Mercurial > repos > iuc > amrfinderplus
annotate amrfinderplus.xml @ 3:ab473abbee98 draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 0f83e13c1a0732970520d63537273b8a3d890dad
| author | iuc |
|---|---|
| date | Tue, 03 Oct 2023 08:30:29 +0000 |
| parents | ff401a72560b |
| children |
| rev | line source |
|---|---|
|
0
d06eb6832e26
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 73f592a7f1c1e9577bbf56a1347bd5c01bb8ea14
iuc
parents:
diff
changeset
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1 <tool id="amrfinderplus" name="AMRFinderPlus" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@"> |
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d06eb6832e26
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 73f592a7f1c1e9577bbf56a1347bd5c01bb8ea14
iuc
parents:
diff
changeset
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2 <description> |
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d06eb6832e26
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 73f592a7f1c1e9577bbf56a1347bd5c01bb8ea14
iuc
parents:
diff
changeset
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3 NCBI Antimicrobial Resistance Gene Finder |
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d06eb6832e26
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 73f592a7f1c1e9577bbf56a1347bd5c01bb8ea14
iuc
parents:
diff
changeset
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4 </description> |
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d06eb6832e26
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 73f592a7f1c1e9577bbf56a1347bd5c01bb8ea14
iuc
parents:
diff
changeset
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5 <macros> |
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d06eb6832e26
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 73f592a7f1c1e9577bbf56a1347bd5c01bb8ea14
iuc
parents:
diff
changeset
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6 <import>macro.xml</import> |
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d06eb6832e26
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 73f592a7f1c1e9577bbf56a1347bd5c01bb8ea14
iuc
parents:
diff
changeset
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7 </macros> |
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d06eb6832e26
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 73f592a7f1c1e9577bbf56a1347bd5c01bb8ea14
iuc
parents:
diff
changeset
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8 <expand macro='edam'/> |
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d06eb6832e26
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 73f592a7f1c1e9577bbf56a1347bd5c01bb8ea14
iuc
parents:
diff
changeset
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9 <expand macro="requirements"/> |
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d06eb6832e26
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 73f592a7f1c1e9577bbf56a1347bd5c01bb8ea14
iuc
parents:
diff
changeset
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10 <expand macro="version_command"/> |
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d06eb6832e26
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 73f592a7f1c1e9577bbf56a1347bd5c01bb8ea14
iuc
parents:
diff
changeset
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11 |
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d06eb6832e26
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 73f592a7f1c1e9577bbf56a1347bd5c01bb8ea14
iuc
parents:
diff
changeset
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12 <command detect_errors="aggressive"><![CDATA[ |
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d06eb6832e26
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 73f592a7f1c1e9577bbf56a1347bd5c01bb8ea14
iuc
parents:
diff
changeset
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13 amrfinder |
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d06eb6832e26
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 73f592a7f1c1e9577bbf56a1347bd5c01bb8ea14
iuc
parents:
diff
changeset
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14 #*====================================== |
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d06eb6832e26
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 73f592a7f1c1e9577bbf56a1347bd5c01bb8ea14
iuc
parents:
diff
changeset
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15 CPU option |
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d06eb6832e26
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 73f592a7f1c1e9577bbf56a1347bd5c01bb8ea14
iuc
parents:
diff
changeset
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16 ======================================*# |
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d06eb6832e26
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 73f592a7f1c1e9577bbf56a1347bd5c01bb8ea14
iuc
parents:
diff
changeset
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17 --threads \${GALAXY_SLOTS:-1} |
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d06eb6832e26
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 73f592a7f1c1e9577bbf56a1347bd5c01bb8ea14
iuc
parents:
diff
changeset
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18 #*====================================== |
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d06eb6832e26
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 73f592a7f1c1e9577bbf56a1347bd5c01bb8ea14
iuc
parents:
diff
changeset
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19 DATABASE |
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d06eb6832e26
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 73f592a7f1c1e9577bbf56a1347bd5c01bb8ea14
iuc
parents:
diff
changeset
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20 ======================================*# |
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d06eb6832e26
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 73f592a7f1c1e9577bbf56a1347bd5c01bb8ea14
iuc
parents:
diff
changeset
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21 --database '$input_option.amrfinder_db_select.fields.path' |
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d06eb6832e26
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 73f592a7f1c1e9577bbf56a1347bd5c01bb8ea14
iuc
parents:
diff
changeset
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22 #*====================================== |
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d06eb6832e26
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 73f592a7f1c1e9577bbf56a1347bd5c01bb8ea14
iuc
parents:
diff
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23 INPUT TYPE |
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d06eb6832e26
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 73f592a7f1c1e9577bbf56a1347bd5c01bb8ea14
iuc
parents:
diff
changeset
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24 ======================================*# |
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d06eb6832e26
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 73f592a7f1c1e9577bbf56a1347bd5c01bb8ea14
iuc
parents:
diff
changeset
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25 #if $input_option.input_mode.input_select == 'nucleotide' |
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d06eb6832e26
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 73f592a7f1c1e9577bbf56a1347bd5c01bb8ea14
iuc
parents:
diff
changeset
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26 --nucleotide $input_option.input_mode.nucleotide_input |
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d06eb6832e26
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 73f592a7f1c1e9577bbf56a1347bd5c01bb8ea14
iuc
parents:
diff
changeset
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27 #if $input_option.input_mode.nucleotide_flank5_size > 0 |
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d06eb6832e26
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 73f592a7f1c1e9577bbf56a1347bd5c01bb8ea14
iuc
parents:
diff
changeset
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28 --nucleotide_flank5_size $input_option.input_mode.nucleotide_flank5_size |
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d06eb6832e26
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 73f592a7f1c1e9577bbf56a1347bd5c01bb8ea14
iuc
parents:
diff
changeset
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29 --nucleotide_flank5_output 'amrfinderplus_flanking_sequence_output.fasta' |
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d06eb6832e26
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 73f592a7f1c1e9577bbf56a1347bd5c01bb8ea14
iuc
parents:
diff
changeset
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30 #end if |
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d06eb6832e26
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 73f592a7f1c1e9577bbf56a1347bd5c01bb8ea14
iuc
parents:
diff
changeset
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31 --nucleotide_output 'amrfinderplus_nucleotide_output.fasta' |
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d06eb6832e26
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 73f592a7f1c1e9577bbf56a1347bd5c01bb8ea14
iuc
parents:
diff
changeset
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32 #elif $input_option.input_mode.input_select == 'protein' |
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d06eb6832e26
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 73f592a7f1c1e9577bbf56a1347bd5c01bb8ea14
iuc
parents:
diff
changeset
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33 --protein $input_option.input_mode.protein_input |
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d06eb6832e26
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 73f592a7f1c1e9577bbf56a1347bd5c01bb8ea14
iuc
parents:
diff
changeset
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34 #if $input_option.input_mode.gff_annotation |
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d06eb6832e26
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 73f592a7f1c1e9577bbf56a1347bd5c01bb8ea14
iuc
parents:
diff
changeset
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35 --gff $input_option.input_mode.gff_annotation |
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d06eb6832e26
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 73f592a7f1c1e9577bbf56a1347bd5c01bb8ea14
iuc
parents:
diff
changeset
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36 #end if |
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d06eb6832e26
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 73f592a7f1c1e9577bbf56a1347bd5c01bb8ea14
iuc
parents:
diff
changeset
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37 #if $input_option.input_mode.annotation_format |
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d06eb6832e26
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 73f592a7f1c1e9577bbf56a1347bd5c01bb8ea14
iuc
parents:
diff
changeset
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38 --annotation_format $input_option.input_mode.annotation_format |
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d06eb6832e26
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 73f592a7f1c1e9577bbf56a1347bd5c01bb8ea14
iuc
parents:
diff
changeset
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39 #end if |
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d06eb6832e26
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 73f592a7f1c1e9577bbf56a1347bd5c01bb8ea14
iuc
parents:
diff
changeset
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40 --protein_output 'amrfinderplus_protein_output.fasta' |
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d06eb6832e26
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 73f592a7f1c1e9577bbf56a1347bd5c01bb8ea14
iuc
parents:
diff
changeset
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41 #else |
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d06eb6832e26
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 73f592a7f1c1e9577bbf56a1347bd5c01bb8ea14
iuc
parents:
diff
changeset
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42 --nucleotide $input_option.input_mode.nucleotide_input |
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d06eb6832e26
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 73f592a7f1c1e9577bbf56a1347bd5c01bb8ea14
iuc
parents:
diff
changeset
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43 #if $input_option.input_mode.nucleotide_flank5_size and $input_option.input_mode.nucleotide_flank5_size > 0 |
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d06eb6832e26
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 73f592a7f1c1e9577bbf56a1347bd5c01bb8ea14
iuc
parents:
diff
changeset
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44 --nucleotide_flank5_size $input_option.input_mode.nucleotide_flank5_size |
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d06eb6832e26
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 73f592a7f1c1e9577bbf56a1347bd5c01bb8ea14
iuc
parents:
diff
changeset
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45 --nucleotide_flank5_output 'amrfinderplus_flanking_sequence_output.fasta' |
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d06eb6832e26
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 73f592a7f1c1e9577bbf56a1347bd5c01bb8ea14
iuc
parents:
diff
changeset
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46 #end if |
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d06eb6832e26
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 73f592a7f1c1e9577bbf56a1347bd5c01bb8ea14
iuc
parents:
diff
changeset
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47 --protein $input_option.input_mode.protein_input |
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d06eb6832e26
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 73f592a7f1c1e9577bbf56a1347bd5c01bb8ea14
iuc
parents:
diff
changeset
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48 --gff $input_option.input_mode.gff_annotation |
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d06eb6832e26
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 73f592a7f1c1e9577bbf56a1347bd5c01bb8ea14
iuc
parents:
diff
changeset
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49 --annotation_format $input_option.input_mode.annotation_format |
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d06eb6832e26
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 73f592a7f1c1e9577bbf56a1347bd5c01bb8ea14
iuc
parents:
diff
changeset
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50 --nucleotide_output 'amrfinderplus_nucleotide_output.fasta' |
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d06eb6832e26
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 73f592a7f1c1e9577bbf56a1347bd5c01bb8ea14
iuc
parents:
diff
changeset
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51 --protein_output 'amrfinderplus_protein_output.fasta' |
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d06eb6832e26
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 73f592a7f1c1e9577bbf56a1347bd5c01bb8ea14
iuc
parents:
diff
changeset
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52 #end if |
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d06eb6832e26
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 73f592a7f1c1e9577bbf56a1347bd5c01bb8ea14
iuc
parents:
diff
changeset
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53 #*====================================== |
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d06eb6832e26
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 73f592a7f1c1e9577bbf56a1347bd5c01bb8ea14
iuc
parents:
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54 ORGANISM PART |
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d06eb6832e26
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 73f592a7f1c1e9577bbf56a1347bd5c01bb8ea14
iuc
parents:
diff
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55 ======================================*# |
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d06eb6832e26
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 73f592a7f1c1e9577bbf56a1347bd5c01bb8ea14
iuc
parents:
diff
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56 #if $organism_options.organism_conditionnal.organism_select |
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d06eb6832e26
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 73f592a7f1c1e9577bbf56a1347bd5c01bb8ea14
iuc
parents:
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57 --organism '$organism_options.organism_conditionnal.organism' |
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d06eb6832e26
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 73f592a7f1c1e9577bbf56a1347bd5c01bb8ea14
iuc
parents:
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58 #if $organism_options.organism_conditionnal.mutation_all |
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d06eb6832e26
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 73f592a7f1c1e9577bbf56a1347bd5c01bb8ea14
iuc
parents:
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59 $organism_options.organism_conditionnal.mutation_all 'mutation_all_report.tsv' |
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d06eb6832e26
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 73f592a7f1c1e9577bbf56a1347bd5c01bb8ea14
iuc
parents:
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60 #end if |
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d06eb6832e26
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 73f592a7f1c1e9577bbf56a1347bd5c01bb8ea14
iuc
parents:
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61 #if $options.plus |
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d06eb6832e26
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 73f592a7f1c1e9577bbf56a1347bd5c01bb8ea14
iuc
parents:
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62 $organism_options.organism_conditionnal.report_common |
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d06eb6832e26
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 73f592a7f1c1e9577bbf56a1347bd5c01bb8ea14
iuc
parents:
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63 #end if |
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d06eb6832e26
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 73f592a7f1c1e9577bbf56a1347bd5c01bb8ea14
iuc
parents:
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64 #end if |
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d06eb6832e26
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 73f592a7f1c1e9577bbf56a1347bd5c01bb8ea14
iuc
parents:
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65 #*====================================== |
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d06eb6832e26
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 73f592a7f1c1e9577bbf56a1347bd5c01bb8ea14
iuc
parents:
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66 OPTIONS |
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d06eb6832e26
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 73f592a7f1c1e9577bbf56a1347bd5c01bb8ea14
iuc
parents:
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67 ======================================*# |
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d06eb6832e26
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 73f592a7f1c1e9577bbf56a1347bd5c01bb8ea14
iuc
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68 --ident_min '$options.ident_min' |
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d06eb6832e26
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 73f592a7f1c1e9577bbf56a1347bd5c01bb8ea14
iuc
parents:
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69 --coverage_min '$options.coverage_min' |
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d06eb6832e26
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 73f592a7f1c1e9577bbf56a1347bd5c01bb8ea14
iuc
parents:
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70 #if '$options.translation_table' |
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d06eb6832e26
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 73f592a7f1c1e9577bbf56a1347bd5c01bb8ea14
iuc
parents:
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71 --translation_table '$options.translation_table' |
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d06eb6832e26
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 73f592a7f1c1e9577bbf56a1347bd5c01bb8ea14
iuc
parents:
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72 #end if |
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d06eb6832e26
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 73f592a7f1c1e9577bbf56a1347bd5c01bb8ea14
iuc
parents:
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73 #if '$options.name' |
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d06eb6832e26
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 73f592a7f1c1e9577bbf56a1347bd5c01bb8ea14
iuc
parents:
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74 --name '$options.name' |
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d06eb6832e26
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 73f592a7f1c1e9577bbf56a1347bd5c01bb8ea14
iuc
parents:
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75 #end if |
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d06eb6832e26
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 73f592a7f1c1e9577bbf56a1347bd5c01bb8ea14
iuc
parents:
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76 $options.plus |
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d06eb6832e26
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 73f592a7f1c1e9577bbf56a1347bd5c01bb8ea14
iuc
parents:
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77 $options.report_all_equal |
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d06eb6832e26
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78 $options.print_node |
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79 --output 'amrfinderplus_report.tsv' |
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80 |
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81 ]]></command> |
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82 <inputs> |
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83 <!-- DB and file INPUT --> |
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84 <section name="input_option" title="Input/Output options" expanded="true"> |
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85 <param name="amrfinder_db_select" type="select" label="The amrfinderplus database"> |
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86 <options from_data_table="amrfinderplus_database"> |
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87 <validator message="No amrfinderplus database is available" type="no_options"/> |
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88 </options> |
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89 </param> |
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90 <conditional name="input_mode"> |
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91 <param name="input_select" type="select" label="Choose input type" help="Choose the type of files (nucleotide and/or protein to be analyzed)"> |
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92 <option value="nucleotide">Nucleotide</option> |
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93 <option value="protein">Protein</option> |
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94 <option value="nucl_prot">Nucleotide and Protein</option> |
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95 </param> |
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96 <when value="nucleotide"> |
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97 <expand macro="nucl_input" option="false"/> |
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98 <param argument="--nucleotide_flank5_size" optional="true" type="integer" min="0" value="0" label="5' flanking sequence size added with sequence match"/> |
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99 </when> |
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100 <when value="protein"> |
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101 <expand macro="prot_input" option="false"/> |
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102 <expand macro="annotation_type" option="true"/> |
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103 </when> |
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104 <when value="nucl_prot"> |
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105 <expand macro="nucl_input" option="false"/> |
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106 <expand macro="prot_input" option="false"/> |
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107 <expand macro="annotation_type" option="false"/> |
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108 <param argument="--nucleotide_flank5_size" optional="true" type="integer" min="0" value="0" label="5' flanking sequence size added with sequence match"/> |
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109 </when> |
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110 </conditional> |
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111 </section> |
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112 <!-- ORGANISM OPTIONS --> |
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113 <section name="organism_options" title="Organism options"> |
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114 <conditional name="organism_conditionnal"> |
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115 <param name="organism_select" type="select" label="Add organism specifications"> |
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116 <option value="" selected="true">No specifications</option> |
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117 <option value="add_organism">Add organism specifications</option> |
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118 </param> |
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119 <when value="add_organism"> |
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120 <param argument="--organism" type="select" optional="false" label="Taxonomy group point mutation" help="Choose a taxonomic group to point mutation screening"> |
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121 <option value="Acinetobacter_baumannii">Acinetobacter_baumannii</option> |
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122 <option value="Burkholderia_cepacia">Burkholderia_cepacia</option> |
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123 <option value="Burkholderia_pseudomallei">Burkholderia_pseudomallei</option> |
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124 <option value="Campylobacter">Campylobacter</option> |
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125 <option value="Citrobacter_freundii">Citrobacter_freundii</option> |
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126 <option value="Clostridioides_difficile">Clostridioides_difficile</option> |
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127 <option value="Enterobacter_cloacae">Enterobacter_cloacae</option> |
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128 <option value="Enterococcus_faecalis">Enterococcus_faecalis</option> |
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129 <option value="Enterococcus_faecium">Enterococcus_faecium</option> |
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130 <option value="Escherichia">Escherichia</option> |
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131 <option value="Klebsiella_aerogenes">Klebsiella_aerogenes</option> |
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132 <option value="Klebsiella_oxytoca">Klebsiella_oxytoca</option> |
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133 <option value="Klebsiella_pneumoniae">Klebsiella_pneumoniae</option> |
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134 <option value="Neisseria_gonorrhoeae">Neisseria_gonorrhoeae</option> |
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135 <option value="Neisseria_meningitidis">Neisseria_meningitidis</option> |
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136 <option value="Pseudomonas_aeruginosa">Pseudomonas_aeruginosa</option> |
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137 <option value="Salmonella">Salmonella</option> |
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138 <option value="Serratia_marcescens">Serratia_marcescens</option> |
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139 <option value="Staphylococcus_aureus">Staphylococcus_aureus</option> |
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140 <option value="Staphylococcus_pseudintermedius">Staphylococcus_pseudintermedius</option> |
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141 <option value="Streptococcus_agalactiae">Streptococcus_agalactiae</option> |
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142 <option value="Streptococcus_pneumoniae">Streptococcus_pneumoniae</option> |
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143 <option value="Streptococcus_pyogenes">Streptococcus_pyogenes</option> |
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144 <option value="Vibrio_cholerae">Vibrio_cholerae</option> |
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145 </param> |
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146 <param argument="--mutation_all" type="boolean" truevalue="--mutation_all" falsevalue="" label="Report genotypes at all locations screened for point mutations"/> |
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147 <param argument="--report_common" type="boolean" truevalue="--report_common" falsevalue="" |
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148 label="Report proteins common to a taxonomy group (need the plus and organism options)"/> |
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149 </when> |
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150 <when value=""> |
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151 </when> |
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152 </conditional> |
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153 </section> |
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154 <!-- OPTIONS --> |
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155 <section name="options" title="Options"> |
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156 <param argument="--ident_min" type="float" min="-1" max="1" value="-1" label="Minimum identity" |
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157 help="Minimum proportion of identical amino acids in alignment. -1 means use a curated threshold if it exists and 0.9 otherwise (default: -1)"/> |
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158 <param argument="--coverage_min" type="float" min="0" max="1" value="0.5" label="Minimum coverage" |
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159 help="Minimum coverage of the reference protein (0 to 1, default: 0.5)"/> |
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160 <param argument="--translation_table" type="select" optional="true" label="Translation table" help="NCBI genetic code for translated BLAST (default: bacterial table 11)"> |
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161 <option value="1">1 Standard code</option> |
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162 <option value="2">2 Vertebrate mitochondrial</option> |
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163 <option value="3">3 Yeast mitochondrial</option> |
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164 <option value="4">4 Mold, Protozoan, and Coelenterate Mitochondrial and the Mycoplasma/Spiroplasma</option> |
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165 <option value="5">5 Invertebrate mitochondrial</option> |
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166 <option value="6">6 Ciliate, dasycladacean and hexamita nuclear</option> |
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167 <option value="9">9 Echinoderm and flatworm mitochondrial</option> |
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168 <option value="10">10 Euplotid nuclear</option> |
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169 <option value="11" selected="true">11 Bacterial, Archaeal and Plant Plastid</option> |
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170 <option value="12">12 Alternative yeast nuclear</option> |
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171 <option value="13">13 Ascidian mitochondrial</option> |
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172 <option value="14">14 Alternative flatworm mitochondrial</option> |
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173 <option value="16">16 Chlorophycean mitochondrial</option> |
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174 <option value="21">21 Trematode Mitochondrial</option> |
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175 <option value="22">22 Scenedesmus obliquus Mitochondrial</option> |
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176 <option value="23">23 Thraustochytrium Mitochondrial</option> |
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177 <option value="24">24 Rhabdopleuridae Mitochondrial</option> |
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178 <option value="25">25 Candidate Division SR1 and Gracilibacteria</option> |
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179 <option value="26">26 Pachysolen tannophilus Nuclear</option> |
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180 <option value="27">27 Karyorelict Nuclear</option> |
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181 <option value="28">28 Condylostoma Nuclear</option> |
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182 <option value="29">29 Mesodinium nuclear</option> |
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183 <option value="30">30 Peritrich nuclear</option> |
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184 <option value="31">31 Blastocrithidia nuclear</option> |
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185 <option value="33">33 Cephalodiscidae mitochondrial</option> |
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186 </param> |
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187 <param argument="--plus" type="boolean" truevalue="--plus" falsevalue="" label="Add the plus genes to the report"/> |
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188 <param argument="--report_all_equal" type="boolean" truevalue="--report_all_equal" falsevalue="" label="Report all equally-scoring BLAST and HMM matches"/> |
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189 <param argument="--print_node" type="boolean" truevalue="--print_node" falsevalue="" label="print hierarchy node (family)"/> |
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190 <param argument="--name" type="text" label="First column name" help="Text to be added as the first column 'name' to all rows of the report"/> |
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191 </section> |
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192 </inputs> |
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193 <outputs> |
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194 <data name="amrfinderplus_report" format="tabular" from_work_dir="amrfinderplus_report.tsv" label="${tool.name} on ${on_string}: AMRFinderPlus report"/> |
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195 <data name="mutation_all_report" format="tabular" from_work_dir="mutation_all_report.tsv" label="${tool.name} on ${on_string}: Point mutation report"> |
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196 <filter> organism_options['organism_conditionnal']['organism_select'] == "add_organism" and organism_options['organism_conditionnal']['mutation_all'] is True </filter> |
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197 </data> |
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198 <data name="protein_output" format="fasta" from_work_dir="amrfinderplus_protein_output.fasta" label="${tool.name} on ${on_string}: Protein identified sequences"> |
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199 <filter> input_option['input_mode']['input_select'] in ['protein', 'nucl_prot']</filter> |
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200 </data> |
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201 <data name="nucleotide_output" format="fasta" from_work_dir="amrfinderplus_nucleotide_output.fasta" label="${tool.name} on ${on_string}: Nucleotide identified sequences"> |
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202 <filter> input_option['input_mode']['input_select'] in ['nucleotide', 'nucl_prot'] </filter> |
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203 </data> |
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204 <data name="nucleotide_flank5_output" format="fasta" from_work_dir="amrfinderplus_flanking_sequence_output.fasta" |
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205 label="${tool.name} on ${on_string}: Nucleotide sequences with 5' flanking regions"> |
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206 <filter> input_option['input_mode']['input_select'] in ['nucleotide', 'nucl_prot'] and input_option['input_mode']['nucleotide_flank5_size'] != 0 </filter> |
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207 </data> |
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208 </outputs> |
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209 <tests> |
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210 <test expect_num_outputs="2"> <!-- TEST_1 simple nucleotide input --> |
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211 <section name="input_option"> |
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212 <param name="amrfinder_db_select" value="V3.11.1-2023-04-17.1"/> |
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213 <conditional name="input_mode"> |
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214 <param name="input_select" value="nucleotide"/> |
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215 <param name="nucleotide_input" value="enterococcus_faecalis.fna"/> |
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216 </conditional> |
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217 </section> |
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218 <output name="amrfinderplus_report" value="test_1/amrfinderplus_results.tsv" ftype="tabular" lines_diff="1"/> |
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219 <output name="nucleotide_output" value="test_1/amrfinderplus_nucleotide_output.fasta" ftype="fasta" lines_diff="1"/> |
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220 </test> |
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221 <test expect_num_outputs="3"> <!-- TEST_2 nucleotide input and full options --> |
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0
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222 <section name="input_option"> |
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223 <param name="amrfinder_db_select" value="V3.11.1-2023-04-17.1"/> |
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224 <conditional name="input_mode"> |
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225 <param name="input_select" value="nucleotide"/> |
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226 <param name="nucleotide_input" value="enterococcus_faecalis.fna"/> |
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227 <param name="nucleotide_flank5_size" value="150"/> |
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228 </conditional> |
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229 </section> |
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230 <section name="organism_options"> |
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231 <conditional name="organism_conditionnal"> |
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232 <param name="organism_select" value="add_organism"/> |
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233 <param name="organism" value="Enterococcus_faecalis"/> |
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234 <param name="report_common" value="true"/> |
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235 </conditional> |
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236 </section> |
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237 <section name="options"> |
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238 <param name="ident_min" value="1"/> |
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239 <param name="coverage_min" value="0.1"/> |
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240 <param name="translation_table" value="11"/> |
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241 <param name="plus" value="true"/> |
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242 <param name="report_all_equal" value="true"/> |
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243 <param name="print_node" value="true"/> |
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244 <param name="name" value="test_2"/> |
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245 <param name="log" value="true"/> |
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246 </section> |
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247 <output name="amrfinderplus_report" value="test_2/amrfinderplus_results.tsv" ftype="tabular" lines_diff="1"/> |
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248 <output name="nucleotide_output" value="test_2/amrfinderplus_nucleotide_output.fasta" ftype="fasta" lines_diff="1"/> |
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249 <output name="nucleotide_flank5_output" value="test_2/amrfinderplus_flanking_output.fasta" ftype="fasta" lines_diff="1"/> |
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250 </test> |
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251 <test expect_num_outputs="2"> <!-- TEST_3 nucleotide input and several options --> |
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252 <section name="input_option"> |
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253 <param name="amrfinder_db_select" value="V3.11.1-2023-04-17.1"/> |
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254 <conditional name="input_mode"> |
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255 <param name="input_select" value="nucleotide"/> |
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256 <param name="nucleotide_input" value="enterococcus_faecalis.fna"/> |
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257 </conditional> |
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258 </section> |
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259 <section name="organism_options"> |
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260 <conditional name="organism_conditionnal"> |
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261 <param name="organism_select" value="add_organism"/> |
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262 <param name="organism" value="Enterococcus_faecalis"/> |
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263 <param name="report_common" value="true"/> |
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264 </conditional> |
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265 </section> |
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266 <section name="options"> |
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267 <param name="report_all_equal" value="true"/> |
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268 </section> |
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269 <output name="amrfinderplus_report" value="test_3/amrfinderplus_results.tsv" ftype="tabular" lines_diff="1"/> |
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270 <output name="nucleotide_output" value="test_3/amrfinderplus_nucleotide_output.fasta" ftype="fasta" lines_diff="1"/> |
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271 </test> |
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272 <test expect_num_outputs="2"> <!-- TEST_4 simple protein input --> |
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273 <section name="input_option"> |
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274 <param name="amrfinder_db_select" value="V3.11.1-2023-04-17.1"/> |
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275 <conditional name="input_mode"> |
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276 <param name="input_select" value="protein"/> |
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277 <param name="protein_input" value="enterococcus_faecalis.faa"/> |
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278 </conditional> |
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279 </section> |
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280 <output name="amrfinderplus_report" value="test_4/amrfinderplus_results.tsv" ftype="tabular" lines_diff="1"/> |
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281 <output name="protein_output" value="test_4/amrfinderplus_protein_output.fasta" ftype="fasta" lines_diff="1"/> |
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282 </test> |
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1
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283 <test expect_num_outputs="2"> <!-- TEST_5 protein input and full options to gff3 and bakta --> |
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0
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284 <section name="input_option"> |
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285 <param name="amrfinder_db_select" value="V3.11.1-2023-04-17.1"/> |
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286 <conditional name="input_mode"> |
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287 <param name="input_select" value="protein"/> |
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288 <param name="protein_input" value="enterococcus_faecalis.faa"/> |
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289 <param name="gff_annotation" value="enterococcus_faecalis_bakta.gff3"/> |
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290 <param name="annotation_format" value="bakta"/> |
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291 </conditional> |
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292 </section> |
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293 <section name="organism_options"> |
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294 <conditional name="organism_conditionnal"> |
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295 <param name="organism_select" value="add_organism"/> |
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296 <param name="organism" value="Enterococcus_faecalis"/> |
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297 <param name="report_common" value="true"/> |
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298 </conditional> |
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299 </section> |
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300 <section name="options"> |
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301 <param name="ident_min" value="0.1"/> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 73f592a7f1c1e9577bbf56a1347bd5c01bb8ea14
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302 <param name="coverage_min" value="0.4"/> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 73f592a7f1c1e9577bbf56a1347bd5c01bb8ea14
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303 <param name="translation_table" value="11"/> |
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d06eb6832e26
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 73f592a7f1c1e9577bbf56a1347bd5c01bb8ea14
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304 <param name="plus" value="true"/> |
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d06eb6832e26
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 73f592a7f1c1e9577bbf56a1347bd5c01bb8ea14
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305 <param name="report_all_equal" value="true"/> |
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d06eb6832e26
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 73f592a7f1c1e9577bbf56a1347bd5c01bb8ea14
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306 <param name="print_node" value="true"/> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 73f592a7f1c1e9577bbf56a1347bd5c01bb8ea14
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307 <param name="name" value="test_5"/> |
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d06eb6832e26
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 73f592a7f1c1e9577bbf56a1347bd5c01bb8ea14
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308 </section> |
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d06eb6832e26
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 73f592a7f1c1e9577bbf56a1347bd5c01bb8ea14
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309 <output name="amrfinderplus_report" value="test_5/amrfinderplus_results.tsv" ftype="tabular" lines_diff="1"/> |
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d06eb6832e26
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 73f592a7f1c1e9577bbf56a1347bd5c01bb8ea14
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310 <output name="protein_output" value="test_5/amrfinderplus_nucleotide_output.fasta" ftype="fasta" lines_diff="1"/> |
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d06eb6832e26
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 73f592a7f1c1e9577bbf56a1347bd5c01bb8ea14
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311 </test> |
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d06eb6832e26
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 73f592a7f1c1e9577bbf56a1347bd5c01bb8ea14
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312 <test expect_num_outputs="2"> <!-- TEST_6 protein input and prokka annotation --> |
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d06eb6832e26
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 73f592a7f1c1e9577bbf56a1347bd5c01bb8ea14
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313 <section name="input_option"> |
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d06eb6832e26
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 73f592a7f1c1e9577bbf56a1347bd5c01bb8ea14
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314 <param name="amrfinder_db_select" value="V3.11.1-2023-04-17.1"/> |
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d06eb6832e26
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 73f592a7f1c1e9577bbf56a1347bd5c01bb8ea14
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315 <conditional name="input_mode"> |
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d06eb6832e26
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 73f592a7f1c1e9577bbf56a1347bd5c01bb8ea14
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316 <param name="input_select" value="protein"/> |
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d06eb6832e26
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 73f592a7f1c1e9577bbf56a1347bd5c01bb8ea14
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317 <param name="protein_input" value="PROKKA_05252023.faa"/> |
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d06eb6832e26
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 73f592a7f1c1e9577bbf56a1347bd5c01bb8ea14
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318 <param name="gff_annotation" value="PROKKA_05252023.gff"/> |
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d06eb6832e26
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 73f592a7f1c1e9577bbf56a1347bd5c01bb8ea14
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319 <param name="annotation_format" value="prokka"/> |
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d06eb6832e26
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 73f592a7f1c1e9577bbf56a1347bd5c01bb8ea14
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320 </conditional> |
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d06eb6832e26
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321 </section> |
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d06eb6832e26
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 73f592a7f1c1e9577bbf56a1347bd5c01bb8ea14
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322 <output name="amrfinderplus_report" value="test_6/amrfinderplus_results.tsv" ftype="tabular" lines_diff="1"/> |
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d06eb6832e26
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 73f592a7f1c1e9577bbf56a1347bd5c01bb8ea14
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323 <output name="protein_output" value="test_6/amrfinderplus_protein_output.fasta" ftype="fasta" lines_diff="1"/> |
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d06eb6832e26
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 73f592a7f1c1e9577bbf56a1347bd5c01bb8ea14
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324 </test> |
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d06eb6832e26
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 73f592a7f1c1e9577bbf56a1347bd5c01bb8ea14
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325 <test expect_num_outputs="2"> <!-- TEST_7 protein input and genbank default annotation --> |
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d06eb6832e26
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 73f592a7f1c1e9577bbf56a1347bd5c01bb8ea14
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326 <section name="input_option"> |
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d06eb6832e26
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 73f592a7f1c1e9577bbf56a1347bd5c01bb8ea14
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327 <param name="amrfinder_db_select" value="V3.11.1-2023-04-17.1"/> |
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d06eb6832e26
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 73f592a7f1c1e9577bbf56a1347bd5c01bb8ea14
iuc
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328 <conditional name="input_mode"> |
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d06eb6832e26
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 73f592a7f1c1e9577bbf56a1347bd5c01bb8ea14
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329 <param name="input_select" value="protein"/> |
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d06eb6832e26
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 73f592a7f1c1e9577bbf56a1347bd5c01bb8ea14
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330 <param name="protein_input" value="input_ncbi.faa"/> |
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d06eb6832e26
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 73f592a7f1c1e9577bbf56a1347bd5c01bb8ea14
iuc
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331 <param name="gff_annotation" value="annotation_ncbi.gff3"/> |
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d06eb6832e26
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 73f592a7f1c1e9577bbf56a1347bd5c01bb8ea14
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332 </conditional> |
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d06eb6832e26
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333 </section> |
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d06eb6832e26
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334 <output name="amrfinderplus_report" value="test_7/amrfinderplus_results.tsv" ftype="tabular" lines_diff="1"/> |
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d06eb6832e26
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 73f592a7f1c1e9577bbf56a1347bd5c01bb8ea14
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335 <output name="protein_output" value="test_7/amrfinderplus_protein_output.fasta" ftype="fasta" lines_diff="1"/> |
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d06eb6832e26
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 73f592a7f1c1e9577bbf56a1347bd5c01bb8ea14
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336 </test> |
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1
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diff
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337 <test expect_num_outputs="3"> <!-- TEST_8 both protein and nucleotide input --> |
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0
d06eb6832e26
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 73f592a7f1c1e9577bbf56a1347bd5c01bb8ea14
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338 <section name="input_option"> |
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d06eb6832e26
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 73f592a7f1c1e9577bbf56a1347bd5c01bb8ea14
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339 <param name="amrfinder_db_select" value="V3.11.1-2023-04-17.1"/> |
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d06eb6832e26
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 73f592a7f1c1e9577bbf56a1347bd5c01bb8ea14
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340 <conditional name="input_mode"> |
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d06eb6832e26
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 73f592a7f1c1e9577bbf56a1347bd5c01bb8ea14
iuc
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341 <param name="input_select" value="nucl_prot"/> |
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d06eb6832e26
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 73f592a7f1c1e9577bbf56a1347bd5c01bb8ea14
iuc
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342 <param name="protein_input" value="enterococcus_faecalis.faa"/> |
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d06eb6832e26
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 73f592a7f1c1e9577bbf56a1347bd5c01bb8ea14
iuc
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343 <param name="nucleotide_input" value="enterococcus_faecalis.fna"/> |
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d06eb6832e26
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 73f592a7f1c1e9577bbf56a1347bd5c01bb8ea14
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344 <param name="gff_annotation" value="enterococcus_faecalis_bakta.gff3"/> |
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345 <param name="annotation_format" value="bakta"/> |
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d06eb6832e26
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 73f592a7f1c1e9577bbf56a1347bd5c01bb8ea14
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346 </conditional> |
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d06eb6832e26
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347 </section> |
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d06eb6832e26
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348 <section name="organism_options"> |
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349 <conditional name="organism_conditionnal"> |
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d06eb6832e26
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 73f592a7f1c1e9577bbf56a1347bd5c01bb8ea14
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350 <param name="organism_select" value="add_organism"/> |
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d06eb6832e26
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 73f592a7f1c1e9577bbf56a1347bd5c01bb8ea14
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351 <param name="organism" value="Enterococcus_faecalis"/> |
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d06eb6832e26
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 73f592a7f1c1e9577bbf56a1347bd5c01bb8ea14
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352 </conditional> |
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d06eb6832e26
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353 </section> |
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d06eb6832e26
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354 <output name="amrfinderplus_report" value="test_8/amrfinderplus_results.tsv" ftype="tabular" lines_diff="1"/> |
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d06eb6832e26
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 73f592a7f1c1e9577bbf56a1347bd5c01bb8ea14
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355 <output name="protein_output" value="test_8/amrfinderplus_protein_output.fasta" ftype="fasta" lines_diff="1"/> |
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d06eb6832e26
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 73f592a7f1c1e9577bbf56a1347bd5c01bb8ea14
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356 <output name="nucleotide_output" value="test_8/amrfinderplus_nucleotide_output.fasta" ftype="fasta" lines_diff="1"/> |
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1
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357 </test> |
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358 <test expect_num_outputs="4"> <!-- TEST_9 rast annotation and mutation all results --> |
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ff401a72560b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit a93148583b30aebf45c816a5d671e710aeff6fbf
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359 <section name="input_option"> |
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ff401a72560b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit a93148583b30aebf45c816a5d671e710aeff6fbf
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360 <param name="amrfinder_db_select" value="V3.11.1-2023-04-17.1"/> |
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ff401a72560b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit a93148583b30aebf45c816a5d671e710aeff6fbf
iuc
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361 <conditional name="input_mode"> |
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ff401a72560b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit a93148583b30aebf45c816a5d671e710aeff6fbf
iuc
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362 <param name="input_select" value="nucl_prot"/> |
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ff401a72560b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit a93148583b30aebf45c816a5d671e710aeff6fbf
iuc
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363 <param name="protein_input" value="e_faecalis_rast.faa"/> |
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ff401a72560b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit a93148583b30aebf45c816a5d671e710aeff6fbf
iuc
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364 <param name="nucleotide_input" value="e_faecalis_rast.fna"/> |
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ff401a72560b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit a93148583b30aebf45c816a5d671e710aeff6fbf
iuc
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365 <param name="gff_annotation" value="e_faecalis_rast.gff"/> |
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ff401a72560b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit a93148583b30aebf45c816a5d671e710aeff6fbf
iuc
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366 <param name="annotation_format" value="rast"/> |
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ff401a72560b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit a93148583b30aebf45c816a5d671e710aeff6fbf
iuc
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367 </conditional> |
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iuc
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368 </section> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit a93148583b30aebf45c816a5d671e710aeff6fbf
iuc
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369 <section name="organism_options"> |
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ff401a72560b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit a93148583b30aebf45c816a5d671e710aeff6fbf
iuc
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370 <conditional name="organism_conditionnal"> |
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ff401a72560b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit a93148583b30aebf45c816a5d671e710aeff6fbf
iuc
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371 <param name="organism_select" value="add_organism"/> |
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ff401a72560b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit a93148583b30aebf45c816a5d671e710aeff6fbf
iuc
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372 <param name="organism" value="Enterococcus_faecalis"/> |
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ff401a72560b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit a93148583b30aebf45c816a5d671e710aeff6fbf
iuc
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373 <param name="mutation_all" value="true"/> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit a93148583b30aebf45c816a5d671e710aeff6fbf
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374 </conditional> |
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375 </section> |
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376 <section name="options"> |
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ff401a72560b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit a93148583b30aebf45c816a5d671e710aeff6fbf
iuc
parents:
0
diff
changeset
|
377 <param name="ident_min" value="0.1"/> |
|
ff401a72560b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit a93148583b30aebf45c816a5d671e710aeff6fbf
iuc
parents:
0
diff
changeset
|
378 <param name="coverage_min" value="0.1"/> |
|
ff401a72560b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit a93148583b30aebf45c816a5d671e710aeff6fbf
iuc
parents:
0
diff
changeset
|
379 <param name="plus" value="true"/> |
|
ff401a72560b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit a93148583b30aebf45c816a5d671e710aeff6fbf
iuc
parents:
0
diff
changeset
|
380 <param name="print_node" value="true"/> |
|
ff401a72560b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit a93148583b30aebf45c816a5d671e710aeff6fbf
iuc
parents:
0
diff
changeset
|
381 <param name="name" value="test_5"/> |
|
ff401a72560b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit a93148583b30aebf45c816a5d671e710aeff6fbf
iuc
parents:
0
diff
changeset
|
382 </section> |
|
ff401a72560b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit a93148583b30aebf45c816a5d671e710aeff6fbf
iuc
parents:
0
diff
changeset
|
383 <output name="amrfinderplus_report" value="test_9/amrfinderplus_results.tsv" ftype="tabular" lines_diff="1"/> |
|
ff401a72560b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit a93148583b30aebf45c816a5d671e710aeff6fbf
iuc
parents:
0
diff
changeset
|
384 <output name="protein_output" value="test_9/amrfinderplus_protein_output.fasta" ftype="fasta" lines_diff="1"/> |
|
ff401a72560b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit a93148583b30aebf45c816a5d671e710aeff6fbf
iuc
parents:
0
diff
changeset
|
385 <output name="nucleotide_output" value="test_9/amrfinderplus_nucleotide_output.fasta" ftype="fasta" lines_diff="1"/> |
|
ff401a72560b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit a93148583b30aebf45c816a5d671e710aeff6fbf
iuc
parents:
0
diff
changeset
|
386 <output name="mutation_all_report" value="test_9/amrfinderplus_mutation_all.tsv" ftype="tabular" lines_diff="1"/> |
|
0
d06eb6832e26
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 73f592a7f1c1e9577bbf56a1347bd5c01bb8ea14
iuc
parents:
diff
changeset
|
387 </test> |
|
d06eb6832e26
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 73f592a7f1c1e9577bbf56a1347bd5c01bb8ea14
iuc
parents:
diff
changeset
|
388 </tests> |
|
d06eb6832e26
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 73f592a7f1c1e9577bbf56a1347bd5c01bb8ea14
iuc
parents:
diff
changeset
|
389 <help><![CDATA[ |
|
d06eb6832e26
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 73f592a7f1c1e9577bbf56a1347bd5c01bb8ea14
iuc
parents:
diff
changeset
|
390 **What it does** |
|
d06eb6832e26
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 73f592a7f1c1e9577bbf56a1347bd5c01bb8ea14
iuc
parents:
diff
changeset
|
391 |
|
d06eb6832e26
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 73f592a7f1c1e9577bbf56a1347bd5c01bb8ea14
iuc
parents:
diff
changeset
|
392 AMRFinderPlus is a tool to find acquired antimicrobial resistance genes and point mutations in protein and/or assembled nucleotide sequences. |
|
d06eb6832e26
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 73f592a7f1c1e9577bbf56a1347bd5c01bb8ea14
iuc
parents:
diff
changeset
|
393 |
|
d06eb6832e26
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 73f592a7f1c1e9577bbf56a1347bd5c01bb8ea14
iuc
parents:
diff
changeset
|
394 **Input file analysis** |
|
d06eb6832e26
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 73f592a7f1c1e9577bbf56a1347bd5c01bb8ea14
iuc
parents:
diff
changeset
|
395 |
|
d06eb6832e26
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 73f592a7f1c1e9577bbf56a1347bd5c01bb8ea14
iuc
parents:
diff
changeset
|
396 AMRFinderPlus can check in nucleotide and/or protein fasta file |
|
d06eb6832e26
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 73f592a7f1c1e9577bbf56a1347bd5c01bb8ea14
iuc
parents:
diff
changeset
|
397 When protein file is provided, sensitivity is higher if you add an annotation file |
|
d06eb6832e26
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 73f592a7f1c1e9577bbf56a1347bd5c01bb8ea14
iuc
parents:
diff
changeset
|
398 |
|
d06eb6832e26
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 73f592a7f1c1e9577bbf56a1347bd5c01bb8ea14
iuc
parents:
diff
changeset
|
399 **Organism options** |
|
d06eb6832e26
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 73f592a7f1c1e9577bbf56a1347bd5c01bb8ea14
iuc
parents:
diff
changeset
|
400 |
|
d06eb6832e26
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 73f592a7f1c1e9577bbf56a1347bd5c01bb8ea14
iuc
parents:
diff
changeset
|
401 With organism informations AMRFinderPlus screens known resistance causing point mutations and blacklisting of common, non-informative genes. |
|
d06eb6832e26
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 73f592a7f1c1e9577bbf56a1347bd5c01bb8ea14
iuc
parents:
diff
changeset
|
402 |
|
d06eb6832e26
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 73f592a7f1c1e9577bbf56a1347bd5c01bb8ea14
iuc
parents:
diff
changeset
|
403 The **mutation_all** option make a new output file containing all detected variants from the reference sequence. |
|
d06eb6832e26
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 73f592a7f1c1e9577bbf56a1347bd5c01bb8ea14
iuc
parents:
diff
changeset
|
404 |
|
d06eb6832e26
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 73f592a7f1c1e9577bbf56a1347bd5c01bb8ea14
iuc
parents:
diff
changeset
|
405 This file allows you to distinguish between called point mutations that were the sensitive variant and the point mutations that could not be called because the sequence was not found. |
|
d06eb6832e26
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 73f592a7f1c1e9577bbf56a1347bd5c01bb8ea14
iuc
parents:
diff
changeset
|
406 |
|
d06eb6832e26
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 73f592a7f1c1e9577bbf56a1347bd5c01bb8ea14
iuc
parents:
diff
changeset
|
407 +---------------------------------+------------------+-----------------------------+------------------------------------------------------------+ |
|
d06eb6832e26
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 73f592a7f1c1e9577bbf56a1347bd5c01bb8ea14
iuc
parents:
diff
changeset
|
408 | Organism option | Point mutations | Blacklisted plus genes | Notes | |
|
d06eb6832e26
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 73f592a7f1c1e9577bbf56a1347bd5c01bb8ea14
iuc
parents:
diff
changeset
|
409 +=================================+==================+=============================+============================================================+ |
|
d06eb6832e26
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 73f592a7f1c1e9577bbf56a1347bd5c01bb8ea14
iuc
parents:
diff
changeset
|
410 | Acinetobacter_baumannii | X | | Use for the A. baumannii-calcoaceticus species complex | |
|
d06eb6832e26
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 73f592a7f1c1e9577bbf56a1347bd5c01bb8ea14
iuc
parents:
diff
changeset
|
411 +---------------------------------+------------------+-----------------------------+------------------------------------------------------------+ |
|
d06eb6832e26
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 73f592a7f1c1e9577bbf56a1347bd5c01bb8ea14
iuc
parents:
diff
changeset
|
412 | Burkholderia_cepacia | X | | Use for the Burkholderia cepacia species complex | |
|
d06eb6832e26
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 73f592a7f1c1e9577bbf56a1347bd5c01bb8ea14
iuc
parents:
diff
changeset
|
413 +---------------------------------+------------------+-----------------------------+------------------------------------------------------------+ |
|
d06eb6832e26
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 73f592a7f1c1e9577bbf56a1347bd5c01bb8ea14
iuc
parents:
diff
changeset
|
414 | Burkholderia_pseudomallei | X | | Use for the Burkholderia pseudomallei species complex | |
|
d06eb6832e26
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 73f592a7f1c1e9577bbf56a1347bd5c01bb8ea14
iuc
parents:
diff
changeset
|
415 +---------------------------------+------------------+-----------------------------+------------------------------------------------------------+ |
|
d06eb6832e26
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 73f592a7f1c1e9577bbf56a1347bd5c01bb8ea14
iuc
parents:
diff
changeset
|
416 | Campylobacter | X | | Use for C. coli and C. jejuni | |
|
d06eb6832e26
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 73f592a7f1c1e9577bbf56a1347bd5c01bb8ea14
iuc
parents:
diff
changeset
|
417 +---------------------------------+------------------+-----------------------------+------------------------------------------------------------+ |
|
d06eb6832e26
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 73f592a7f1c1e9577bbf56a1347bd5c01bb8ea14
iuc
parents:
diff
changeset
|
418 | Citrobacter_freundii | X | | | |
|
d06eb6832e26
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 73f592a7f1c1e9577bbf56a1347bd5c01bb8ea14
iuc
parents:
diff
changeset
|
419 +---------------------------------+------------------+-----------------------------+------------------------------------------------------------+ |
|
d06eb6832e26
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 73f592a7f1c1e9577bbf56a1347bd5c01bb8ea14
iuc
parents:
diff
changeset
|
420 | Clostridioides_difficile | X | | | |
|
d06eb6832e26
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 73f592a7f1c1e9577bbf56a1347bd5c01bb8ea14
iuc
parents:
diff
changeset
|
421 +---------------------------------+------------------+-----------------------------+------------------------------------------------------------+ |
|
d06eb6832e26
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 73f592a7f1c1e9577bbf56a1347bd5c01bb8ea14
iuc
parents:
diff
changeset
|
422 | Enterobacter_cloacae | X | | | |
|
d06eb6832e26
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 73f592a7f1c1e9577bbf56a1347bd5c01bb8ea14
iuc
parents:
diff
changeset
|
423 +---------------------------------+------------------+-----------------------------+------------------------------------------------------------+ |
|
d06eb6832e26
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 73f592a7f1c1e9577bbf56a1347bd5c01bb8ea14
iuc
parents:
diff
changeset
|
424 | Enterococcus_faecalis | X | | | |
|
d06eb6832e26
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 73f592a7f1c1e9577bbf56a1347bd5c01bb8ea14
iuc
parents:
diff
changeset
|
425 +---------------------------------+------------------+-----------------------------+------------------------------------------------------------+ |
|
d06eb6832e26
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 73f592a7f1c1e9577bbf56a1347bd5c01bb8ea14
iuc
parents:
diff
changeset
|
426 | Enterococcus_faecium | X | | Use for E. hirae | |
|
d06eb6832e26
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 73f592a7f1c1e9577bbf56a1347bd5c01bb8ea14
iuc
parents:
diff
changeset
|
427 +---------------------------------+------------------+-----------------------------+------------------------------------------------------------+ |
|
d06eb6832e26
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 73f592a7f1c1e9577bbf56a1347bd5c01bb8ea14
iuc
parents:
diff
changeset
|
428 | Escherichia | X | X | Use for Shigella and Escherichia | |
|
d06eb6832e26
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 73f592a7f1c1e9577bbf56a1347bd5c01bb8ea14
iuc
parents:
diff
changeset
|
429 +---------------------------------+------------------+-----------------------------+------------------------------------------------------------+ |
|
d06eb6832e26
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 73f592a7f1c1e9577bbf56a1347bd5c01bb8ea14
iuc
parents:
diff
changeset
|
430 | Klebsiella_oxytoca | X | X | | |
|
d06eb6832e26
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 73f592a7f1c1e9577bbf56a1347bd5c01bb8ea14
iuc
parents:
diff
changeset
|
431 +---------------------------------+------------------+-----------------------------+------------------------------------------------------------+ |
|
d06eb6832e26
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 73f592a7f1c1e9577bbf56a1347bd5c01bb8ea14
iuc
parents:
diff
changeset
|
432 | Klebsiella_pneumoniae | X | X | Use for K. pneumoniae species complex and K. aerogenes | |
|
d06eb6832e26
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 73f592a7f1c1e9577bbf56a1347bd5c01bb8ea14
iuc
parents:
diff
changeset
|
433 +---------------------------------+------------------+-----------------------------+------------------------------------------------------------+ |
|
d06eb6832e26
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 73f592a7f1c1e9577bbf56a1347bd5c01bb8ea14
iuc
parents:
diff
changeset
|
434 | Neisseria_gonorrhoeae | X | | | |
|
d06eb6832e26
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 73f592a7f1c1e9577bbf56a1347bd5c01bb8ea14
iuc
parents:
diff
changeset
|
435 +---------------------------------+------------------+-----------------------------+------------------------------------------------------------+ |
|
d06eb6832e26
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 73f592a7f1c1e9577bbf56a1347bd5c01bb8ea14
iuc
parents:
diff
changeset
|
436 | Neisseria_meningitidis | X | | | |
|
d06eb6832e26
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 73f592a7f1c1e9577bbf56a1347bd5c01bb8ea14
iuc
parents:
diff
changeset
|
437 +---------------------------------+------------------+-----------------------------+------------------------------------------------------------+ |
|
d06eb6832e26
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 73f592a7f1c1e9577bbf56a1347bd5c01bb8ea14
iuc
parents:
diff
changeset
|
438 | Pseudomonas_aeruginosa | X | | | |
|
d06eb6832e26
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 73f592a7f1c1e9577bbf56a1347bd5c01bb8ea14
iuc
parents:
diff
changeset
|
439 +---------------------------------+------------------+-----------------------------+------------------------------------------------------------+ |
|
d06eb6832e26
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 73f592a7f1c1e9577bbf56a1347bd5c01bb8ea14
iuc
parents:
diff
changeset
|
440 | Salmonella | X | X | | |
|
d06eb6832e26
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 73f592a7f1c1e9577bbf56a1347bd5c01bb8ea14
iuc
parents:
diff
changeset
|
441 +---------------------------------+------------------+-----------------------------+------------------------------------------------------------+ |
|
d06eb6832e26
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 73f592a7f1c1e9577bbf56a1347bd5c01bb8ea14
iuc
parents:
diff
changeset
|
442 | Serratia_marcescens | X | | | |
|
d06eb6832e26
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 73f592a7f1c1e9577bbf56a1347bd5c01bb8ea14
iuc
parents:
diff
changeset
|
443 +---------------------------------+------------------+-----------------------------+------------------------------------------------------------+ |
|
d06eb6832e26
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 73f592a7f1c1e9577bbf56a1347bd5c01bb8ea14
iuc
parents:
diff
changeset
|
444 | Staphylococcus_aureus | X | | | |
|
d06eb6832e26
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 73f592a7f1c1e9577bbf56a1347bd5c01bb8ea14
iuc
parents:
diff
changeset
|
445 +---------------------------------+------------------+-----------------------------+------------------------------------------------------------+ |
|
d06eb6832e26
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 73f592a7f1c1e9577bbf56a1347bd5c01bb8ea14
iuc
parents:
diff
changeset
|
446 | Staphylococcus_pseudintermedius | X | X | | |
|
d06eb6832e26
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 73f592a7f1c1e9577bbf56a1347bd5c01bb8ea14
iuc
parents:
diff
changeset
|
447 +---------------------------------+------------------+-----------------------------+------------------------------------------------------------+ |
|
d06eb6832e26
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 73f592a7f1c1e9577bbf56a1347bd5c01bb8ea14
iuc
parents:
diff
changeset
|
448 | Streptococcus_agalactiae | X | | | |
|
d06eb6832e26
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 73f592a7f1c1e9577bbf56a1347bd5c01bb8ea14
iuc
parents:
diff
changeset
|
449 +---------------------------------+------------------+-----------------------------+------------------------------------------------------------+ |
|
d06eb6832e26
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 73f592a7f1c1e9577bbf56a1347bd5c01bb8ea14
iuc
parents:
diff
changeset
|
450 | Streptococcus_pneumoniae | X | | Use for S. pneumoniae and S. mitis | |
|
d06eb6832e26
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 73f592a7f1c1e9577bbf56a1347bd5c01bb8ea14
iuc
parents:
diff
changeset
|
451 +---------------------------------+------------------+-----------------------------+------------------------------------------------------------+ |
|
d06eb6832e26
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 73f592a7f1c1e9577bbf56a1347bd5c01bb8ea14
iuc
parents:
diff
changeset
|
452 | Streptococcus_pyogenes | X | | | |
|
d06eb6832e26
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 73f592a7f1c1e9577bbf56a1347bd5c01bb8ea14
iuc
parents:
diff
changeset
|
453 +---------------------------------+------------------+-----------------------------+------------------------------------------------------------+ |
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d06eb6832e26
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 73f592a7f1c1e9577bbf56a1347bd5c01bb8ea14
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454 | Vibrio_cholerae | X | | | |
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d06eb6832e26
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 73f592a7f1c1e9577bbf56a1347bd5c01bb8ea14
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455 +---------------------------------+------------------+-----------------------------+------------------------------------------------------------+ |
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d06eb6832e26
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 73f592a7f1c1e9577bbf56a1347bd5c01bb8ea14
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456 |
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d06eb6832e26
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 73f592a7f1c1e9577bbf56a1347bd5c01bb8ea14
iuc
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457 |
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d06eb6832e26
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 73f592a7f1c1e9577bbf56a1347bd5c01bb8ea14
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458 **Supplementary options** |
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d06eb6832e26
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 73f592a7f1c1e9577bbf56a1347bd5c01bb8ea14
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459 - *nucleotide 5' flanking size* to extract nucleotide matches and a range of nucleotide in 5' |
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d06eb6832e26
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 73f592a7f1c1e9577bbf56a1347bd5c01bb8ea14
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460 - *Minimum identity* to choose threshold in amino acids alignemnt. -1 for a high curation threshold. |
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d06eb6832e26
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 73f592a7f1c1e9577bbf56a1347bd5c01bb8ea14
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461 - *Minimum coverage* Coverage to protein alignment. |
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d06eb6832e26
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 73f592a7f1c1e9577bbf56a1347bd5c01bb8ea14
iuc
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462 - *Translation table* by default AMRFinderPlus work on bacteria but can be modified to some other Phyla. |
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d06eb6832e26
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 73f592a7f1c1e9577bbf56a1347bd5c01bb8ea14
iuc
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463 - *Plus* option provide more information related to virulence, stress response ... |
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d06eb6832e26
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 73f592a7f1c1e9577bbf56a1347bd5c01bb8ea14
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464 |
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d06eb6832e26
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 73f592a7f1c1e9577bbf56a1347bd5c01bb8ea14
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465 **Output files** |
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d06eb6832e26
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 73f592a7f1c1e9577bbf56a1347bd5c01bb8ea14
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466 |
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d06eb6832e26
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 73f592a7f1c1e9577bbf56a1347bd5c01bb8ea14
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467 AMRFinderPlus can generate some differents files : |
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d06eb6832e26
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 73f592a7f1c1e9577bbf56a1347bd5c01bb8ea14
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468 - The AMRFinderPlus report with identified protein, gene and AMR related informations. |
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d06eb6832e26
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 73f592a7f1c1e9577bbf56a1347bd5c01bb8ea14
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469 - A report with all detected variants from the reference sequence. |
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d06eb6832e26
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 73f592a7f1c1e9577bbf56a1347bd5c01bb8ea14
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470 - The protein and/ort nucleotide matched sequences. |
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d06eb6832e26
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 73f592a7f1c1e9577bbf56a1347bd5c01bb8ea14
iuc
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471 - Only when nucleotide a nucleotide fasta file could be provided with 5' flanking regions. |
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d06eb6832e26
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 73f592a7f1c1e9577bbf56a1347bd5c01bb8ea14
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472 |
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d06eb6832e26
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 73f592a7f1c1e9577bbf56a1347bd5c01bb8ea14
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473 |
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d06eb6832e26
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 73f592a7f1c1e9577bbf56a1347bd5c01bb8ea14
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474 ]]></help> |
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d06eb6832e26
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 73f592a7f1c1e9577bbf56a1347bd5c01bb8ea14
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475 <expand macro="citations"/> |
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d06eb6832e26
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 73f592a7f1c1e9577bbf56a1347bd5c01bb8ea14
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476 </tool> |