Mercurial > repos > nml > staramr
annotate staramr_search.xml @ 17:141afacabcfa draft
planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit e752f6e09372d3513de79d85baa619c5f5065303
author | nml |
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date | Thu, 31 Aug 2023 15:55:49 +0000 |
parents | 4d83eccf5f81 |
children | 3b22de20bd4b |
rev | line source |
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15
be818ae858e4
planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit e92a931da272a26f3a16e7b1d31c432890a6fdb3
nml
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1 <tool id="staramr_search" name="staramr" version="@VERSION@+galaxy0" profile="16.04"> |
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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> |
17
141afacabcfa
planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit e752f6e09372d3513de79d85baa619c5f5065303
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4 <token name="@VERSION@">0.10.0</token> |
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930893c83a1a
planemo upload for repository https://github.com/phac-nml/staramr commit 0794053d021c92d4dd7459abca46d4bf823d7203
nml
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5 </macros> |
0
fef5aff062c7
planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
nml
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6 <requirements> |
5
930893c83a1a
planemo upload for repository https://github.com/phac-nml/staramr commit 0794053d021c92d4dd7459abca46d4bf823d7203
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7 <requirement type="package" version="@VERSION@">staramr</requirement> |
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be818ae858e4
planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit e92a931da272a26f3a16e7b1d31c432890a6fdb3
nml
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8 <!-- The staramr conda package includes the mlst software, but the list of schemes |
be818ae858e4
planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit e92a931da272a26f3a16e7b1d31c432890a6fdb3
nml
parents:
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9 changes depending on the version. I specify the exact version here to make sure |
be818ae858e4
planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit e92a931da272a26f3a16e7b1d31c432890a6fdb3
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parents:
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10 the list of schemes provided is consistent --> |
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4d83eccf5f81
planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit 7483ccd266d271a05704b1eced996a653b50ee84
nml
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11 <requirement type="package" version="2.23.0">mlst</requirement> |
0
fef5aff062c7
planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
nml
parents:
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12 </requirements> |
5
930893c83a1a
planemo upload for repository https://github.com/phac-nml/staramr commit 0794053d021c92d4dd7459abca46d4bf823d7203
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13 <version_command>staramr --version</version_command> |
0
fef5aff062c7
planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
nml
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14 <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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15 #import re |
3801ea82c888
planemo upload for repository https://github.com/phac-nml/staramr commit 1b3cd6d32c357a59fa437e29ede4a6c1e78427f8
nml
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16 |
0
fef5aff062c7
planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
nml
parents:
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17 #set $named_genomes = '' |
fef5aff062c7
planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
nml
parents:
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18 #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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19 #set $_named_genome = re.sub(r'(\s|\(|\)|\/)', '_', '"{}.fasta"'.format($genome.element_identifier)) |
da787fc8b740
planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit f1641993d71fc04fadf20753a63cc72a412f4af5
nml
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20 ln -s '$genome' $_named_genome && |
0
fef5aff062c7
planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
nml
parents:
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21 #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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changeset
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22 #end for |
fef5aff062c7
planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
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parents:
diff
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23 |
15
be818ae858e4
planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit e92a931da272a26f3a16e7b1d31c432890a6fdb3
nml
parents:
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24 #set $excel_proper_extension = 'results.xlsx' |
be818ae858e4
planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit e92a931da272a26f3a16e7b1d31c432890a6fdb3
nml
parents:
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25 ln -s '$excel' $excel_proper_extension && |
0
fef5aff062c7
planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
nml
parents:
diff
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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 staramr search |
fef5aff062c7
planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
nml
parents:
diff
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28 |
fef5aff062c7
planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
nml
parents:
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29 --nprocs "\${GALAXY_SLOTS:-1}" |
fef5aff062c7
planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
nml
parents:
diff
changeset
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30 |
10
7573a6c11c4d
"planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit 69b939934ff9f503c7314cdbe6e3cb08e5f84db5"
nml
parents:
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31 --genome-size-lower-bound $advanced.genome_size_lower_bound |
7573a6c11c4d
"planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit 69b939934ff9f503c7314cdbe6e3cb08e5f84db5"
nml
parents:
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32 --genome-size-upper-bound $advanced.genome_size_upper_bound |
7573a6c11c4d
"planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit 69b939934ff9f503c7314cdbe6e3cb08e5f84db5"
nml
parents:
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33 --minimum-N50-value $advanced.minimum_N50_value |
7573a6c11c4d
"planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit 69b939934ff9f503c7314cdbe6e3cb08e5f84db5"
nml
parents:
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34 --minimum-contig-length $advanced.minimum_contig_length |
7573a6c11c4d
"planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit 69b939934ff9f503c7314cdbe6e3cb08e5f84db5"
nml
parents:
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35 --unacceptable-number-contigs $advanced.unacceptable_number_contigs |
7573a6c11c4d
"planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit 69b939934ff9f503c7314cdbe6e3cb08e5f84db5"
nml
parents:
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36 |
0
fef5aff062c7
planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
nml
parents:
diff
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37 --pid-threshold $advanced.pid_threshold |
fef5aff062c7
planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
nml
parents:
diff
changeset
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38 --percent-length-overlap-resfinder $advanced.plength_resfinder |
6
3c09557ac425
planemo upload for repository https://github.com/phac-nml/staramr commit 52535d98ad1e03c83c93f230abf966613b4b8fa2
nml
parents:
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39 --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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40 --percent-length-overlap-pointfinder $advanced.plength_pointfinder |
fef5aff062c7
planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
nml
parents:
diff
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41 |
13
2fd4d4c9c5c2
"planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit f328deb1fae95c3418e86bc1f1a2b2034b2f7c3e"
nml
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42 #if str($advanced.mlst_scheme) != 'auto': |
2fd4d4c9c5c2
"planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit f328deb1fae95c3418e86bc1f1a2b2034b2f7c3e"
nml
parents:
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43 --mlst-scheme '${advanced.mlst_scheme}' |
2fd4d4c9c5c2
"planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit f328deb1fae95c3418e86bc1f1a2b2034b2f7c3e"
nml
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44 #end if |
2fd4d4c9c5c2
"planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit f328deb1fae95c3418e86bc1f1a2b2034b2f7c3e"
nml
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45 |
0
fef5aff062c7
planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
nml
parents:
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46 $advanced.report_all_blast |
fef5aff062c7
planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
nml
parents:
diff
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47 $advanced.exclude_negatives |
fef5aff062c7
planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
nml
parents:
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48 $advanced.exclude_resistance_phenotypes |
fef5aff062c7
planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
nml
parents:
diff
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49 |
4
1e8ec0f861ff
planemo upload for repository https://github.com/phac-nml/staramr commit fd6c4338e65d6a33900da6fe7ae6f507105d3446
nml
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50 #if str($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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51 --exclude-genes-file '${advanced.exclude_genes.exclude_genes_file}' |
1e8ec0f861ff
planemo upload for repository https://github.com/phac-nml/staramr commit fd6c4338e65d6a33900da6fe7ae6f507105d3446
nml
parents:
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52 #elif str($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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53 --no-exclude-genes |
1e8ec0f861ff
planemo upload for repository https://github.com/phac-nml/staramr commit fd6c4338e65d6a33900da6fe7ae6f507105d3446
nml
parents:
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54 #end if |
1e8ec0f861ff
planemo upload for repository https://github.com/phac-nml/staramr commit fd6c4338e65d6a33900da6fe7ae6f507105d3446
nml
parents:
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55 |
17
141afacabcfa
planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit e752f6e09372d3513de79d85baa619c5f5065303
nml
parents:
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56 |
141afacabcfa
planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit e752f6e09372d3513de79d85baa619c5f5065303
nml
parents:
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57 #if str($advanced.complex_mutations.complex_mutations_condition) == 'custom' |
141afacabcfa
planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit e752f6e09372d3513de79d85baa619c5f5065303
nml
parents:
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58 --complex-mutations-file '${advanced.complex_mutations.complex_mutations_file}' |
141afacabcfa
planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit e752f6e09372d3513de79d85baa619c5f5065303
nml
parents:
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59 #end if |
141afacabcfa
planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit e752f6e09372d3513de79d85baa619c5f5065303
nml
parents:
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60 |
6
3c09557ac425
planemo upload for repository https://github.com/phac-nml/staramr commit 52535d98ad1e03c83c93f230abf966613b4b8fa2
nml
parents:
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61 #if str($advanced.plasmidfinder_type) != 'include_all' |
3c09557ac425
planemo upload for repository https://github.com/phac-nml/staramr commit 52535d98ad1e03c83c93f230abf966613b4b8fa2
nml
parents:
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62 --plasmidfinder-database-type '${advanced.plasmidfinder_type}' |
3c09557ac425
planemo upload for repository https://github.com/phac-nml/staramr commit 52535d98ad1e03c83c93f230abf966613b4b8fa2
nml
parents:
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63 #end if |
3c09557ac425
planemo upload for repository https://github.com/phac-nml/staramr commit 52535d98ad1e03c83c93f230abf966613b4b8fa2
nml
parents:
5
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64 |
15
be818ae858e4
planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit e92a931da272a26f3a16e7b1d31c432890a6fdb3
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65 --output-summary '$summary' |
be818ae858e4
planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit e92a931da272a26f3a16e7b1d31c432890a6fdb3
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66 --output-detailed-summary '$detailed_summary' |
be818ae858e4
planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit e92a931da272a26f3a16e7b1d31c432890a6fdb3
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67 --output-resfinder '$resfinder' |
be818ae858e4
planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit e92a931da272a26f3a16e7b1d31c432890a6fdb3
nml
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68 --output-plasmidfinder '$plasmidfinder' |
be818ae858e4
planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit e92a931da272a26f3a16e7b1d31c432890a6fdb3
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69 --output-settings '$settings' |
be818ae858e4
planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit e92a931da272a26f3a16e7b1d31c432890a6fdb3
nml
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70 --output-excel '$excel_proper_extension' |
be818ae858e4
planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit e92a931da272a26f3a16e7b1d31c432890a6fdb3
nml
parents:
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71 --output-mlst '$mlst' |
0
fef5aff062c7
planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
nml
parents:
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72 |
fef5aff062c7
planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
nml
parents:
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73 --output-hits-dir staramr_hits |
fef5aff062c7
planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
nml
parents:
diff
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74 |
15
be818ae858e4
planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit e92a931da272a26f3a16e7b1d31c432890a6fdb3
nml
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75 #if str($pointfinder_db.use_pointfinder) != 'disabled' |
be818ae858e4
planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit e92a931da272a26f3a16e7b1d31c432890a6fdb3
nml
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76 --output-pointfinder '$pointfinder' |
be818ae858e4
planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit e92a931da272a26f3a16e7b1d31c432890a6fdb3
nml
parents:
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77 #if str($pointfinder_db.use_pointfinder) == 'custom' |
be818ae858e4
planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit e92a931da272a26f3a16e7b1d31c432890a6fdb3
nml
parents:
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78 --pointfinder-organism '${pointfinder_db.pointfinder_custom}' |
be818ae858e4
planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit e92a931da272a26f3a16e7b1d31c432890a6fdb3
nml
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79 #else |
be818ae858e4
planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit e92a931da272a26f3a16e7b1d31c432890a6fdb3
nml
parents:
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80 --pointfinder-organism '${pointfinder_db.use_pointfinder}' |
be818ae858e4
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81 #end if |
0
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82 #end if |
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83 |
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84 $named_genomes |
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85 ]]></command> |
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86 <inputs> |
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87 <param type="data" name="genomes" format="fasta" multiple="true"/> |
15
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88 <conditional name="pointfinder_db"> |
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planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit e92a931da272a26f3a16e7b1d31c432890a6fdb3
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89 <param name="use_pointfinder" type="select" label="Enable scanning for point mutations using the PointFinder database"> |
16
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90 <option value="disabled" selected="true">Disable PointFinder</option> |
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91 <option value="campylobacter">Campylobacter</option> |
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planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit 7483ccd266d271a05704b1eced996a653b50ee84
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92 <option value="enterococcus_faecalis">enterococcus_faecalis</option> |
4d83eccf5f81
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93 <option value="enterococcus_faecium">enterococcus_faecium</option> |
4d83eccf5f81
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94 <option value="escherichia_coli">escherichia_coli</option> |
4d83eccf5f81
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95 <option value="helicobacter_pylori">helicobacter_pylori</option> |
15
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96 <option value="salmonella">Salmonella</option> |
be818ae858e4
planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit e92a931da272a26f3a16e7b1d31c432890a6fdb3
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97 <option value="custom">Unvalidated</option> |
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98 </param> |
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99 <!-- These three values don't have any additional parameters as they are used as-is to control the PointFinder organism --> |
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100 <when value="disabled"/> |
16
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101 <when value="campylobacter"/> |
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102 <when value="enterococcus_faecalis"/> |
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103 <when value="enterococcus_faecium"/> |
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104 <when value="escherichia_coli"/> |
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105 <when value="helicobacter_pylori"/> |
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106 <when value="salmonella"/> |
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107 |
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108 <!-- This option provides the ability to select among a number of custom/unvalidated PointFinder organisms --> |
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109 <when value="custom"> |
16
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110 <param name="pointfinder_custom" type="select" label="PointFinder organism (unvalidated)" help="Select one of the unvalidated PointFinder organisms to use for scanning for point mutations. These have not been fully validated as compatible with staramr so caution is recommended when interpreting results."> |
15
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111 <option value="klebsiella">klebsiella</option> |
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112 <option value="mycobacterium_tuberculosis">mycobacterium_tuberculosis</option> |
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113 <option value="neisseria_gonorrhoeae">neisseria_gonorrhoeae</option> |
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114 <option value="plasmodium_falciparum">plasmodium_falciparum</option> |
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115 <option value="staphylococcus_aureus">staphylococcus_aureus</option> |
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planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit e92a931da272a26f3a16e7b1d31c432890a6fdb3
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116 </param> |
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117 </when> |
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118 </conditional> |
0
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119 <section name="advanced" title="Advanced options" expanded="false"> |
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120 <param name="pid_threshold" type="float" label="Percent identity threshold for BLAST" value="98.0" |
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121 min="0" max="100" help="(--pid-threshold)" /> |
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122 <param name="plength_resfinder" type="float" label="Percent length overlap of BLAST hit for ResFinder database" value="60.0" |
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123 min="0" max="100" help="(--percent-length-overlap-resfinder)" /> |
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124 <param name="plength_pointfinder" type="float" label="Percent length overlap of BLAST hit for PointFinder database" value="95.0" |
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125 min="0" max="100" help="(--percent-length-overlap-pointfinder)" /> |
6
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126 <param name="plength_plasmidfinder" type="float" label="Percent length overlap of BLAST hit for PlasmidFinder database" value="60.0" |
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127 min="0" max="100" help="(--percent-length-overlap-plasmidfinder)" /> |
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7573a6c11c4d
"planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit 69b939934ff9f503c7314cdbe6e3cb08e5f84db5"
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128 <param name="genome_size_lower_bound" type="integer" label="The lower bound for our genome size for the quality metrics" value="4000000" |
7573a6c11c4d
"planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit 69b939934ff9f503c7314cdbe6e3cb08e5f84db5"
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129 help="(--genome-size-lower-bound)" /> |
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"planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit 69b939934ff9f503c7314cdbe6e3cb08e5f84db5"
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130 <param name="genome_size_upper_bound" type="integer" label="The upper bound for our genome size for the quality metrics" value="6000000" |
7573a6c11c4d
"planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit 69b939934ff9f503c7314cdbe6e3cb08e5f84db5"
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131 help="(--genome-size-upper-bound)" /> |
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"planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit 69b939934ff9f503c7314cdbe6e3cb08e5f84db5"
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132 <param name="minimum_N50_value" type="integer" label="The minimum N50 value for the quality metrics" value="10000" |
7573a6c11c4d
"planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit 69b939934ff9f503c7314cdbe6e3cb08e5f84db5"
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133 help="(--minimum-N50-value)" /> |
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"planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit 69b939934ff9f503c7314cdbe6e3cb08e5f84db5"
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134 <param name="minimum_contig_length" type="integer" label="The minimum contig length for the quality metrics" value="300" |
7573a6c11c4d
"planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit 69b939934ff9f503c7314cdbe6e3cb08e5f84db5"
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135 help="(--minimum-contig-length)" /> |
7573a6c11c4d
"planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit 69b939934ff9f503c7314cdbe6e3cb08e5f84db5"
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136 <param name="unacceptable_number_contigs" type="integer" label="The number of contigs, under the minimum contig length which is unacceptable for the quality metrics" value="1000" |
7573a6c11c4d
"planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit 69b939934ff9f503c7314cdbe6e3cb08e5f84db5"
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137 help="(--unacceptable-number-contigs)" /> |
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138 <param name="report_all_blast" type="boolean" label="Report all BLAST results" truevalue="--report-all-blast" falsevalue="" |
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139 help="Report all BLAST results (includes overlapping hits, mainly for debugging)" /> |
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140 <param name="exclude_negatives" type="boolean" label="Exclude negative (non-resistant) results" truevalue="--exclude-negatives" falsevalue="" /> |
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141 <param name="exclude_resistance_phenotypes" type="boolean" label="Exclude resistance phenotypes" truevalue="--exclude-resistance-phenotypes" falsevalue="" /> |
13
2fd4d4c9c5c2
"planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit f328deb1fae95c3418e86bc1f1a2b2034b2f7c3e"
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142 <param name="mlst_scheme" type="select" label="MLST Scheme"> |
15
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143 <option value="auto" selected="true">Automatic</option> |
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planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit e92a931da272a26f3a16e7b1d31c432890a6fdb3
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144 <option value="aactinomycetemcomitans">aactinomycetemcomitans</option> |
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145 <option value="abaumannii">abaumannii</option> |
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146 <option value="abaumannii_2">abaumannii_2</option> |
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planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit e92a931da272a26f3a16e7b1d31c432890a6fdb3
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147 <option value="achromobacter">achromobacter</option> |
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planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit e92a931da272a26f3a16e7b1d31c432890a6fdb3
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148 <option value="aeromonas">aeromonas</option> |
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149 <option value="aphagocytophilum">aphagocytophilum</option> |
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planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit e92a931da272a26f3a16e7b1d31c432890a6fdb3
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150 <option value="arcobacter">arcobacter</option> |
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151 <option value="bbacilliformis">bbacilliformis</option> |
be818ae858e4
planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit e92a931da272a26f3a16e7b1d31c432890a6fdb3
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152 <option value="bcc">bcc</option> |
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153 <option value="bcereus">bcereus</option> |
be818ae858e4
planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit e92a931da272a26f3a16e7b1d31c432890a6fdb3
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154 <option value="bfragilis">bfragilis</option> |
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planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit e92a931da272a26f3a16e7b1d31c432890a6fdb3
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|
155 <option value="bhenselae">bhenselae</option> |
be818ae858e4
planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit e92a931da272a26f3a16e7b1d31c432890a6fdb3
nml
parents:
14
diff
changeset
|
156 <option value="blicheniformis_14">blicheniformis_14</option> |
be818ae858e4
planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit e92a931da272a26f3a16e7b1d31c432890a6fdb3
nml
parents:
14
diff
changeset
|
157 <option value="bordetella_3">bordetella_3</option> |
be818ae858e4
planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit e92a931da272a26f3a16e7b1d31c432890a6fdb3
nml
parents:
14
diff
changeset
|
158 <option value="borrelia">borrelia</option> |
be818ae858e4
planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit e92a931da272a26f3a16e7b1d31c432890a6fdb3
nml
parents:
14
diff
changeset
|
159 <option value="bpseudomallei">bpseudomallei</option> |
be818ae858e4
planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit e92a931da272a26f3a16e7b1d31c432890a6fdb3
nml
parents:
14
diff
changeset
|
160 <option value="brachyspira">brachyspira</option> |
be818ae858e4
planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit e92a931da272a26f3a16e7b1d31c432890a6fdb3
nml
parents:
14
diff
changeset
|
161 <option value="brachyspira_2">brachyspira_2</option> |
be818ae858e4
planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit e92a931da272a26f3a16e7b1d31c432890a6fdb3
nml
parents:
14
diff
changeset
|
162 <option value="brachyspira_3">brachyspira_3</option> |
be818ae858e4
planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit e92a931da272a26f3a16e7b1d31c432890a6fdb3
nml
parents:
14
diff
changeset
|
163 <option value="brachyspira_4">brachyspira_4</option> |
be818ae858e4
planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit e92a931da272a26f3a16e7b1d31c432890a6fdb3
nml
parents:
14
diff
changeset
|
164 <option value="brachyspira_5">brachyspira_5</option> |
be818ae858e4
planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit e92a931da272a26f3a16e7b1d31c432890a6fdb3
nml
parents:
14
diff
changeset
|
165 <option value="brucella">brucella</option> |
be818ae858e4
planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit e92a931da272a26f3a16e7b1d31c432890a6fdb3
nml
parents:
14
diff
changeset
|
166 <option value="bsubtilis">bsubtilis</option> |
be818ae858e4
planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit e92a931da272a26f3a16e7b1d31c432890a6fdb3
nml
parents:
14
diff
changeset
|
167 <option value="bwashoensis">bwashoensis</option> |
be818ae858e4
planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit e92a931da272a26f3a16e7b1d31c432890a6fdb3
nml
parents:
14
diff
changeset
|
168 <option value="campylobacter">campylobacter</option> |
be818ae858e4
planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit e92a931da272a26f3a16e7b1d31c432890a6fdb3
nml
parents:
14
diff
changeset
|
169 <option value="campylobacter_nonjejuni">campylobacter_nonjejuni</option> |
be818ae858e4
planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit e92a931da272a26f3a16e7b1d31c432890a6fdb3
nml
parents:
14
diff
changeset
|
170 <option value="campylobacter_nonjejuni_2">campylobacter_nonjejuni_2</option> |
be818ae858e4
planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit e92a931da272a26f3a16e7b1d31c432890a6fdb3
nml
parents:
14
diff
changeset
|
171 <option value="campylobacter_nonjejuni_3">campylobacter_nonjejuni_3</option> |
be818ae858e4
planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit e92a931da272a26f3a16e7b1d31c432890a6fdb3
nml
parents:
14
diff
changeset
|
172 <option value="campylobacter_nonjejuni_4">campylobacter_nonjejuni_4</option> |
be818ae858e4
planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit e92a931da272a26f3a16e7b1d31c432890a6fdb3
nml
parents:
14
diff
changeset
|
173 <option value="campylobacter_nonjejuni_5">campylobacter_nonjejuni_5</option> |
be818ae858e4
planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit e92a931da272a26f3a16e7b1d31c432890a6fdb3
nml
parents:
14
diff
changeset
|
174 <option value="campylobacter_nonjejuni_6">campylobacter_nonjejuni_6</option> |
be818ae858e4
planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit e92a931da272a26f3a16e7b1d31c432890a6fdb3
nml
parents:
14
diff
changeset
|
175 <option value="campylobacter_nonjejuni_7">campylobacter_nonjejuni_7</option> |
be818ae858e4
planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit e92a931da272a26f3a16e7b1d31c432890a6fdb3
nml
parents:
14
diff
changeset
|
176 <option value="campylobacter_nonjejuni_8">campylobacter_nonjejuni_8</option> |
be818ae858e4
planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit e92a931da272a26f3a16e7b1d31c432890a6fdb3
nml
parents:
14
diff
changeset
|
177 <option value="campylobacter_nonjejuni_9">campylobacter_nonjejuni_9</option> |
be818ae858e4
planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit e92a931da272a26f3a16e7b1d31c432890a6fdb3
nml
parents:
14
diff
changeset
|
178 <option value="cbotulinum">cbotulinum</option> |
be818ae858e4
planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit e92a931da272a26f3a16e7b1d31c432890a6fdb3
nml
parents:
14
diff
changeset
|
179 <option value="cdifficile">cdifficile</option> |
be818ae858e4
planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit e92a931da272a26f3a16e7b1d31c432890a6fdb3
nml
parents:
14
diff
changeset
|
180 <option value="cfreundii">cfreundii</option> |
be818ae858e4
planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit e92a931da272a26f3a16e7b1d31c432890a6fdb3
nml
parents:
14
diff
changeset
|
181 <option value="chlamydiales">chlamydiales</option> |
be818ae858e4
planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit e92a931da272a26f3a16e7b1d31c432890a6fdb3
nml
parents:
14
diff
changeset
|
182 <option value="cmaltaromaticum">cmaltaromaticum</option> |
be818ae858e4
planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit e92a931da272a26f3a16e7b1d31c432890a6fdb3
nml
parents:
14
diff
changeset
|
183 <option value="cperfringens">cperfringens</option> |
be818ae858e4
planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit e92a931da272a26f3a16e7b1d31c432890a6fdb3
nml
parents:
14
diff
changeset
|
184 <option value="cronobacter">cronobacter</option> |
be818ae858e4
planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit e92a931da272a26f3a16e7b1d31c432890a6fdb3
nml
parents:
14
diff
changeset
|
185 <option value="csepticum">csepticum</option> |
be818ae858e4
planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit e92a931da272a26f3a16e7b1d31c432890a6fdb3
nml
parents:
14
diff
changeset
|
186 <option value="diphtheria_3">diphtheria_3</option> |
be818ae858e4
planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit e92a931da272a26f3a16e7b1d31c432890a6fdb3
nml
parents:
14
diff
changeset
|
187 <option value="dnodosus">dnodosus</option> |
be818ae858e4
planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit e92a931da272a26f3a16e7b1d31c432890a6fdb3
nml
parents:
14
diff
changeset
|
188 <option value="ecloacae">ecloacae</option> |
be818ae858e4
planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit e92a931da272a26f3a16e7b1d31c432890a6fdb3
nml
parents:
14
diff
changeset
|
189 <option value="ecoli">ecoli</option> |
be818ae858e4
planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit e92a931da272a26f3a16e7b1d31c432890a6fdb3
nml
parents:
14
diff
changeset
|
190 <option value="ecoli_achtman_4">ecoli_achtman_4</option> |
be818ae858e4
planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit e92a931da272a26f3a16e7b1d31c432890a6fdb3
nml
parents:
14
diff
changeset
|
191 <option value="edwardsiella">edwardsiella</option> |
be818ae858e4
planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit e92a931da272a26f3a16e7b1d31c432890a6fdb3
nml
parents:
14
diff
changeset
|
192 <option value="efaecalis">efaecalis</option> |
be818ae858e4
planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit e92a931da272a26f3a16e7b1d31c432890a6fdb3
nml
parents:
14
diff
changeset
|
193 <option value="efaecium">efaecium</option> |
be818ae858e4
planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit e92a931da272a26f3a16e7b1d31c432890a6fdb3
nml
parents:
14
diff
changeset
|
194 <option value="fpsychrophilum">fpsychrophilum</option> |
be818ae858e4
planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit e92a931da272a26f3a16e7b1d31c432890a6fdb3
nml
parents:
14
diff
changeset
|
195 <option value="gallibacterium">gallibacterium</option> |
be818ae858e4
planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit e92a931da272a26f3a16e7b1d31c432890a6fdb3
nml
parents:
14
diff
changeset
|
196 <option value="geotrichum">geotrichum</option> |
be818ae858e4
planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit e92a931da272a26f3a16e7b1d31c432890a6fdb3
nml
parents:
14
diff
changeset
|
197 <option value="hcinaedi">hcinaedi</option> |
be818ae858e4
planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit e92a931da272a26f3a16e7b1d31c432890a6fdb3
nml
parents:
14
diff
changeset
|
198 <option value="helicobacter">helicobacter</option> |
be818ae858e4
planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit e92a931da272a26f3a16e7b1d31c432890a6fdb3
nml
parents:
14
diff
changeset
|
199 <option value="hinfluenzae">hinfluenzae</option> |
be818ae858e4
planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit e92a931da272a26f3a16e7b1d31c432890a6fdb3
nml
parents:
14
diff
changeset
|
200 <option value="hparasuis">hparasuis</option> |
be818ae858e4
planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit e92a931da272a26f3a16e7b1d31c432890a6fdb3
nml
parents:
14
diff
changeset
|
201 <option value="hsuis">hsuis</option> |
be818ae858e4
planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit e92a931da272a26f3a16e7b1d31c432890a6fdb3
nml
parents:
14
diff
changeset
|
202 <option value="kaerogenes">kaerogenes</option> |
be818ae858e4
planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit e92a931da272a26f3a16e7b1d31c432890a6fdb3
nml
parents:
14
diff
changeset
|
203 <option value="kingella">kingella</option> |
be818ae858e4
planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit e92a931da272a26f3a16e7b1d31c432890a6fdb3
nml
parents:
14
diff
changeset
|
204 <option value="klebsiella">klebsiella</option> |
be818ae858e4
planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit e92a931da272a26f3a16e7b1d31c432890a6fdb3
nml
parents:
14
diff
changeset
|
205 <option value="koxytoca">koxytoca</option> |
be818ae858e4
planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit e92a931da272a26f3a16e7b1d31c432890a6fdb3
nml
parents:
14
diff
changeset
|
206 <option value="leptospira">leptospira</option> |
be818ae858e4
planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit e92a931da272a26f3a16e7b1d31c432890a6fdb3
nml
parents:
14
diff
changeset
|
207 <option value="leptospira_2">leptospira_2</option> |
be818ae858e4
planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit e92a931da272a26f3a16e7b1d31c432890a6fdb3
nml
parents:
14
diff
changeset
|
208 <option value="leptospira_3">leptospira_3</option> |
be818ae858e4
planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit e92a931da272a26f3a16e7b1d31c432890a6fdb3
nml
parents:
14
diff
changeset
|
209 <option value="liberibacter">liberibacter</option> |
be818ae858e4
planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit e92a931da272a26f3a16e7b1d31c432890a6fdb3
nml
parents:
14
diff
changeset
|
210 <option value="listeria_2">listeria_2</option> |
be818ae858e4
planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit e92a931da272a26f3a16e7b1d31c432890a6fdb3
nml
parents:
14
diff
changeset
|
211 <option value="llactis_phage">llactis_phage</option> |
be818ae858e4
planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit e92a931da272a26f3a16e7b1d31c432890a6fdb3
nml
parents:
14
diff
changeset
|
212 <option value="lsalivarius">lsalivarius</option> |
be818ae858e4
planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit e92a931da272a26f3a16e7b1d31c432890a6fdb3
nml
parents:
14
diff
changeset
|
213 <option value="mabscessus">mabscessus</option> |
be818ae858e4
planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit e92a931da272a26f3a16e7b1d31c432890a6fdb3
nml
parents:
14
diff
changeset
|
214 <option value="magalactiae">magalactiae</option> |
be818ae858e4
planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit e92a931da272a26f3a16e7b1d31c432890a6fdb3
nml
parents:
14
diff
changeset
|
215 <option value="manserisalpingitidis">manserisalpingitidis</option> |
be818ae858e4
planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit e92a931da272a26f3a16e7b1d31c432890a6fdb3
nml
parents:
14
diff
changeset
|
216 <option value="mbovis_2">mbovis_2</option> |
be818ae858e4
planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit e92a931da272a26f3a16e7b1d31c432890a6fdb3
nml
parents:
14
diff
changeset
|
217 <option value="mcanis">mcanis</option> |
be818ae858e4
planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit e92a931da272a26f3a16e7b1d31c432890a6fdb3
nml
parents:
14
diff
changeset
|
218 <option value="mcaseolyticus">mcaseolyticus</option> |
be818ae858e4
planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit e92a931da272a26f3a16e7b1d31c432890a6fdb3
nml
parents:
14
diff
changeset
|
219 <option value="mcatarrhalis_achtman_6">mcatarrhalis_achtman_6</option> |
be818ae858e4
planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit e92a931da272a26f3a16e7b1d31c432890a6fdb3
nml
parents:
14
diff
changeset
|
220 <option value="mflocculare">mflocculare</option> |
be818ae858e4
planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit e92a931da272a26f3a16e7b1d31c432890a6fdb3
nml
parents:
14
diff
changeset
|
221 <option value="mgallisepticum">mgallisepticum</option> |
be818ae858e4
planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit e92a931da272a26f3a16e7b1d31c432890a6fdb3
nml
parents:
14
diff
changeset
|
222 <option value="mgallisepticum_2">mgallisepticum_2</option> |
be818ae858e4
planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit e92a931da272a26f3a16e7b1d31c432890a6fdb3
nml
parents:
14
diff
changeset
|
223 <option value="mhaemolytica">mhaemolytica</option> |
be818ae858e4
planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit e92a931da272a26f3a16e7b1d31c432890a6fdb3
nml
parents:
14
diff
changeset
|
224 <option value="mhominis_3">mhominis_3</option> |
be818ae858e4
planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit e92a931da272a26f3a16e7b1d31c432890a6fdb3
nml
parents:
14
diff
changeset
|
225 <option value="mhyopneumoniae">mhyopneumoniae</option> |
be818ae858e4
planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit e92a931da272a26f3a16e7b1d31c432890a6fdb3
nml
parents:
14
diff
changeset
|
226 <option value="mhyorhinis">mhyorhinis</option> |
be818ae858e4
planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit e92a931da272a26f3a16e7b1d31c432890a6fdb3
nml
parents:
14
diff
changeset
|
227 <option value="miowae">miowae</option> |
be818ae858e4
planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit e92a931da272a26f3a16e7b1d31c432890a6fdb3
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228 <option value="mplutonius">mplutonius</option> |
be818ae858e4
planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit e92a931da272a26f3a16e7b1d31c432890a6fdb3
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229 <option value="mpneumoniae">mpneumoniae</option> |
be818ae858e4
planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit e92a931da272a26f3a16e7b1d31c432890a6fdb3
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230 <option value="msciuri">msciuri</option> |
be818ae858e4
planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit e92a931da272a26f3a16e7b1d31c432890a6fdb3
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231 <option value="msynoviae">msynoviae</option> |
be818ae858e4
planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit e92a931da272a26f3a16e7b1d31c432890a6fdb3
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232 <option value="mycobacteria_2">mycobacteria_2</option> |
be818ae858e4
planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit e92a931da272a26f3a16e7b1d31c432890a6fdb3
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233 <option value="neisseria">neisseria</option> |
be818ae858e4
planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit e92a931da272a26f3a16e7b1d31c432890a6fdb3
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234 <option value="oralstrep">oralstrep</option> |
be818ae858e4
planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit e92a931da272a26f3a16e7b1d31c432890a6fdb3
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235 <option value="orhinotracheale">orhinotracheale</option> |
be818ae858e4
planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit e92a931da272a26f3a16e7b1d31c432890a6fdb3
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236 <option value="otsutsugamushi">otsutsugamushi</option> |
be818ae858e4
planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit e92a931da272a26f3a16e7b1d31c432890a6fdb3
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237 <option value="pacnes_3">pacnes_3</option> |
be818ae858e4
planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit e92a931da272a26f3a16e7b1d31c432890a6fdb3
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238 <option value="paeruginosa">paeruginosa</option> |
be818ae858e4
planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit e92a931da272a26f3a16e7b1d31c432890a6fdb3
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239 <option value="pdamselae">pdamselae</option> |
be818ae858e4
planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit e92a931da272a26f3a16e7b1d31c432890a6fdb3
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240 <option value="pfluorescens">pfluorescens</option> |
be818ae858e4
planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit e92a931da272a26f3a16e7b1d31c432890a6fdb3
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241 <option value="pgingivalis">pgingivalis</option> |
be818ae858e4
planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit e92a931da272a26f3a16e7b1d31c432890a6fdb3
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242 <option value="plarvae">plarvae</option> |
be818ae858e4
planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit e92a931da272a26f3a16e7b1d31c432890a6fdb3
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243 <option value="pmultocida">pmultocida</option> |
be818ae858e4
planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit e92a931da272a26f3a16e7b1d31c432890a6fdb3
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244 <option value="pmultocida_2">pmultocida_2</option> |
be818ae858e4
planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit e92a931da272a26f3a16e7b1d31c432890a6fdb3
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245 <option value="ppentosaceus">ppentosaceus</option> |
be818ae858e4
planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit e92a931da272a26f3a16e7b1d31c432890a6fdb3
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246 <option value="pputida">pputida</option> |
be818ae858e4
planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit e92a931da272a26f3a16e7b1d31c432890a6fdb3
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247 <option value="psalmonis">psalmonis</option> |
be818ae858e4
planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit e92a931da272a26f3a16e7b1d31c432890a6fdb3
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248 <option value="ranatipestifer">ranatipestifer</option> |
be818ae858e4
planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit e92a931da272a26f3a16e7b1d31c432890a6fdb3
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249 <option value="rhodococcus">rhodococcus</option> |
be818ae858e4
planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit e92a931da272a26f3a16e7b1d31c432890a6fdb3
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250 <option value="sagalactiae">sagalactiae</option> |
be818ae858e4
planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit e92a931da272a26f3a16e7b1d31c432890a6fdb3
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251 <option value="saureus">saureus</option> |
be818ae858e4
planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit e92a931da272a26f3a16e7b1d31c432890a6fdb3
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252 <option value="sbsec">sbsec</option> |
be818ae858e4
planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit e92a931da272a26f3a16e7b1d31c432890a6fdb3
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253 <option value="scanis">scanis</option> |
be818ae858e4
planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit e92a931da272a26f3a16e7b1d31c432890a6fdb3
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254 <option value="schromogenes">schromogenes</option> |
be818ae858e4
planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit e92a931da272a26f3a16e7b1d31c432890a6fdb3
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255 <option value="sdysgalactiae">sdysgalactiae</option> |
be818ae858e4
planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit e92a931da272a26f3a16e7b1d31c432890a6fdb3
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256 <option value="senterica_achtman_2">senterica_achtman_2</option> |
be818ae858e4
planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit e92a931da272a26f3a16e7b1d31c432890a6fdb3
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257 <option value="sepidermidis">sepidermidis</option> |
be818ae858e4
planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit e92a931da272a26f3a16e7b1d31c432890a6fdb3
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258 <option value="sgallolyticus">sgallolyticus</option> |
be818ae858e4
planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit e92a931da272a26f3a16e7b1d31c432890a6fdb3
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259 <option value="shaemolyticus">shaemolyticus</option> |
be818ae858e4
planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit e92a931da272a26f3a16e7b1d31c432890a6fdb3
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260 <option value="shewanella">shewanella</option> |
be818ae858e4
planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit e92a931da272a26f3a16e7b1d31c432890a6fdb3
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261 <option value="shominis">shominis</option> |
be818ae858e4
planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit e92a931da272a26f3a16e7b1d31c432890a6fdb3
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262 <option value="sinorhizobium">sinorhizobium</option> |
be818ae858e4
planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit e92a931da272a26f3a16e7b1d31c432890a6fdb3
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263 <option value="smaltophilia">smaltophilia</option> |
be818ae858e4
planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit e92a931da272a26f3a16e7b1d31c432890a6fdb3
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264 <option value="spneumoniae">spneumoniae</option> |
be818ae858e4
planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit e92a931da272a26f3a16e7b1d31c432890a6fdb3
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265 <option value="spseudintermedius">spseudintermedius</option> |
be818ae858e4
planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit e92a931da272a26f3a16e7b1d31c432890a6fdb3
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266 <option value="spyogenes">spyogenes</option> |
be818ae858e4
planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit e92a931da272a26f3a16e7b1d31c432890a6fdb3
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267 <option value="ssuis">ssuis</option> |
be818ae858e4
planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit e92a931da272a26f3a16e7b1d31c432890a6fdb3
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268 <option value="staphlugdunensis">staphlugdunensis</option> |
be818ae858e4
planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit e92a931da272a26f3a16e7b1d31c432890a6fdb3
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269 <option value="sthermophilus">sthermophilus</option> |
be818ae858e4
planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit e92a931da272a26f3a16e7b1d31c432890a6fdb3
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270 <option value="streptomyces">streptomyces</option> |
be818ae858e4
planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit e92a931da272a26f3a16e7b1d31c432890a6fdb3
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271 <option value="streptothermophilus">streptothermophilus</option> |
be818ae858e4
planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit e92a931da272a26f3a16e7b1d31c432890a6fdb3
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272 <option value="suberis">suberis</option> |
be818ae858e4
planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit e92a931da272a26f3a16e7b1d31c432890a6fdb3
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273 <option value="szooepidemicus">szooepidemicus</option> |
be818ae858e4
planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit e92a931da272a26f3a16e7b1d31c432890a6fdb3
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274 <option value="taylorella">taylorella</option> |
be818ae858e4
planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit e92a931da272a26f3a16e7b1d31c432890a6fdb3
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275 <option value="tenacibaculum">tenacibaculum</option> |
be818ae858e4
planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit e92a931da272a26f3a16e7b1d31c432890a6fdb3
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276 <option value="tpallidum">tpallidum</option> |
be818ae858e4
planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit e92a931da272a26f3a16e7b1d31c432890a6fdb3
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277 <option value="ureaplasma">ureaplasma</option> |
be818ae858e4
planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit e92a931da272a26f3a16e7b1d31c432890a6fdb3
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278 <option value="vcholerae">vcholerae</option> |
be818ae858e4
planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit e92a931da272a26f3a16e7b1d31c432890a6fdb3
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279 <option value="vcholerae_2">vcholerae_2</option> |
be818ae858e4
planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit e92a931da272a26f3a16e7b1d31c432890a6fdb3
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280 <option value="vibrio">vibrio</option> |
be818ae858e4
planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit e92a931da272a26f3a16e7b1d31c432890a6fdb3
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281 <option value="vparahaemolyticus">vparahaemolyticus</option> |
be818ae858e4
planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit e92a931da272a26f3a16e7b1d31c432890a6fdb3
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282 <option value="vtapetis">vtapetis</option> |
be818ae858e4
planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit e92a931da272a26f3a16e7b1d31c432890a6fdb3
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283 <option value="vvulnificus">vvulnificus</option> |
be818ae858e4
planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit e92a931da272a26f3a16e7b1d31c432890a6fdb3
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284 <option value="wolbachia">wolbachia</option> |
be818ae858e4
planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit e92a931da272a26f3a16e7b1d31c432890a6fdb3
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285 <option value="xfastidiosa">xfastidiosa</option> |
be818ae858e4
planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit e92a931da272a26f3a16e7b1d31c432890a6fdb3
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286 <option value="ypseudotuberculosis_achtman_3">ypseudotuberculosis_achtman_3</option> |
be818ae858e4
planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit e92a931da272a26f3a16e7b1d31c432890a6fdb3
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287 <option value="yruckeri">yruckeri</option> |
13
2fd4d4c9c5c2
"planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit f328deb1fae95c3418e86bc1f1a2b2034b2f7c3e"
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288 </param> |
4
1e8ec0f861ff
planemo upload for repository https://github.com/phac-nml/staramr commit fd6c4338e65d6a33900da6fe7ae6f507105d3446
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289 <conditional name="exclude_genes"> |
1e8ec0f861ff
planemo upload for repository https://github.com/phac-nml/staramr commit fd6c4338e65d6a33900da6fe7ae6f507105d3446
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290 <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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291 <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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292 <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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293 <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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294 </param> |
1e8ec0f861ff
planemo upload for repository https://github.com/phac-nml/staramr commit fd6c4338e65d6a33900da6fe7ae6f507105d3446
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295 <when value="default" /> |
1e8ec0f861ff
planemo upload for repository https://github.com/phac-nml/staramr commit fd6c4338e65d6a33900da6fe7ae6f507105d3446
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296 <when value="custom"> |
1e8ec0f861ff
planemo upload for repository https://github.com/phac-nml/staramr commit fd6c4338e65d6a33900da6fe7ae6f507105d3446
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297 <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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298 </when> |
1e8ec0f861ff
planemo upload for repository https://github.com/phac-nml/staramr commit fd6c4338e65d6a33900da6fe7ae6f507105d3446
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299 <when value="none" /> |
17
141afacabcfa
planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit e752f6e09372d3513de79d85baa619c5f5065303
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300 </conditional> |
141afacabcfa
planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit e752f6e09372d3513de79d85baa619c5f5065303
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301 <conditional name="complex_mutations"> |
141afacabcfa
planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit e752f6e09372d3513de79d85baa619c5f5065303
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302 <param name="complex_mutations_condition" type="select" label="Provide a custom list of complex mutations"> |
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303 <option value="default" selected="true">Use default list of complex mutations</option> |
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planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit e752f6e09372d3513de79d85baa619c5f5065303
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304 <option value="custom">Provide a custom list of complex mutations</option> |
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planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit e752f6e09372d3513de79d85baa619c5f5065303
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305 </param> |
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planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit e752f6e09372d3513de79d85baa619c5f5065303
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306 <when value="default" /> |
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307 <when value="custom"> |
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308 <param type="data" name="complex_mutations_file" format="txt,tabular" label="Complex mutations file" help="Pass a file containing a list of complex mutations to group (if present) in the PointFinder results" /> |
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309 </when> |
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310 </conditional> |
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311 <param name="plasmidfinder_type" type="select" label="Specify PlasmidFinder Database type"> |
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312 <option value="include_all" selected="true">Include all available database types</option> |
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313 <option value="gram_positive">Gram Positive</option> |
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314 <option value="enterobacteriaceae">Enterobacteriaceae</option> |
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315 </param> |
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316 </section> |
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317 </inputs> |
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318 <outputs> |
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"planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit f328deb1fae95c3418e86bc1f1a2b2034b2f7c3e"
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319 <data format="tabular" name="mlst" label="${tool.name} on ${on_string}: mlst.tsv" /> |
0
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planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
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320 <data format="tabular" name="summary" label="${tool.name} on ${on_string}: summary.tsv" /> |
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321 <data format="tabular" name="detailed_summary" label="${tool.name} on ${on_string}: detailed_summary.tsv" /> |
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322 <data format="tabular" name="resfinder" label="${tool.name} on ${on_string}: resfinder.tsv" /> |
6
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323 <data format="tabular" name="plasmidfinder" label="${tool.name} on ${on_string}: plasmidfinder.tsv" /> |
0
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planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
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324 <data format="tabular" name="pointfinder" label="${tool.name} on ${on_string}: pointfinder.tsv"> |
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325 <filter>pointfinder_db['use_pointfinder'] != "disabled"</filter> |
0
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326 </data> |
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planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
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327 <data format="txt" name="settings" label="${tool.name} on ${on_string}: settings.txt" /> |
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328 <data format="xlsx" name="excel" label="${tool.name} on ${on_string}: results.xlsx" /> |
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planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
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329 <collection name="blast_hits" type="list" label="${tool.name} on ${on_string}: hits"> |
fef5aff062c7
planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
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330 <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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331 </collection> |
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332 </outputs> |
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333 <tests> |
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334 <test expect_num_outputs="9"> |
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planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit e92a931da272a26f3a16e7b1d31c432890a6fdb3
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335 <param name="genomes" value="16S-rc_gyrA-rc_beta-lactam.fsa" ftype="fasta" /> |
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"planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit f328deb1fae95c3418e86bc1f1a2b2034b2f7c3e"
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336 <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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337 |
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338 <output name="summary" file="test1-summary.tsv" ftype="tabular" /> |
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339 <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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340 <output name="resfinder" file="test1-resfinder.tsv" ftype="tabular" /> |
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planemo upload for repository https://github.com/phac-nml/staramr commit 52535d98ad1e03c83c93f230abf966613b4b8fa2
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341 <output name="plasmidfinder" file="test1-plasmidfinder.tsv" ftype="tabular" /> |
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planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit e752f6e09372d3513de79d85baa619c5f5065303
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342 <output name="pointfinder" file="test1-pointfinder.tsv" ftype="tabular" /> |
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planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
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343 <output_collection name="blast_hits" type="list"> |
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planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit e92a931da272a26f3a16e7b1d31c432890a6fdb3
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344 <element name="resfinder_16S-rc_gyrA-rc_beta-lactam.fsa" file="test1-hits/resfinder_16S-rc_gyrA-rc_beta-lactam.fsa" ftype="fasta" /> |
be818ae858e4
planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit e92a931da272a26f3a16e7b1d31c432890a6fdb3
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345 <element name="pointfinder_16S-rc_gyrA-rc_beta-lactam.fsa" file="test1-hits/pointfinder_16S-rc_gyrA-rc_beta-lactam.fsa" ftype="fasta" /> |
0
fef5aff062c7
planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
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346 </output_collection> |
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347 </test> |
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348 <test expect_num_outputs="9"> |
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planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit e92a931da272a26f3a16e7b1d31c432890a6fdb3
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349 <param name="genomes" value="16S-rc_gyrA-rc_beta-lactam.fsa" ftype="fasta" /> |
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350 <param name="use_pointfinder" value="escherichia_coli" /> |
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planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit e92a931da272a26f3a16e7b1d31c432890a6fdb3
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351 |
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planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit e92a931da272a26f3a16e7b1d31c432890a6fdb3
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352 <output name="summary" file="test1-summary-ecoli.tsv" ftype="tabular" /> |
be818ae858e4
planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit e92a931da272a26f3a16e7b1d31c432890a6fdb3
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353 <output name="detailed_summary" file="test1-detailed-summary-ecoli.tsv" ftype="tabular" /> |
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planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit e92a931da272a26f3a16e7b1d31c432890a6fdb3
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354 <output name="resfinder" file="test1-resfinder.tsv" ftype="tabular" /> |
be818ae858e4
planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit e92a931da272a26f3a16e7b1d31c432890a6fdb3
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355 <output name="plasmidfinder" file="test1-plasmidfinder.tsv" ftype="tabular" /> |
be818ae858e4
planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit e92a931da272a26f3a16e7b1d31c432890a6fdb3
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356 <output name="pointfinder" file="test1-pointfinder-ecoli.tsv" ftype="tabular" /> |
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planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit e92a931da272a26f3a16e7b1d31c432890a6fdb3
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357 </test> |
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358 <test expect_num_outputs="8"> |
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planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit e92a931da272a26f3a16e7b1d31c432890a6fdb3
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359 <param name="genomes" value="16S-rc_gyrA-rc_beta-lactam.fsa" ftype="fasta" /> |
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360 |
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planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
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361 <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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362 <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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363 <output_collection name="blast_hits" type="list"> |
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be818ae858e4
planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit e92a931da272a26f3a16e7b1d31c432890a6fdb3
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364 <element name="resfinder_16S-rc_gyrA-rc_beta-lactam.fsa" file="test2-hits/resfinder_16S-rc_gyrA-rc_beta-lactam.fsa" ftype="fasta" /> |
0
fef5aff062c7
planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
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365 </output_collection> |
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planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
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366 </test> |
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367 <test expect_num_outputs="8"> |
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planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit e92a931da272a26f3a16e7b1d31c432890a6fdb3
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368 <param name="genomes" value="16S-rc_gyrA-rc_beta-lactam.fsa" ftype="fasta" /> |
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"planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit f328deb1fae95c3418e86bc1f1a2b2034b2f7c3e"
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369 <section name="advanced"> |
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planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit e92a931da272a26f3a16e7b1d31c432890a6fdb3
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370 <param name="mlst_scheme" value="listeria_2" /> |
13
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"planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit f328deb1fae95c3418e86bc1f1a2b2034b2f7c3e"
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371 </section> |
2fd4d4c9c5c2
"planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit f328deb1fae95c3418e86bc1f1a2b2034b2f7c3e"
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372 <output name="mlst" file="mlst.tsv" ftype="tabular" /> |
2fd4d4c9c5c2
"planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit f328deb1fae95c3418e86bc1f1a2b2034b2f7c3e"
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373 </test> |
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planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit e752f6e09372d3513de79d85baa619c5f5065303
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374 <test expect_num_outputs="8"> |
15
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planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit e92a931da272a26f3a16e7b1d31c432890a6fdb3
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375 <param name="genomes" value="16S-rc_gyrA-rc_beta-lactam.fsa" ftype="fasta" /> |
0
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planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
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|
376 <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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|
377 |
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planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
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|
378 <output name="summary" file="test3-summary.tsv" ftype="tabular" /> |
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379 </test> |
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380 <test expect_num_outputs="8"> |
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381 <param name="genomes" value="16S rc_gyrA rc_beta-lactam spaces (extra:characters).fsa" ftype="fasta" /> |
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382 <param name="pid_threshold" value="99.8" /> |
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383 |
3801ea82c888
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384 <output name="summary" file="test4-summary.tsv" ftype="tabular" /> |
3801ea82c888
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385 </test> |
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386 <test expect_num_outputs="8"> |
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planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit e92a931da272a26f3a16e7b1d31c432890a6fdb3
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387 <param name="genomes" value="test-aminoglycoside.fsa" ftype="fasta" /> |
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388 |
1e8ec0f861ff
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389 <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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390 </test> |
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391 <test expect_num_outputs="8"> |
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planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit e92a931da272a26f3a16e7b1d31c432890a6fdb3
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392 <param name="genomes" value="test-aminoglycoside.fsa" ftype="fasta" /> |
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393 <param name="exclude_genes_condition" value="none" /> |
1e8ec0f861ff
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394 |
1e8ec0f861ff
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395 <output name="summary" file="test6-summary.tsv" ftype="tabular" /> |
1e8ec0f861ff
planemo upload for repository https://github.com/phac-nml/staramr commit fd6c4338e65d6a33900da6fe7ae6f507105d3446
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396 </test> |
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planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit e752f6e09372d3513de79d85baa619c5f5065303
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397 <test expect_num_outputs="8"> |
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planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit e92a931da272a26f3a16e7b1d31c432890a6fdb3
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398 <param name="genomes" value="test-aminoglycoside.fsa" ftype="fasta" /> |
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399 <param name="exclude_genes_condition" value="custom" /> |
1e8ec0f861ff
planemo upload for repository https://github.com/phac-nml/staramr commit fd6c4338e65d6a33900da6fe7ae6f507105d3446
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400 <param name="exclude_genes_file" value="genes_to_exclude.tsv" /> |
1e8ec0f861ff
planemo upload for repository https://github.com/phac-nml/staramr commit fd6c4338e65d6a33900da6fe7ae6f507105d3446
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401 |
1e8ec0f861ff
planemo upload for repository https://github.com/phac-nml/staramr commit fd6c4338e65d6a33900da6fe7ae6f507105d3446
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402 <output name="summary" file="test5-summary.tsv" ftype="tabular" /> |
1e8ec0f861ff
planemo upload for repository https://github.com/phac-nml/staramr commit fd6c4338e65d6a33900da6fe7ae6f507105d3446
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403 </test> |
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planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit e752f6e09372d3513de79d85baa619c5f5065303
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404 <test expect_num_outputs="8"> |
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planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit e92a931da272a26f3a16e7b1d31c432890a6fdb3
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405 <param name="genomes" value="test-aminoglycoside.fsa" ftype="fasta" /> |
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7573a6c11c4d
"planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit 69b939934ff9f503c7314cdbe6e3cb08e5f84db5"
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406 <param name="genome_size_lower_bound" value="1" /> |
7573a6c11c4d
"planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit 69b939934ff9f503c7314cdbe6e3cb08e5f84db5"
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407 <param name="genome_size_upper_bound" value="10" /> |
7573a6c11c4d
"planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit 69b939934ff9f503c7314cdbe6e3cb08e5f84db5"
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408 |
7573a6c11c4d
"planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit 69b939934ff9f503c7314cdbe6e3cb08e5f84db5"
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409 <output name="summary" file="test8-summary.tsv" ftype="tabular"/> |
7573a6c11c4d
"planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit 69b939934ff9f503c7314cdbe6e3cb08e5f84db5"
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410 </test> |
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planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
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411 </tests> |
fef5aff062c7
planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
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412 <help><![CDATA[ |
fef5aff062c7
planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
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413 staramr |
fef5aff062c7
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414 ======= |
fef5aff062c7
planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
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415 |
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4d83eccf5f81
planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit 7483ccd266d271a05704b1eced996a653b50ee84
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416 staramr_ scans bacterial genome contigs against both the ResFinder_, PlasmidFinder_ and PointFinder_ databases (used by their respective webservices_) and compiles a summary report of detected antimicrobial resistance genes. |
0
fef5aff062c7
planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
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417 |
fef5aff062c7
planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
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418 Usage |
fef5aff062c7
planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
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419 ----- |
fef5aff062c7
planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
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420 |
fef5aff062c7
planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
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421 1. Select your genome contigs (in FASTA format). |
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422 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). |
0
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planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
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423 3. Run the tool. |
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planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
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424 |
4
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425 Input |
1e8ec0f861ff
planemo upload for repository https://github.com/phac-nml/staramr commit fd6c4338e65d6a33900da6fe7ae6f507105d3446
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426 ----- |
1e8ec0f861ff
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427 |
1e8ec0f861ff
planemo upload for repository https://github.com/phac-nml/staramr commit fd6c4338e65d6a33900da6fe7ae6f507105d3446
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428 Genomes |
1e8ec0f861ff
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429 ``````` |
1e8ec0f861ff
planemo upload for repository https://github.com/phac-nml/staramr commit fd6c4338e65d6a33900da6fe7ae6f507105d3446
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430 |
1e8ec0f861ff
planemo upload for repository https://github.com/phac-nml/staramr commit fd6c4338e65d6a33900da6fe7ae6f507105d3446
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431 staramr_ takes as input one or more assembled genomes (in FASTA format) to search for AMR genes. |
1e8ec0f861ff
planemo upload for repository https://github.com/phac-nml/staramr commit fd6c4338e65d6a33900da6fe7ae6f507105d3446
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432 |
1e8ec0f861ff
planemo upload for repository https://github.com/phac-nml/staramr commit fd6c4338e65d6a33900da6fe7ae6f507105d3446
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433 Exclude genes file |
1e8ec0f861ff
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434 `````````````````` |
1e8ec0f861ff
planemo upload for repository https://github.com/phac-nml/staramr commit fd6c4338e65d6a33900da6fe7ae6f507105d3446
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435 |
1e8ec0f861ff
planemo upload for repository https://github.com/phac-nml/staramr commit fd6c4338e65d6a33900da6fe7ae6f507105d3446
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436 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: |
1e8ec0f861ff
planemo upload for repository https://github.com/phac-nml/staramr commit fd6c4338e65d6a33900da6fe7ae6f507105d3446
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437 |
1e8ec0f861ff
planemo upload for repository https://github.com/phac-nml/staramr commit fd6c4338e65d6a33900da6fe7ae6f507105d3446
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438 :: |
1e8ec0f861ff
planemo upload for repository https://github.com/phac-nml/staramr commit fd6c4338e65d6a33900da6fe7ae6f507105d3446
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439 |
1e8ec0f861ff
planemo upload for repository https://github.com/phac-nml/staramr commit fd6c4338e65d6a33900da6fe7ae6f507105d3446
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440 #gene_id |
1e8ec0f861ff
planemo upload for repository https://github.com/phac-nml/staramr commit fd6c4338e65d6a33900da6fe7ae6f507105d3446
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441 aac(6')-Iaa_1_NC_003197 |
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3c09557ac425
planemo upload for repository https://github.com/phac-nml/staramr commit 52535d98ad1e03c83c93f230abf966613b4b8fa2
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442 ColpVC_1__JX133088 |
4
1e8ec0f861ff
planemo upload for repository https://github.com/phac-nml/staramr commit fd6c4338e65d6a33900da6fe7ae6f507105d3446
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443 |
0
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planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
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444 Output |
fef5aff062c7
planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
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445 ------ |
fef5aff062c7
planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
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446 |
9
61a3e97aa865
"planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit 07b1134fbf48f0f94e6060b861651e1ab48cde71"
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447 There are 6 different output files produced by `staramr` as well as a collection of additional files. |
61a3e97aa865
"planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit 07b1134fbf48f0f94e6060b861651e1ab48cde71"
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448 |
61a3e97aa865
"planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit 07b1134fbf48f0f94e6060b861651e1ab48cde71"
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449 mlst.tsv |
61a3e97aa865
"planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit 07b1134fbf48f0f94e6060b861651e1ab48cde71"
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450 ```````````````````` |
61a3e97aa865
"planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit 07b1134fbf48f0f94e6060b861651e1ab48cde71"
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451 |
61a3e97aa865
"planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit 07b1134fbf48f0f94e6060b861651e1ab48cde71"
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452 A tabular file of each multi-locus sequence type (MLST) and it's corresponding locus/alleles, one genome per line. |
61a3e97aa865
"planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit 07b1134fbf48f0f94e6060b861651e1ab48cde71"
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453 |
61a3e97aa865
"planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit 07b1134fbf48f0f94e6060b861651e1ab48cde71"
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|
454 +------------+--------------+-----------------------------------+------------+------------+------------+------------+------------+------------+------------+ |
61a3e97aa865
"planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit 07b1134fbf48f0f94e6060b861651e1ab48cde71"
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455 | Isolate ID | Scheme | Sequence Type | Locus 1 | Locus 2 | Locus 3 | Locus 4 | Locus 5 | Locus 6 | Locus 7 | |
61a3e97aa865
"planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit 07b1134fbf48f0f94e6060b861651e1ab48cde71"
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456 +============+==============+===================================+============+============+============+============+============+============+============+ |
61a3e97aa865
"planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit 07b1134fbf48f0f94e6060b861651e1ab48cde71"
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457 | SRR1952908 | senterica | 11 | aroC(5) | dnaN(2) | hemD(3) | hisD(7) | purE(6) | sucA(6) | thrA(11) | |
61a3e97aa865
"planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit 07b1134fbf48f0f94e6060b861651e1ab48cde71"
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458 +------------+--------------+-----------------------------------+------------+------------+------------+------------+------------+------------+---+--------+ |
61a3e97aa865
"planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit 07b1134fbf48f0f94e6060b861651e1ab48cde71"
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459 | SRR1952926 | senterica | 11 | aroC(5) | dnaN(2) | hemD(3) | hisD(7) | purE(6) | sucA(6) | thrA(11) | |
61a3e97aa865
"planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit 07b1134fbf48f0f94e6060b861651e1ab48cde71"
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changeset
|
460 +------------+--------------+-----------------------------------+------------+------------+------------+------------+------------+------------+------------+ |
61a3e97aa865
"planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit 07b1134fbf48f0f94e6060b861651e1ab48cde71"
nml
parents:
8
diff
changeset
|
461 |
0
fef5aff062c7
planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
nml
parents:
diff
changeset
|
462 |
fef5aff062c7
planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
nml
parents:
diff
changeset
|
463 summary.tsv |
fef5aff062c7
planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
nml
parents:
diff
changeset
|
464 ``````````` |
fef5aff062c7
planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
nml
parents:
diff
changeset
|
465 |
fef5aff062c7
planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
nml
parents:
diff
changeset
|
466 A summary of all detected AMR genes/mutations in each genome, one genome per line. |
fef5aff062c7
planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
nml
parents:
diff
changeset
|
467 |
13
2fd4d4c9c5c2
"planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit f328deb1fae95c3418e86bc1f1a2b2034b2f7c3e"
nml
parents:
12
diff
changeset
|
468 +------------+----------------+-----------------------------------------------------------+-----------------------------------------------------------------------------------------------------------+-------------------------------------+-----------+---------------+---------------+-----------+---------------------------------------------------+-------------------------+ |
11
5f43703968cf
"planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit 65ffe1cd11ac6108adf483d3e83856a5466df79c"
nml
parents:
10
diff
changeset
|
469 | Isolate ID | Quality Module | Genotype | Predicted Phenotype | Plasmid | Scheme | Sequence Type | Genome Length | N50 value | Number of Contigs Greater Than Or Equal To 300 bp | Quality Module Feedback | |
13
2fd4d4c9c5c2
"planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit f328deb1fae95c3418e86bc1f1a2b2034b2f7c3e"
nml
parents:
12
diff
changeset
|
470 +============+================+===========================================================+===========================================================================================================+=====================================+===========+===============+===============+===========+===================================================+=========================+ |
11
5f43703968cf
"planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit 65ffe1cd11ac6108adf483d3e83856a5466df79c"
nml
parents:
10
diff
changeset
|
471 | SRR1952908 | Passed | 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 | senterica | 11 | 4796082 | 225419 | 59 | | |
13
2fd4d4c9c5c2
"planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit f328deb1fae95c3418e86bc1f1a2b2034b2f7c3e"
nml
parents:
12
diff
changeset
|
472 +------------+----------------+-----------------------------------------------------------+-----------------------------------------------------------------------------------------------------------+-------------------------------------+-----------+---------------+---------------+-----------+---------------------------------------------------+-------------------------+ |
11
5f43703968cf
"planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit 65ffe1cd11ac6108adf483d3e83856a5466df79c"
nml
parents:
10
diff
changeset
|
473 | SRR1952926 | Passed | blaTEM-57, gyrA (S83Y), tet(A) | ampicillin, ciprofloxacin I/R, nalidixic acid, tetracycline | ColpVC, IncFIB(S), IncFII(S), IncI1 | senterica | 11 | 4794071 | 225380 | 50 | | |
13
2fd4d4c9c5c2
"planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit f328deb1fae95c3418e86bc1f1a2b2034b2f7c3e"
nml
parents:
12
diff
changeset
|
474 +------------+----------------+-----------------------------------------------------------+-----------------------------------------------------------------------------------------------------------+-------------------------------------+-----------+---------------+---------------+-----------+---------------------------------------------------+-------------------------+ |
11
5f43703968cf
"planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit 65ffe1cd11ac6108adf483d3e83856a5466df79c"
nml
parents:
10
diff
changeset
|
475 |
6
3c09557ac425
planemo upload for repository https://github.com/phac-nml/staramr commit 52535d98ad1e03c83c93f230abf966613b4b8fa2
nml
parents:
5
diff
changeset
|
476 |
3c09557ac425
planemo upload for repository https://github.com/phac-nml/staramr commit 52535d98ad1e03c83c93f230abf966613b4b8fa2
nml
parents:
5
diff
changeset
|
477 detailed_summary.tsv |
3c09557ac425
planemo upload for repository https://github.com/phac-nml/staramr commit 52535d98ad1e03c83c93f230abf966613b4b8fa2
nml
parents:
5
diff
changeset
|
478 ```````````````````` |
3c09557ac425
planemo upload for repository https://github.com/phac-nml/staramr commit 52535d98ad1e03c83c93f230abf966613b4b8fa2
nml
parents:
5
diff
changeset
|
479 |
7
f1adc47e017a
planemo upload for repository https://github.com/phac-nml/staramr commit dad82f0ddadb5e106a54d5aa6609918325e49d23
nml
parents:
6
diff
changeset
|
480 A detailed summary of all detected AMR genes/mutations/plasmids in each genome/type, one gene/type per line. |
6
3c09557ac425
planemo upload for repository https://github.com/phac-nml/staramr commit 52535d98ad1e03c83c93f230abf966613b4b8fa2
nml
parents:
5
diff
changeset
|
481 |
7
f1adc47e017a
planemo upload for repository https://github.com/phac-nml/staramr commit dad82f0ddadb5e106a54d5aa6609918325e49d23
nml
parents:
6
diff
changeset
|
482 +------------+--------------+-----------------------------------+-----------+----------+-------------------------+-------------+--------+--------+-----------+------------+ |
f1adc47e017a
planemo upload for repository https://github.com/phac-nml/staramr commit dad82f0ddadb5e106a54d5aa6609918325e49d23
nml
parents:
6
diff
changeset
|
483 | Isolate ID | Gene/Plasmid | Predicted Phenotype | %Identity | %Overlap | HSP Length/Total Length | Contig | Start | End | Accession | Data Type | |
f1adc47e017a
planemo upload for repository https://github.com/phac-nml/staramr commit dad82f0ddadb5e106a54d5aa6609918325e49d23
nml
parents:
6
diff
changeset
|
484 +============+==============+===================================+===========+==========+=========================+=============+========+========+===========+============+ |
f1adc47e017a
planemo upload for repository https://github.com/phac-nml/staramr commit dad82f0ddadb5e106a54d5aa6609918325e49d23
nml
parents:
6
diff
changeset
|
485 | SRR1952908 | ColpVC | | 98.96 | 100 | 193/193 | contig00038 | 1618 | 1426 | JX133088 | Plasmid | |
f1adc47e017a
planemo upload for repository https://github.com/phac-nml/staramr commit dad82f0ddadb5e106a54d5aa6609918325e49d23
nml
parents:
6
diff
changeset
|
486 +------------+--------------+-----------------------------------+-----------+----------+-------------------------+-------------+--------+--------+-----------+------------+ |
f1adc47e017a
planemo upload for repository https://github.com/phac-nml/staramr commit dad82f0ddadb5e106a54d5aa6609918325e49d23
nml
parents:
6
diff
changeset
|
487 | SRR1952908 | IncFIB(S) | | 98.91 | 100 | 643/643 | contig00024 | 10302 | 9660 | FN432031 | Plasmid | |
f1adc47e017a
planemo upload for repository https://github.com/phac-nml/staramr commit dad82f0ddadb5e106a54d5aa6609918325e49d23
nml
parents:
6
diff
changeset
|
488 +------------+--------------+-----------------------------------+-----------+----------+-------------------------+-------------+--------+--------+-----------+------------+ |
f1adc47e017a
planemo upload for repository https://github.com/phac-nml/staramr commit dad82f0ddadb5e106a54d5aa6609918325e49d23
nml
parents:
6
diff
changeset
|
489 | SRR1952908 | IncFII(S) | | 100 | 100 | 262/262 | contig00024 | 54294 | 54555 | CP000858 | Plasmid | |
f1adc47e017a
planemo upload for repository https://github.com/phac-nml/staramr commit dad82f0ddadb5e106a54d5aa6609918325e49d23
nml
parents:
6
diff
changeset
|
490 +------------+--------------+-----------------------------------+-----------+----------+-------------------------+-------------+--------+--------+-----------+------------+ |
f1adc47e017a
planemo upload for repository https://github.com/phac-nml/staramr commit dad82f0ddadb5e106a54d5aa6609918325e49d23
nml
parents:
6
diff
changeset
|
491 | 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
|
492 +------------+--------------+-----------------------------------+-----------+----------+-------------------------+-------------+--------+--------+-----------+------------+ |
f1adc47e017a
planemo upload for repository https://github.com/phac-nml/staramr commit dad82f0ddadb5e106a54d5aa6609918325e49d23
nml
parents:
6
diff
changeset
|
493 | 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
|
494 +------------+--------------+-----------------------------------+-----------+----------+-------------------------+-------------+--------+--------+-----------+------------+ |
f1adc47e017a
planemo upload for repository https://github.com/phac-nml/staramr commit dad82f0ddadb5e106a54d5aa6609918325e49d23
nml
parents:
6
diff
changeset
|
495 | 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
|
496 +------------+--------------+-----------------------------------+-----------+----------+-------------------------+-------------+--------+--------+-----------+------------+ |
f1adc47e017a
planemo upload for repository https://github.com/phac-nml/staramr commit dad82f0ddadb5e106a54d5aa6609918325e49d23
nml
parents:
6
diff
changeset
|
497 | 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
|
498 +------------+--------------+-----------------------------------+-----------+----------+-------------------------+-------------+--------+--------+-----------+------------+ |
f1adc47e017a
planemo upload for repository https://github.com/phac-nml/staramr commit dad82f0ddadb5e106a54d5aa6609918325e49d23
nml
parents:
6
diff
changeset
|
499 | 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:
6
diff
changeset
|
500 +------------+--------------+-----------------------------------+-----------+----------+-------------------------+-------------+--------+--------+-----------+------------+ |
f1adc47e017a
planemo upload for repository https://github.com/phac-nml/staramr commit dad82f0ddadb5e106a54d5aa6609918325e49d23
nml
parents:
6
diff
changeset
|
501 | 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
|
502 +------------+--------------+-----------------------------------+-----------+----------+-------------------------+-------------+--------+--------+-----------+------------+ |
f1adc47e017a
planemo upload for repository https://github.com/phac-nml/staramr commit dad82f0ddadb5e106a54d5aa6609918325e49d23
nml
parents:
6
diff
changeset
|
503 | 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
|
504 +------------+--------------+-----------------------------------+-----------+----------+-------------------------+-------------+--------+--------+-----------+------------+ |
f1adc47e017a
planemo upload for repository https://github.com/phac-nml/staramr commit dad82f0ddadb5e106a54d5aa6609918325e49d23
nml
parents:
6
diff
changeset
|
505 | 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:
6
diff
changeset
|
506 +------------+--------------+-----------------------------------+-----------+----------+-------------------------+-------------+--------+--------+-----------+------------+ |
f1adc47e017a
planemo upload for repository https://github.com/phac-nml/staramr commit dad82f0ddadb5e106a54d5aa6609918325e49d23
nml
parents:
6
diff
changeset
|
507 | 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:
6
diff
changeset
|
508 +------------+--------------+-----------------------------------+-----------+----------+-------------------------+-------------+--------+--------+-----------+------------+ |
f1adc47e017a
planemo upload for repository https://github.com/phac-nml/staramr commit dad82f0ddadb5e106a54d5aa6609918325e49d23
nml
parents:
6
diff
changeset
|
509 | 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:
6
diff
changeset
|
510 +------------+--------------+-----------------------------------+-----------+----------+-------------------------+-------------+--------+--------+-----------+------------+ |
f1adc47e017a
planemo upload for repository https://github.com/phac-nml/staramr commit dad82f0ddadb5e106a54d5aa6609918325e49d23
nml
parents:
6
diff
changeset
|
511 | 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:
6
diff
changeset
|
512 +------------+--------------+-----------------------------------+-----------+----------+-------------------------+-------------+--------+--------+-----------+------------+ |
f1adc47e017a
planemo upload for repository https://github.com/phac-nml/staramr commit dad82f0ddadb5e106a54d5aa6609918325e49d23
nml
parents:
6
diff
changeset
|
513 | 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
|
514 +------------+--------------+-----------------------------------+-----------+----------+-------------------------+-------------+--------+--------+-----------+------------+ |
f1adc47e017a
planemo upload for repository https://github.com/phac-nml/staramr commit dad82f0ddadb5e106a54d5aa6609918325e49d23
nml
parents:
6
diff
changeset
|
515 | 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
|
516 +------------+--------------+-----------------------------------+-----------+----------+-------------------------+-------------+--------+--------+-----------+------------+ |
f1adc47e017a
planemo upload for repository https://github.com/phac-nml/staramr commit dad82f0ddadb5e106a54d5aa6609918325e49d23
nml
parents:
6
diff
changeset
|
517 | 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
|
518 +------------+--------------+-----------------------------------+-----------+----------+-------------------------+-------------+--------+--------+-----------+------------+ |
f1adc47e017a
planemo upload for repository https://github.com/phac-nml/staramr commit dad82f0ddadb5e106a54d5aa6609918325e49d23
nml
parents:
6
diff
changeset
|
519 | 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:
6
diff
changeset
|
520 +------------+--------------+-----------------------------------+-----------+----------+-------------------------+-------------+--------+--------+-----------+------------+ |
6
3c09557ac425
planemo upload for repository https://github.com/phac-nml/staramr commit 52535d98ad1e03c83c93f230abf966613b4b8fa2
nml
parents:
5
diff
changeset
|
521 |
0
fef5aff062c7
planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
nml
parents:
diff
changeset
|
522 |
fef5aff062c7
planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
nml
parents:
diff
changeset
|
523 resfinder.tsv |
fef5aff062c7
planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
nml
parents:
diff
changeset
|
524 ````````````` |
fef5aff062c7
planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
nml
parents:
diff
changeset
|
525 |
fef5aff062c7
planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
nml
parents:
diff
changeset
|
526 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
nml
parents:
diff
changeset
|
527 |
fef5aff062c7
planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
nml
parents:
diff
changeset
|
528 +------------+------------+----------------------+------------+-----------+--------------------------+--------------+--------+-------+-----------+ |
fef5aff062c7
planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
nml
parents:
diff
changeset
|
529 | 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
|
530 +============+============+======================+============+===========+==========================+==============+========+=======+===========+ |
fef5aff062c7
planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
nml
parents:
diff
changeset
|
531 | 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
|
532 +------------+------------+----------------------+------------+-----------+--------------------------+--------------+--------+-------+-----------+ |
fef5aff062c7
planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
nml
parents:
diff
changeset
|
533 | 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
|
534 +------------+------------+----------------------+------------+-----------+--------------------------+--------------+--------+-------+-----------+ |
fef5aff062c7
planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
nml
parents:
diff
changeset
|
535 | 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
|
536 +------------+------------+----------------------+------------+-----------+--------------------------+--------------+--------+-------+-----------+ |
fef5aff062c7
planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
nml
parents:
diff
changeset
|
537 | 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
|
538 +------------+------------+----------------------+------------+-----------+--------------------------+--------------+--------+-------+-----------+ |
fef5aff062c7
planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
nml
parents:
diff
changeset
|
539 | 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
|
540 +------------+------------+----------------------+------------+-----------+--------------------------+--------------+--------+-------+-----------+ |
fef5aff062c7
planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
nml
parents:
diff
changeset
|
541 | 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
|
542 +------------+------------+----------------------+------------+-----------+--------------------------+--------------+--------+-------+-----------+ |
fef5aff062c7
planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
nml
parents:
diff
changeset
|
543 | 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
|
544 +------------+------------+----------------------+------------+-----------+--------------------------+--------------+--------+-------+-----------+ |
fef5aff062c7
planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
nml
parents:
diff
changeset
|
545 | 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
|
546 +------------+------------+----------------------+------------+-----------+--------------------------+--------------+--------+-------+-----------+ |
fef5aff062c7
planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
nml
parents:
diff
changeset
|
547 |
6
3c09557ac425
planemo upload for repository https://github.com/phac-nml/staramr commit 52535d98ad1e03c83c93f230abf966613b4b8fa2
nml
parents:
5
diff
changeset
|
548 plasmidfinder.tsv |
3c09557ac425
planemo upload for repository https://github.com/phac-nml/staramr commit 52535d98ad1e03c83c93f230abf966613b4b8fa2
nml
parents:
5
diff
changeset
|
549 ````````````````` |
3c09557ac425
planemo upload for repository https://github.com/phac-nml/staramr commit 52535d98ad1e03c83c93f230abf966613b4b8fa2
nml
parents:
5
diff
changeset
|
550 |
7
f1adc47e017a
planemo upload for repository https://github.com/phac-nml/staramr commit dad82f0ddadb5e106a54d5aa6609918325e49d23
nml
parents:
6
diff
changeset
|
551 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
nml
parents:
5
diff
changeset
|
552 |
3c09557ac425
planemo upload for repository https://github.com/phac-nml/staramr commit 52535d98ad1e03c83c93f230abf966613b4b8fa2
nml
parents:
5
diff
changeset
|
553 +------------+-----------+-----------+----------+-------------------------+-------------+-------+-------+-----------+ |
7
f1adc47e017a
planemo upload for repository https://github.com/phac-nml/staramr commit dad82f0ddadb5e106a54d5aa6609918325e49d23
nml
parents:
6
diff
changeset
|
554 | 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
|
555 +============+===========+===========+==========+=========================+=============+=======+=======+===========+ |
3c09557ac425
planemo upload for repository https://github.com/phac-nml/staramr commit 52535d98ad1e03c83c93f230abf966613b4b8fa2
nml
parents:
5
diff
changeset
|
556 | 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
|
557 +------------+-----------+-----------+----------+-------------------------+-------------+-------+-------+-----------+ |
3c09557ac425
planemo upload for repository https://github.com/phac-nml/staramr commit 52535d98ad1e03c83c93f230abf966613b4b8fa2
nml
parents:
5
diff
changeset
|
558 | 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
|
559 +------------+-----------+-----------+----------+-------------------------+-------------+-------+-------+-----------+ |
3c09557ac425
planemo upload for repository https://github.com/phac-nml/staramr commit 52535d98ad1e03c83c93f230abf966613b4b8fa2
nml
parents:
5
diff
changeset
|
560 | 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
|
561 +------------+-----------+-----------+----------+-------------------------+-------------+-------+-------+-----------+ |
3c09557ac425
planemo upload for repository https://github.com/phac-nml/staramr commit 52535d98ad1e03c83c93f230abf966613b4b8fa2
nml
parents:
5
diff
changeset
|
562 | 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
|
563 +------------+-----------+-----------+----------+-------------------------+-------------+-------+-------+-----------+ |
3c09557ac425
planemo upload for repository https://github.com/phac-nml/staramr commit 52535d98ad1e03c83c93f230abf966613b4b8fa2
nml
parents:
5
diff
changeset
|
564 | SRR1952926 | ColpVC | 98.96 | 100 | 193/193 | contig00037 | 657 | 849 | JX133088 | |
3c09557ac425
planemo upload for repository https://github.com/phac-nml/staramr commit 52535d98ad1e03c83c93f230abf966613b4b8fa2
nml
parents:
5
diff
changeset
|
565 +------------+-----------+-----------+----------+-------------------------+-------------+-------+-------+-----------+ |
3c09557ac425
planemo upload for repository https://github.com/phac-nml/staramr commit 52535d98ad1e03c83c93f230abf966613b4b8fa2
nml
parents:
5
diff
changeset
|
566 | SRR1952926 | IncFIB(S) | 98.91 | 100 | 643/643 | contig00021 | 10302 | 9660 | FN432031 | |
3c09557ac425
planemo upload for repository https://github.com/phac-nml/staramr commit 52535d98ad1e03c83c93f230abf966613b4b8fa2
nml
parents:
5
diff
changeset
|
567 +------------+-----------+-----------+----------+-------------------------+-------------+-------+-------+-----------+ |
3c09557ac425
planemo upload for repository https://github.com/phac-nml/staramr commit 52535d98ad1e03c83c93f230abf966613b4b8fa2
nml
parents:
5
diff
changeset
|
568 | SRR1952926 | IncFII(S) | 100 | 100 | 262/262 | contig00021 | 54294 | 54555 | CP000858 | |
3c09557ac425
planemo upload for repository https://github.com/phac-nml/staramr commit 52535d98ad1e03c83c93f230abf966613b4b8fa2
nml
parents:
5
diff
changeset
|
569 +------------+-----------+-----------+----------+-------------------------+-------------+-------+-------+-----------+ |
3c09557ac425
planemo upload for repository https://github.com/phac-nml/staramr commit 52535d98ad1e03c83c93f230abf966613b4b8fa2
nml
parents:
5
diff
changeset
|
570 | SRR1952926 | IncI1 | 100 | 100 | 142/142 | contig00017 | 3907 | 3766 | AP005147 | |
3c09557ac425
planemo upload for repository https://github.com/phac-nml/staramr commit 52535d98ad1e03c83c93f230abf966613b4b8fa2
nml
parents:
5
diff
changeset
|
571 +------------+-----------+-----------+----------+-------------------------+-------------+-------+-------+-----------+ |
3c09557ac425
planemo upload for repository https://github.com/phac-nml/staramr commit 52535d98ad1e03c83c93f230abf966613b4b8fa2
nml
parents:
5
diff
changeset
|
572 |
0
fef5aff062c7
planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
nml
parents:
diff
changeset
|
573 pointfinder.tsv |
fef5aff062c7
planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
nml
parents:
diff
changeset
|
574 ``````````````` |
fef5aff062c7
planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
nml
parents:
diff
changeset
|
575 |
fef5aff062c7
planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
nml
parents:
diff
changeset
|
576 A tabular file of each AMR point mutation and additional BLAST information from the **PointFinder** database, one gene per line. |
fef5aff062c7
planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
nml
parents:
diff
changeset
|
577 |
fef5aff062c7
planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
nml
parents:
diff
changeset
|
578 +-------------+--------------+------------------------------------+--------+-----------+----------------------+------------+-----------+--------------------------+--------------+---------+--------+ |
fef5aff062c7
planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
nml
parents:
diff
changeset
|
579 | Isolate ID | Gene | Predicted Phenotype | Type | Position | Mutation | %Identity | %Overlap | HSP Length/Total Length | Contig | Start | End | |
fef5aff062c7
planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
nml
parents:
diff
changeset
|
580 +=============+==============+====================================+========+===========+======================+============+===========+==========================+==============+=========+========+ |
fef5aff062c7
planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
nml
parents:
diff
changeset
|
581 | SRR1952908 | gyrA (S83Y) | ciprofloxacin I/R, nalidixic acid | codon | 83 | TCC -> TAC (S -> Y) | 99.96 | 100.00 | 2637/2637 | contig00008 | 22801 | 20165 | |
fef5aff062c7
planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
nml
parents:
diff
changeset
|
582 +-------------+--------------+------------------------------------+--------+-----------+----------------------+------------+-----------+--------------------------+--------------+---------+--------+ |
fef5aff062c7
planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
nml
parents:
diff
changeset
|
583 | SRR1952926 | gyrA (S83Y) | ciprofloxacin I/R, nalidixic acid | codon | 83 | TCC -> TAC (S -> Y) | 99.96 | 100.00 | 2637/2637 | contig00011 | 157768 | 160404 | |
fef5aff062c7
planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
nml
parents:
diff
changeset
|
584 +-------------+--------------+------------------------------------+--------+-----------+----------------------+------------+-----------+--------------------------+--------------+---------+--------+ |
fef5aff062c7
planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
nml
parents:
diff
changeset
|
585 |
fef5aff062c7
planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
nml
parents:
diff
changeset
|
586 settings.txt |
fef5aff062c7
planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
nml
parents:
diff
changeset
|
587 ```````````` |
fef5aff062c7
planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
nml
parents:
diff
changeset
|
588 |
fef5aff062c7
planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
nml
parents:
diff
changeset
|
589 The command-line, database versions, and other settings used to run `staramr`. |
fef5aff062c7
planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
nml
parents:
diff
changeset
|
590 |
fef5aff062c7
planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
nml
parents:
diff
changeset
|
591 :: |
fef5aff062c7
planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
nml
parents:
diff
changeset
|
592 |
fef5aff062c7
planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
nml
parents:
diff
changeset
|
593 command_line = staramr search -o out --pointfinder-organism salmonella SRR1952908.fasta SRR1952926.fasta |
11
5f43703968cf
"planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit 65ffe1cd11ac6108adf483d3e83856a5466df79c"
nml
parents:
10
diff
changeset
|
594 version = 0.7.1 |
6
3c09557ac425
planemo upload for repository https://github.com/phac-nml/staramr commit 52535d98ad1e03c83c93f230abf966613b4b8fa2
nml
parents:
5
diff
changeset
|
595 start_time = 2019-04-25 16:01:32 |
3c09557ac425
planemo upload for repository https://github.com/phac-nml/staramr commit 52535d98ad1e03c83c93f230abf966613b4b8fa2
nml
parents:
5
diff
changeset
|
596 end_time = 2019-04-25 16:01:34 |
3c09557ac425
planemo upload for repository https://github.com/phac-nml/staramr commit 52535d98ad1e03c83c93f230abf966613b4b8fa2
nml
parents:
5
diff
changeset
|
597 total_minutes = 0.04 |
0
fef5aff062c7
planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
nml
parents:
diff
changeset
|
598 resfinder_db_dir = staramr/databases/data/dist/resfinder |
fef5aff062c7
planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
nml
parents:
diff
changeset
|
599 resfinder_db_url = https://bitbucket.org/genomicepidemiology/resfinder_db.git |
6
3c09557ac425
planemo upload for repository https://github.com/phac-nml/staramr commit 52535d98ad1e03c83c93f230abf966613b4b8fa2
nml
parents:
5
diff
changeset
|
600 resfinder_db_commit = e8f1eb2585cd9610c4034a54ce7fc4f93aa95535 |
3c09557ac425
planemo upload for repository https://github.com/phac-nml/staramr commit 52535d98ad1e03c83c93f230abf966613b4b8fa2
nml
parents:
5
diff
changeset
|
601 resfinder_db_date = Mon, 16 Jul 2018 16:58 |
0
fef5aff062c7
planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
nml
parents:
diff
changeset
|
602 pointfinder_db_dir = staramr/databases/data/dist/pointfinder |
fef5aff062c7
planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
nml
parents:
diff
changeset
|
603 pointfinder_db_url = https://bitbucket.org/genomicepidemiology/pointfinder_db.git |
6
3c09557ac425
planemo upload for repository https://github.com/phac-nml/staramr commit 52535d98ad1e03c83c93f230abf966613b4b8fa2
nml
parents:
5
diff
changeset
|
604 pointfinder_db_commit = 8706a6363bb29e47e0e398c53043b037c24b99a7 |
3c09557ac425
planemo upload for repository https://github.com/phac-nml/staramr commit 52535d98ad1e03c83c93f230abf966613b4b8fa2
nml
parents:
5
diff
changeset
|
605 pointfinder_db_date = Wed, 04 Jul 2018 14:27 |
3c09557ac425
planemo upload for repository https://github.com/phac-nml/staramr commit 52535d98ad1e03c83c93f230abf966613b4b8fa2
nml
parents:
5
diff
changeset
|
606 plasmidfinder_db_dir = staramr/databases/data/dist/plasmidfinder |
3c09557ac425
planemo upload for repository https://github.com/phac-nml/staramr commit 52535d98ad1e03c83c93f230abf966613b4b8fa2
nml
parents:
5
diff
changeset
|
607 plasmidfinder_db_url = https://bitbucket.org/genomicepidemiology/plasmidfinder_db.git |
3c09557ac425
planemo upload for repository https://github.com/phac-nml/staramr commit 52535d98ad1e03c83c93f230abf966613b4b8fa2
nml
parents:
5
diff
changeset
|
608 plasmidfinder_db_commit = 81919954cbedaff39056610ab584ab4c06011ed8 |
3c09557ac425
planemo upload for repository https://github.com/phac-nml/staramr commit 52535d98ad1e03c83c93f230abf966613b4b8fa2
nml
parents:
5
diff
changeset
|
609 plasmidfinder_db_date = Tue, 20 Nov 2018 08:51 |
0
fef5aff062c7
planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
nml
parents:
diff
changeset
|
610 pointfinder_gene_drug_version = 050218 |
8
da787fc8b740
planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit f1641993d71fc04fadf20753a63cc72a412f4af5
nml
parents:
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diff
changeset
|
611 resfinder_gene_drug_version = 050218.1 |
0
fef5aff062c7
planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
nml
parents:
diff
changeset
|
612 |
fef5aff062c7
planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
nml
parents:
diff
changeset
|
613 results.xlsx |
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planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
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614 ```````````` |
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planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
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615 |
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planemo upload for repository https://github.com/phac-nml/staramr commit 52535d98ad1e03c83c93f230abf966613b4b8fa2
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616 An Excel spreadsheet containing the previous 5 files as separate worksheets. |
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planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
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617 |
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planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
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618 BLAST Hits |
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planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
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619 `````````` |
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planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
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620 |
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planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit f1641993d71fc04fadf20753a63cc72a412f4af5
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621 The dataset collection **hits** stores fasta files of the specific blast hits. |
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planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
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622 |
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planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
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623 Galaxy wrapper written by Aaron Petkau at the National Microbiology Laboratory, Public Health Agency of Canada. |
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planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
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624 |
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planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
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625 .. _staramr: https://github.com/phac-nml/staramr |
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planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
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626 .. _ResFinder: https://bitbucket.org/genomicepidemiology/resfinder_db |
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planemo upload for repository https://github.com/phac-nml/staramr commit 52535d98ad1e03c83c93f230abf966613b4b8fa2
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627 .. _PlasmidFinder: https://bitbucket.org/genomicepidemiology/plasmidfinder_db |
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planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
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628 .. _PointFinder: https://bitbucket.org/genomicepidemiology/pointfinder_db |
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planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit 7483ccd266d271a05704b1eced996a653b50ee84
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629 .. _webservices: http://www.genomicepidemiology.org/services/ |
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planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
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630 ]]></help> |
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planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
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631 <citations> |
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planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
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632 <citation type="bibtex"> |
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planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit e92a931da272a26f3a16e7b1d31c432890a6fdb3
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633 @Article{microorganisms10020292, |
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planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit e92a931da272a26f3a16e7b1d31c432890a6fdb3
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634 AUTHOR = {Bharat, Amrita and Petkau, Aaron and Avery, Brent P. and Chen, Jessica C. and Folster, Jason P. and Carson, Carolee A. and Kearney, Ashley and Nadon, Celine and Mabon, Philip and Thiessen, Jeffrey and Alexander, David C. and Allen, Vanessa and El Bailey, Sameh and Bekal, Sadjia and German, Greg J. and Haldane, David and Hoang, Linda and Chui, Linda and Minion, Jessica and Zahariadis, George and Domselaar, Gary Van and Reid-Smith, Richard J. and Mulvey, Michael R.}, |
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planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit e92a931da272a26f3a16e7b1d31c432890a6fdb3
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635 TITLE = {Correlation between Phenotypic and In Silico Detection of Antimicrobial Resistance in Salmonella enterica in Canada Using Staramr}, |
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planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit e92a931da272a26f3a16e7b1d31c432890a6fdb3
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636 JOURNAL = {Microorganisms}, |
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planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit e92a931da272a26f3a16e7b1d31c432890a6fdb3
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637 VOLUME = {10}, |
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planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit e92a931da272a26f3a16e7b1d31c432890a6fdb3
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638 YEAR = {2022}, |
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639 NUMBER = {2}, |
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planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit e92a931da272a26f3a16e7b1d31c432890a6fdb3
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640 ARTICLE-NUMBER = {292}, |
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planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit e92a931da272a26f3a16e7b1d31c432890a6fdb3
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641 URL = {https://www.mdpi.com/2076-2607/10/2/292}, |
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planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit e92a931da272a26f3a16e7b1d31c432890a6fdb3
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642 ISSN = {2076-2607}, |
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planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit e92a931da272a26f3a16e7b1d31c432890a6fdb3
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643 DOI = {10.3390/microorganisms10020292} |
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planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit e92a931da272a26f3a16e7b1d31c432890a6fdb3
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644 } |
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planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit e92a931da272a26f3a16e7b1d31c432890a6fdb3
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645 </citation> |
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planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
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646 </citations> |
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planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
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647 </tool> |