Mercurial > repos > iuc > integron_finder

annotate integron_finder.xml @ 2:392f100eebcd draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/integron_finder commit bf94533e76d4253a734333e33c2f14f6634f0e79
author iuc
date Sun, 25 Feb 2024 16:08:08 +0000
parents 4768f7f8e93f
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1 <tool id="integron_finder" name="Integron Finder" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
2
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2 <description>is a program that detects integrons in DNA sequences</description>
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3 <macros>
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4 <import>macro.xml</import>
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5 </macros>
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6 <expand macro="edam_info"/>
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7 <expand macro="xrefs"/>
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8 <expand macro="requirements"/>
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9 <command detect_errors="aggressive"><![CDATA[
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10 integron_finder
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11 '$sequence'
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12 --cpu @THREADS@
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13 --keep-tmp
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14 $local_max
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15 #if $type_replicon
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16 $type_replicon
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17 #end if
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18 #if $topology_file
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19 --topology-file '$topology_file'
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20 #end if
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21 $promoter_attI
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22 -dt $settings.attc_settings.dist_thresh
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23 --calin-threshold $settings.attc_settings.calin_threshold
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24 --max-attc-size $settings.attc_settings.max_attc_size
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25 --min-attc-size $settings.attc_settings.min_attc_size
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26 $settings.attc_settings.keep_palindromes
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27 #if $settings.attc_settings.covar_matrix
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28 --attc-model '$settings.attc_settings.covar_matrix'
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29 #end if
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30 $settings.protein_settings.no_proteins
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31 $settings.protein_settings.union_integrases
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32 $settings.protein_settings.func_annot
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33 $gbk
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34 $pdf
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35 && mv Results_Integron_Finder_* Results_Integron_Finder
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36 ]]></command>
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37 <inputs>
1
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38 <param type="data" name="sequence" format="fasta" label="Replicon file" help="Replicon can be entire chromosome, contif, PCR fragments...">
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39 <validator type="expression" message="Integron Finder has problems with large multi FASTA files. Please assembly your sequences or split them up into files smaller 10.000 sequences."><![CDATA[value is not None and value.metadata.sequences <= 10000]]></validator>
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40 </param>
2
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41 <param argument="--local-max" type="boolean" checked="false" truevalue="--local-max" falsevalue="" label="Thorough local detection" help="This option allows a more sensitive search. I will be slower (dependant on the number of hits) if integrons are found, but will be as fast if nothing is detected and will not increase the false positive rate." />
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42 <param name="type_replicon" type="select" optional="true" label="Default replicons topology" help="Set the default topology for replicons, linear, circular (deault: no topology)">
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43 <option value="--linear">linear (--linear)</option>
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44 <option value="--circ">circular (--circ)</option>
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45 </param>
2
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46 <param argument="--topology-file" type="data" format="txt" optional="true" label="Select a topology file from your history"/>
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47 <param argument="--promoter-attI" type="boolean" checked="false" truevalue="--promoter-attI" falsevalue="" label="Search also for promoter and attI sites?" />
0
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48 <param argument="--gbk" type="boolean" checked="false" truevalue="--gbk" falsevalue="" label="Genbank output?" help="Generate a GenBank file with the sequence annotated with the same annotations than .integrons file."/>
2
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49 <param argument="--pdf" type="boolean" checked="false" truevalue="--pdf" falsevalue="" label="PDF output?" help="For each complete integron, a simple graphic of the region is depicted (in pdf format)"/>
0
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50 <section name="settings" title="Advanced Parameters" expanded="False">
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51 <section name="attc_settings" title="Attc options" expanded="False">
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52 <param name="dist_thresh" argument="--distance-thresh" type="integer" value="4000" label="Threshold for clustering (in base)" min="0" help="By default, to cluster an array of attC sites and an integron integrase, they must be less than 4 kb apart. You can here change this value." />
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53 <param name="calin_threshold" type="integer" value="2" label="Threshold to filter CALIN" min="0" help="Keep 'CALIN' only if attC sites number >= calin-threshold" />
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54 <param name="max_attc_size" type="integer" value="200" label="Maximum value for attC size" min="0"/>
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55 <param name="min_attc_size" type="integer" value="40" label="Minimum value for attC size" min="0" />
2
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56 <param argument="--keep-palindromes" type="boolean" checked="false" truevalue="--keep-palindromes" falsevalue="" label="Keep palindromes with the highest evalue" help="For a given hit, if the palindromic version is found, don't remove the one with highest evalue"/>
0
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57 <param name="covar_matrix" argument="--attc-model" type="data" optional="true" format="txt" label="Covariance Matrix" />
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58 </section>
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59 <section name="protein_settings" title="Protein options" expanded="False">
2
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60 <param argument="--no-proteins" type="boolean" checked="false" truevalue="--no-proteins" falsevalue="" label="Just look for attC sites" help="When enabled, it does not annotate CDS and does not find integrase."/>
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61 <param argument="--union-integrases" type="boolean" checked="false" truevalue="--union-integrases" falsevalue="" label="Use the union of the hits" help="Instead of taking intersection of hits from Phage_int profile (Tyr recombinases) and integron_integrase profile, use the union of the hits" />
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62 <param argument="--func-annot" type="boolean" checked="false" truevalue="--func-annot" falsevalue="" label="Annotate cassettes given HMM profiles" />
0
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63 </section>
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64 </section>
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65 <param name="no_logfile" type="boolean" truevalue="true" falsevalue="false" label="Remove log file"/>
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66 </inputs>
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67 <outputs>
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68 <collection type="list" label="Genbank files from [$tool.name] on $[on_string]" name="genbank_out">
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69 <discover_datasets pattern="(?P&lt;designation&gt;.+)\.gbk" format="gbk" visible="false" directory="Results_Integron_Finder/" />
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70 <filter>gbk</filter>
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71 </collection>
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72 <data format="txt" name="integron_log" from_work_dir="Results_Integron_Finder/integron_finder.out" label="Log from [$tool.name] on $[on_string]">
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73 <filter> no_logfile == False</filter>
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74 </data>
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75 <data format="tsv" name="integrons_table" from_work_dir="Results_Integron_Finder/*.integrons" label="Integrons annotations from [$tool.name] on $[on_string]"/>
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76 <data format="tsv" name="summary" from_work_dir="Results_Integron_Finder/*.summary" label="Summary from [$tool.name] on $[on_string]"/>
1ae00120dd24 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bakta/integron_finder commit 6e0d10965c02c249844f1eddd1c7442990695a6a
iuc
parents:
diff changeset
77 <collection type="list" label="Graphic from [$tool.name] on $[on_string]" name="pdf_out">
1ae00120dd24 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bakta/integron_finder commit 6e0d10965c02c249844f1eddd1c7442990695a6a
iuc
parents:
diff changeset
78 <discover_datasets pattern="(?P&lt;designation&gt;.+)\.pdf" format="pdf" visible="false" directory="Results_Integron_Finder/" />
1ae00120dd24 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bakta/integron_finder commit 6e0d10965c02c249844f1eddd1c7442990695a6a
iuc
parents:
diff changeset
79 <filter>pdf</filter>
1ae00120dd24 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bakta/integron_finder commit 6e0d10965c02c249844f1eddd1c7442990695a6a
iuc
parents:
diff changeset
80 </collection>
1ae00120dd24 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bakta/integron_finder commit 6e0d10965c02c249844f1eddd1c7442990695a6a
iuc
parents:
diff changeset
81 </outputs>
1ae00120dd24 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bakta/integron_finder commit 6e0d10965c02c249844f1eddd1c7442990695a6a
iuc
parents:
diff changeset
82 <tests>
1ae00120dd24 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bakta/integron_finder commit 6e0d10965c02c249844f1eddd1c7442990695a6a
iuc
parents:
diff changeset
83 <test expect_num_outputs="3">
1ae00120dd24 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bakta/integron_finder commit 6e0d10965c02c249844f1eddd1c7442990695a6a
iuc
parents:
diff changeset
84 <param name="sequence" value="input.fasta"/>
1ae00120dd24 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bakta/integron_finder commit 6e0d10965c02c249844f1eddd1c7442990695a6a
iuc
parents:
diff changeset
85 <output name="integron_log" value="integron_log" lines_diff="3" />
1ae00120dd24 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bakta/integron_finder commit 6e0d10965c02c249844f1eddd1c7442990695a6a
iuc
parents:
diff changeset
86 <output name="integrons_table" value="test1_integrons_table.tsv" lines_diff="3"/>
1ae00120dd24 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bakta/integron_finder commit 6e0d10965c02c249844f1eddd1c7442990695a6a
iuc
parents:
diff changeset
87 <output name="summary" value="summary.tsv" lines_diff="3"/>
1ae00120dd24 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bakta/integron_finder commit 6e0d10965c02c249844f1eddd1c7442990695a6a
iuc
parents:
diff changeset
88 </test>
1ae00120dd24 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bakta/integron_finder commit 6e0d10965c02c249844f1eddd1c7442990695a6a
iuc
parents:
diff changeset
89 <test expect_num_outputs="2">
1ae00120dd24 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bakta/integron_finder commit 6e0d10965c02c249844f1eddd1c7442990695a6a
iuc
parents:
diff changeset
90 <param name="sequence" value="input.fasta"/>
1ae00120dd24 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bakta/integron_finder commit 6e0d10965c02c249844f1eddd1c7442990695a6a
iuc
parents:
diff changeset
91 <param name="local_max" value="true"/>
1ae00120dd24 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bakta/integron_finder commit 6e0d10965c02c249844f1eddd1c7442990695a6a
iuc
parents:
diff changeset
92 <param name="type_replicon" value="--linear"/>
1ae00120dd24 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bakta/integron_finder commit 6e0d10965c02c249844f1eddd1c7442990695a6a
iuc
parents:
diff changeset
93 <param name="no_logfile" value="true"/>
1ae00120dd24 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bakta/integron_finder commit 6e0d10965c02c249844f1eddd1c7442990695a6a
iuc
parents:
diff changeset
94 <output name="integrons_table" value="test2_integrons_table.tsv" lines_diff="3" />
1ae00120dd24 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bakta/integron_finder commit 6e0d10965c02c249844f1eddd1c7442990695a6a
iuc
parents:
diff changeset
95 <output name="summary" value="summary.tsv" lines_diff="4" />
1ae00120dd24 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bakta/integron_finder commit 6e0d10965c02c249844f1eddd1c7442990695a6a
iuc
parents:
diff changeset
96 </test>
1ae00120dd24 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bakta/integron_finder commit 6e0d10965c02c249844f1eddd1c7442990695a6a
iuc
parents:
diff changeset
97 <test expect_num_outputs="2">
1ae00120dd24 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bakta/integron_finder commit 6e0d10965c02c249844f1eddd1c7442990695a6a
iuc
parents:
diff changeset
98 <param name="sequence" value="input.fasta"/>
1ae00120dd24 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bakta/integron_finder commit 6e0d10965c02c249844f1eddd1c7442990695a6a
iuc
parents:
diff changeset
99 <param name="type_replicon" value="--circ"/>
1ae00120dd24 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bakta/integron_finder commit 6e0d10965c02c249844f1eddd1c7442990695a6a
iuc
parents:
diff changeset
100 <param name="no_logfile" value="true"/>
1ae00120dd24 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bakta/integron_finder commit 6e0d10965c02c249844f1eddd1c7442990695a6a
iuc
parents:
diff changeset
101 <output name="integrons_table" value="test3_integrons_table.tsv" lines_diff="3" />
1ae00120dd24 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bakta/integron_finder commit 6e0d10965c02c249844f1eddd1c7442990695a6a
iuc
parents:
diff changeset
102 <output name="summary" value="summary.tsv" lines_diff="3" />
1ae00120dd24 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bakta/integron_finder commit 6e0d10965c02c249844f1eddd1c7442990695a6a
iuc
parents:
diff changeset
103 </test>
1ae00120dd24 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bakta/integron_finder commit 6e0d10965c02c249844f1eddd1c7442990695a6a
iuc
parents:
diff changeset
104 <test expect_num_outputs="2">
1ae00120dd24 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bakta/integron_finder commit 6e0d10965c02c249844f1eddd1c7442990695a6a
iuc
parents:
diff changeset
105 <param name="sequence" value="input.fasta"/>
1ae00120dd24 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bakta/integron_finder commit 6e0d10965c02c249844f1eddd1c7442990695a6a
iuc
parents:
diff changeset
106 <param name="topology_file" value="topology.txt"/>
1ae00120dd24 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bakta/integron_finder commit 6e0d10965c02c249844f1eddd1c7442990695a6a
iuc
parents:
diff changeset
107 <param name="no_logfile" value="true"/>
1ae00120dd24 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bakta/integron_finder commit 6e0d10965c02c249844f1eddd1c7442990695a6a
iuc
parents:
diff changeset
108 <output name="integrons_table" value="test4_integrons_table.tsv" lines_diff="3" />
1ae00120dd24 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bakta/integron_finder commit 6e0d10965c02c249844f1eddd1c7442990695a6a
iuc
parents:
diff changeset
109 <output name="summary" value="summary.tsv" lines_diff="5" />
1ae00120dd24 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bakta/integron_finder commit 6e0d10965c02c249844f1eddd1c7442990695a6a
iuc
parents:
diff changeset
110 </test>
1ae00120dd24 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bakta/integron_finder commit 6e0d10965c02c249844f1eddd1c7442990695a6a
iuc
parents:
diff changeset
111 <test expect_num_outputs="2">
1ae00120dd24 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bakta/integron_finder commit 6e0d10965c02c249844f1eddd1c7442990695a6a
iuc
parents:
diff changeset
112 <param name="sequence" value="input.fasta"/>
1ae00120dd24 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bakta/integron_finder commit 6e0d10965c02c249844f1eddd1c7442990695a6a
iuc
parents:
diff changeset
113 <param name="promoter_attI" value="true"/>
1ae00120dd24 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bakta/integron_finder commit 6e0d10965c02c249844f1eddd1c7442990695a6a
iuc
parents:
diff changeset
114 <param name="no_logfile" value="true"/>
1ae00120dd24 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bakta/integron_finder commit 6e0d10965c02c249844f1eddd1c7442990695a6a
iuc
parents:
diff changeset
115 <output name="integrons_table" value="test5_integrons_table.tsv" lines_diff="3" />
1ae00120dd24 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bakta/integron_finder commit 6e0d10965c02c249844f1eddd1c7442990695a6a
iuc
parents:
diff changeset
116 <output name="summary" value="summary.tsv" lines_diff="3" />
1ae00120dd24 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bakta/integron_finder commit 6e0d10965c02c249844f1eddd1c7442990695a6a
iuc
parents:
diff changeset
117 </test>
1ae00120dd24 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bakta/integron_finder commit 6e0d10965c02c249844f1eddd1c7442990695a6a
iuc
parents:
diff changeset
118 <test expect_num_outputs="4">
1ae00120dd24 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bakta/integron_finder commit 6e0d10965c02c249844f1eddd1c7442990695a6a
iuc
parents:
diff changeset
119 <param name="sequence" value="input.fasta"/>
1ae00120dd24 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bakta/integron_finder commit 6e0d10965c02c249844f1eddd1c7442990695a6a
iuc
parents:
diff changeset
120 <param name="gbk" value="true"/>
1ae00120dd24 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bakta/integron_finder commit 6e0d10965c02c249844f1eddd1c7442990695a6a
iuc
parents:
diff changeset
121 <param name="pdf" value="true"/>
1ae00120dd24 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bakta/integron_finder commit 6e0d10965c02c249844f1eddd1c7442990695a6a
iuc
parents:
diff changeset
122 <param name="no_logfile" value="true"/>
1ae00120dd24 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bakta/integron_finder commit 6e0d10965c02c249844f1eddd1c7442990695a6a
iuc
parents:
diff changeset
123 <output_collection name="genbank_out" type="list">
1ae00120dd24 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bakta/integron_finder commit 6e0d10965c02c249844f1eddd1c7442990695a6a
iuc
parents:
diff changeset
124 <element name="ACBA.007.P01_13">
1ae00120dd24 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bakta/integron_finder commit 6e0d10965c02c249844f1eddd1c7442990695a6a
iuc
parents:
diff changeset
125 <assert_contents>
1ae00120dd24 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bakta/integron_finder commit 6e0d10965c02c249844f1eddd1c7442990695a6a
iuc
parents:
diff changeset
126 <has_text text="MKTATAPLPPLRSVKVLDQLRERIRYLHYSLRTEQAYVNWVRAFI"/>
1ae00120dd24 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bakta/integron_finder commit 6e0d10965c02c249844f1eddd1c7442990695a6a
iuc
parents:
diff changeset
127 </assert_contents>
1ae00120dd24 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bakta/integron_finder commit 6e0d10965c02c249844f1eddd1c7442990695a6a
iuc
parents:
diff changeset
128 </element>
1ae00120dd24 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bakta/integron_finder commit 6e0d10965c02c249844f1eddd1c7442990695a6a
iuc
parents:
diff changeset
129 </output_collection>
1ae00120dd24 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bakta/integron_finder commit 6e0d10965c02c249844f1eddd1c7442990695a6a
iuc
parents:
diff changeset
130 <output_collection name="pdf_out" type="list">
1ae00120dd24 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bakta/integron_finder commit 6e0d10965c02c249844f1eddd1c7442990695a6a
iuc
parents:
diff changeset
131 <element name="ACBA.007.P01_13_1">
1ae00120dd24 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bakta/integron_finder commit 6e0d10965c02c249844f1eddd1c7442990695a6a
iuc
parents:
diff changeset
132 <assert_contents>
1ae00120dd24 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bakta/integron_finder commit 6e0d10965c02c249844f1eddd1c7442990695a6a
iuc
parents:
diff changeset
133 <has_text text=">"/>
1ae00120dd24 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bakta/integron_finder commit 6e0d10965c02c249844f1eddd1c7442990695a6a
iuc
parents:
diff changeset
134 </assert_contents>
1ae00120dd24 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bakta/integron_finder commit 6e0d10965c02c249844f1eddd1c7442990695a6a
iuc
parents:
diff changeset
135 </element>
1ae00120dd24 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bakta/integron_finder commit 6e0d10965c02c249844f1eddd1c7442990695a6a
iuc
parents:
diff changeset
136 </output_collection>
1ae00120dd24 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bakta/integron_finder commit 6e0d10965c02c249844f1eddd1c7442990695a6a
iuc
parents:
diff changeset
137 <output name="integrons_table" value="test6_integrons_table.tsv" lines_diff="3" />
1ae00120dd24 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bakta/integron_finder commit 6e0d10965c02c249844f1eddd1c7442990695a6a
iuc
parents:
diff changeset
138 <output name="summary" value="summary.tsv" lines_diff="3" />
1ae00120dd24 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bakta/integron_finder commit 6e0d10965c02c249844f1eddd1c7442990695a6a
iuc
parents:
diff changeset
139 </test>
1ae00120dd24 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bakta/integron_finder commit 6e0d10965c02c249844f1eddd1c7442990695a6a
iuc
parents:
diff changeset
140 <test expect_num_outputs="2">
1ae00120dd24 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bakta/integron_finder commit 6e0d10965c02c249844f1eddd1c7442990695a6a
iuc
parents:
diff changeset
141 <param name="sequence" value="input.fasta"/>
1ae00120dd24 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bakta/integron_finder commit 6e0d10965c02c249844f1eddd1c7442990695a6a
iuc
parents:
diff changeset
142 <param name="no_logfile" value="true"/>
1ae00120dd24 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bakta/integron_finder commit 6e0d10965c02c249844f1eddd1c7442990695a6a
iuc
parents:
diff changeset
143 <section name="settings">
1ae00120dd24 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bakta/integron_finder commit 6e0d10965c02c249844f1eddd1c7442990695a6a
iuc
parents:
diff changeset
144 <section name="attc_settings">
1ae00120dd24 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bakta/integron_finder commit 6e0d10965c02c249844f1eddd1c7442990695a6a
iuc
parents:
diff changeset
145 <param name="dist_thresh" value="2000"/>
1ae00120dd24 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bakta/integron_finder commit 6e0d10965c02c249844f1eddd1c7442990695a6a
iuc
parents:
diff changeset
146 <param name="calin_threshold" value="3"/>
1ae00120dd24 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bakta/integron_finder commit 6e0d10965c02c249844f1eddd1c7442990695a6a
iuc
parents:
diff changeset
147 <param name="max_attc_size" value="188"/>
1ae00120dd24 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bakta/integron_finder commit 6e0d10965c02c249844f1eddd1c7442990695a6a
iuc
parents:
diff changeset
148 <param name="min_attc_size" value="30"/>
1ae00120dd24 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bakta/integron_finder commit 6e0d10965c02c249844f1eddd1c7442990695a6a
iuc
parents:
diff changeset
149 <param name="keep_palindromes" value=""/>
1ae00120dd24 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bakta/integron_finder commit 6e0d10965c02c249844f1eddd1c7442990695a6a
iuc
parents:
diff changeset
150 </section>
1ae00120dd24 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bakta/integron_finder commit 6e0d10965c02c249844f1eddd1c7442990695a6a
iuc
parents:
diff changeset
151 </section>
1ae00120dd24 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bakta/integron_finder commit 6e0d10965c02c249844f1eddd1c7442990695a6a
iuc
parents:
diff changeset
152 <output name="integrons_table" value="test7_integrons_table.tsv" lines_diff="3" />
1ae00120dd24 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bakta/integron_finder commit 6e0d10965c02c249844f1eddd1c7442990695a6a
iuc
parents:
diff changeset
153 <output name="summary" value="summary.tsv" lines_diff="3" />
1ae00120dd24 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bakta/integron_finder commit 6e0d10965c02c249844f1eddd1c7442990695a6a
iuc
parents:
diff changeset
154 </test>
1ae00120dd24 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bakta/integron_finder commit 6e0d10965c02c249844f1eddd1c7442990695a6a
iuc
parents:
diff changeset
155 <test expect_num_outputs="2">
1ae00120dd24 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bakta/integron_finder commit 6e0d10965c02c249844f1eddd1c7442990695a6a
iuc
parents:
diff changeset
156 <param name="sequence" value="input.fasta"/>
1ae00120dd24 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bakta/integron_finder commit 6e0d10965c02c249844f1eddd1c7442990695a6a
iuc
parents:
diff changeset
157 <param name="no_logfile" value="true"/>
1ae00120dd24 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bakta/integron_finder commit 6e0d10965c02c249844f1eddd1c7442990695a6a
iuc
parents:
diff changeset
158 <section name="settings">
1ae00120dd24 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bakta/integron_finder commit 6e0d10965c02c249844f1eddd1c7442990695a6a
iuc
parents:
diff changeset
159 <section name="attc_settings">
1ae00120dd24 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bakta/integron_finder commit 6e0d10965c02c249844f1eddd1c7442990695a6a
iuc
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160 <param name="covar_matrix" value="covar.txt"/>
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161 </section>
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162 </section>
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163 <output name="integrons_table" value="test8_integrons_table.tsv" lines_diff="10" />
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164 <output name="summary" value="summary.tsv" lines_diff="3" />
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165 </test>
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166 <test expect_num_outputs="2">
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167 <param name="sequence" value="input.fasta"/>
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168 <param name="no_logfile" value="true"/>
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169 <section name="settings">
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170 <section name="protein_settings">
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171 <param name="no_proteins" value="true"/>
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172 </section>
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173 </section>
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174 <output name="integrons_table" value="test9_integrons_table.tsv" lines_diff="3" />
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175 <output name="summary" value="test9_summary.tsv" lines_diff="3" />
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176 </test>
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177 <test expect_num_outputs="2">
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178 <param name="sequence" value="input.fasta"/>
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179 <param name="no_logfile" value="true"/>
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180 <section name="settings">
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181 <section name="protein_settings">
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182 <param name="union_integrases" value="true" />
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183 <param name="func_annot" value="true"/>
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184 </section>
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185 </section>
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186 <output name="integrons_table" value="test10_integrons_table.tsv" lines_diff="3" />
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187 <output name="summary" value="summary.tsv" lines_diff="3" />
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188 </test>
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189 </tests>
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190 <help><![CDATA[
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191
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192 How does it work ?
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193 ==================
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194
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195 - First, IntegronFinder annotates the DNA sequence's CDS with Prodigal.
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196
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197 - Second, IntegronFinder detects independently integron integrase and *attC*
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198 recombination sites. The Integron integrase is detected by using the intersection
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199 of two HMM profiles:
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200
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201 - one specific of tyrosine-recombinase (PF00589)
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202 - one specific of the integron integrase, near the patch III domain of tyrosine recombinases.
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203
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204 The *attC* recombination site is detected with a covariance model (CM), which
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205 models the secondary structure in addition to the few conserved sequence
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206 positions.
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207
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208
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209 - Third, the results are integrated, and IntegronFinder distinguishes 3 types of
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210 elements:
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211
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212 - complete integron
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213 Integron with integron integrase nearby *attC* site(s)
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214 - In0 element
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215 Integron integrase only, without any *attC* site nearby
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216 - CALIN element
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217 Cluster of *attC* sites Lacking INtegrase nearby.
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218 A rule of thumb to avoid false positive is to filter out singleton of
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219 *attC* site.
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220
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221 IntegronFinder can also annotate gene cassettes (CDS nearby *attC* sites) using
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222 Resfams, a database of HMM profiles aiming at annotating antibiotic resistance
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223 genes. This database is provided but the user can add any other HMM profiles
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224 database of its own interest.
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225
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226 When available, IntegronFinder annotates the promoters and attI sites by pattern
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227 matching.
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228 ]]></help>
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229 <expand macro="citations"/>
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230 </tool>