload for repository https://github.com/phac-nml/staramr commit 52535d98ad1e03c83c93f230abf966613b4b8fa2
nml
parents:
5
diff
changeset
|
322 | SRR1952908 | IncI1 | 100 | 100 | 142/142 | contig00020 | 3907 | 3766 | AP005147 | |
3c09557ac425
planemo upload for repository https://github.com/phac-nml/staramr commit 52535d98ad1e03c83c93f230abf966613b4b8fa2
nml
parents:
5
diff
changeset
|
323 +------------+-----------+-----------+----------+-------------------------+-------------+-------+-------+-----------+ |
3c09557ac425
planemo upload for repository https://github.com/phac-nml/staramr commit 52535d98ad1e03c83c93f230abf966613b4b8fa2
nml
parents:
5
diff
changeset
|
324 | SRR1952926 | ColpVC | 98.96 | 100 | 193/193 | contig00037 | 657 | 849 | JX133088 | |
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325 +------------+-----------+-----------+----------+-------------------------+-------------+-------+-------+-----------+ |
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326 | SRR1952926 | IncFIB(S) | 98.91 | 100 | 643/643 | contig00021 | 10302 | 9660 | FN432031 | |
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327 +------------+-----------+-----------+----------+-------------------------+-------------+-------+-------+-----------+ |
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328 | SRR1952926 | IncFII(S) | 100 | 100 | 262/262 | contig00021 | 54294 | 54555 | CP000858 | |
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329 +------------+-----------+-----------+----------+-------------------------+-------------+-------+-------+-----------+ |
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330 | SRR1952926 | IncI1 | 100 | 100 | 142/142 | contig00017 | 3907 | 3766 | AP005147 | |
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331 +------------+-----------+-----------+----------+-------------------------+-------------+-------+-------+-----------+ |
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332 |
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333 pointfinder.tsv |
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334 ``````````````` |
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335 |
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336 A tabular file of each AMR point mutation and additional BLAST information from the **PointFinder** database, one gene per line. |
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337 |
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338 +-------------+--------------+------------------------------------+--------+-----------+----------------------+------------+-----------+--------------------------+--------------+---------+--------+ |
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339 | Isolate ID | Gene | Predicted Phenotype | Type | Position | Mutation | %Identity | %Overlap | HSP Length/Total Length | Contig | Start | End | |
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340 +=============+==============+====================================+========+===========+======================+============+===========+==========================+==============+=========+========+ |
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341 | SRR1952908 | gyrA (S83Y) | ciprofloxacin I/R, nalidixic acid | codon | 83 | TCC -> TAC (S -> Y) | 99.96 | 100.00 | 2637/2637 | contig00008 | 22801 | 20165 | |
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342 +-------------+--------------+------------------------------------+--------+-----------+----------------------+------------+-----------+--------------------------+--------------+---------+--------+ |
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343 | SRR1952926 | gyrA (S83Y) | ciprofloxacin I/R, nalidixic acid | codon | 83 | TCC -> TAC (S -> Y) | 99.96 | 100.00 | 2637/2637 | contig00011 | 157768 | 160404 | |
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344 +-------------+--------------+------------------------------------+--------+-----------+----------------------+------------+-----------+--------------------------+--------------+---------+--------+ |
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345 |
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346 settings.txt |
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347 ```````````` |
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348 |
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349 The command-line, database versions, and other settings used to run `staramr`. |
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350 |
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351 :: |
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352 |
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353 command_line = staramr search -o out --pointfinder-organism salmonella SRR1952908.fasta SRR1952926.fasta |
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"planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit 07b1134fbf48f0f94e6060b861651e1ab48cde71"
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354 version = 0.6.1 |
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355 start_time = 2019-04-25 16:01:32 |
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356 end_time = 2019-04-25 16:01:34 |
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357 total_minutes = 0.04 |
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358 resfinder_db_dir = staramr/databases/data/dist/resfinder |
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359 resfinder_db_url = https://bitbucket.org/genomicepidemiology/resfinder_db.git |
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360 resfinder_db_commit = e8f1eb2585cd9610c4034a54ce7fc4f93aa95535 |
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361 resfinder_db_date = Mon, 16 Jul 2018 16:58 |
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362 pointfinder_db_dir = staramr/databases/data/dist/pointfinder |
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363 pointfinder_db_url = https://bitbucket.org/genomicepidemiology/pointfinder_db.git |
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364 pointfinder_db_commit = 8706a6363bb29e47e0e398c53043b037c24b99a7 |
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365 pointfinder_db_date = Wed, 04 Jul 2018 14:27 |
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366 plasmidfinder_db_dir = staramr/databases/data/dist/plasmidfinder |
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367 plasmidfinder_db_url = https://bitbucket.org/genomicepidemiology/plasmidfinder_db.git |
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368 plasmidfinder_db_commit = 81919954cbedaff39056610ab584ab4c06011ed8 |
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369 plasmidfinder_db_date = Tue, 20 Nov 2018 08:51 |
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370 pointfinder_gene_drug_version = 050218 |
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371 resfinder_gene_drug_version = 050218.1 |
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372 |
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373 results.xlsx |
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374 ```````````` |
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375 |
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376 An Excel spreadsheet containing the previous 5 files as separate worksheets. |
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377 |
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378 BLAST Hits |
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379 `````````` |
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380 |
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381 The dataset collection **hits** stores fasta files of the specific blast hits. |
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382 |
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383 Galaxy wrapper written by Aaron Petkau at the National Microbiology Laboratory, Public Health Agency of Canada. |
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384 |
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385 .. _staramr: https://github.com/phac-nml/staramr |
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386 .. _ResFinder: https://bitbucket.org/genomicepidemiology/resfinder_db |
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387 .. _PlasmidFinder: https://bitbucket.org/genomicepidemiology/plasmidfinder_db |
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388 .. _PointFinder: https://bitbucket.org/genomicepidemiology/pointfinder_db |
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389 .. _webservice: https://cge.cbs.dtu.dk/services/ResFinder/ |
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390 ]]></help> |
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391 <citations> |
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392 <citation type="bibtex"> |
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393 @misc{githubstaramr, |
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394 author = {Petkau, Aaron}, |
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395 year = {2018}, |
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396 title = {staramr}, |
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397 publisher = {GitHub}, |
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398 journal = {GitHub repository}, |
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399 url = {https://github.com/phac-nml/staramr}, |
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400 }</citation> |
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401 </citations> |
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402 </tool> |