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comparison integron_finder.xml @ 2:9fdd3e97db8d draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/integron_finder commit 13f722da1a2d95586490e8534b9884abe61ba7cd
author iuc
date Tue, 10 Feb 2026 15:53:43 +0000
parents 3d4ae4eb3e98
children
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1:3d4ae4eb3e98 2:9fdd3e97db8d
1 <tool id="integron_finder" name="Integron Finder" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@"> 1 <tool id="integron_finder" name="Integron Finder" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
2 <description> is a program that detects integrons in DNA sequences</description> 2 <description>is a program that detects integrons in DNA sequences</description>
3 <macros> 3 <macros>
4 <import>macro.xml</import> 4 <import>macro.xml</import>
5 </macros> 5 </macros>
6 <expand macro="edam_info"/> 6 <expand macro="edam_info"/>
7 <expand macro="xrefs"/> 7 <expand macro="xrefs"/>
36 ]]></command> 36 ]]></command>
37 <inputs> 37 <inputs>
38 <param type="data" name="sequence" format="fasta" label="Replicon file" help="Replicon can be entire chromosome, contif, PCR fragments..."> 38 <param type="data" name="sequence" format="fasta" label="Replicon file" help="Replicon can be entire chromosome, contif, PCR fragments...">
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> 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>
40 </param> 40 </param>
41 <param name="local_max" 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." /> 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." />
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)"> 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)">
43 <option value="--linear">linear (--linear)</option> 43 <option value="--linear">linear (--linear)</option>
44 <option value="--circ">circular (--circ)</option> 44 <option value="--circ">circular (--circ)</option>
45 </param> 45 </param>
46 <param name="topology_file" argument="--topology-file" type="data" format="txt" optional="true" label="Select a topology file from your history"/> 46 <param argument="--topology-file" type="data" format="txt" optional="true" label="Select a topology file from your history"/>
47 <param name="promoter_attI" argument="--promoter-attI" type="boolean" checked="false" truevalue="--promoter-attI" falsevalue="" label="Search also for promoter and attI sites?" /> 47 <param argument="--promoter-attI" type="boolean" checked="false" truevalue="--promoter-attI" falsevalue="" label="Search also for promoter and attI sites?" />
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."/> 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."/>
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)"/> 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)"/>
50 <section name="settings" title="Advanced Parameters" expanded="False"> 50 <section name="settings" title="Advanced Parameters" expanded="False">
51 <section name="attc_settings" title="Attc options" expanded="False"> 51 <section name="attc_settings" title="Attc options" expanded="False">
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." /> 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." />
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" /> 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" />
54 <param name="max_attc_size" type="integer" value="200" label="Maximum value for attC size" min="0"/> 54 <param name="max_attc_size" type="integer" value="200" label="Maximum value for attC size" min="0"/>
55 <param name="min_attc_size" type="integer" value="40" label="Minimum value for attC size" min="0" /> 55 <param name="min_attc_size" type="integer" value="40" label="Minimum value for attC size" min="0" />
56 <param name="keep_palindromes" 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"/> 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"/>
57 <param name="covar_matrix" argument="--attc-model" type="data" optional="true" format="txt" label="Covariance Matrix" /> 57 <param name="covar_matrix" argument="--attc-model" type="data" optional="true" format="txt" label="Covariance Matrix" />
58 </section> 58 </section>
59 <section name="protein_settings" title="Protein options" expanded="False"> 59 <section name="protein_settings" title="Protein options" expanded="False">
60 <param name="no_proteins" 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."/> 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."/>
61 <param name="union_integrases" 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" /> 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" />
62 <param name="func_annot" argument="--func-annot" type="boolean" checked="false" truevalue="--func-annot" falsevalue="" label="Annotate cassettes given HMM profiles" /> 62 <param argument="--func-annot" type="boolean" checked="false" truevalue="--func-annot" falsevalue="" label="Annotate cassettes given HMM profiles" />
63 </section> 63 </section>
64 </section> 64 </section>
65 <param name="no_logfile" type="boolean" truevalue="true" falsevalue="false" label="Remove log file"/> 65 <param name="no_logfile" type="boolean" truevalue="true" falsevalue="false" label="Remove log file"/>
66 </inputs> 66 </inputs>
67 <outputs> 67 <outputs>
68 <collection type="list" label="Genbank files from [$tool.name] on $[on_string]" name="genbank_out"> 68 <collection type="list" label="${tool.name} on ${on_string}: Genbank " name="genbank_out">
69 <discover_datasets pattern="(?P&lt;designation&gt;.+)\.gbk" format="gbk" visible="false" directory="Results_Integron_Finder/" /> 69 <discover_datasets pattern="(?P&lt;designation&gt;.+)\.gbk" format="genbank" visible="false" directory="Results_Integron_Finder/" />
70 <filter>gbk</filter> 70 <filter>gbk</filter>
71 </collection> 71 </collection>
72 <data format="txt" name="integron_log" from_work_dir="Results_Integron_Finder/integron_finder.out" label="Log from [$tool.name] on $[on_string]"> 72 <data format="txt" name="integron_log" from_work_dir="Results_Integron_Finder/integron_finder.out" label="${tool.name} on ${on_string}: Log">
73 <filter> no_logfile == False</filter> 73 <filter> no_logfile == False</filter>
74 </data> 74 </data>
75 <data format="tsv" name="integrons_table" from_work_dir="Results_Integron_Finder/*.integrons" label="Integrons annotations from [$tool.name] on $[on_string]"/> 75 <data format="tsv" name="integrons_table" from_work_dir="Results_Integron_Finder/*.integrons" label="${tool.name} on ${on_string}: Integron annotations"/>
76 <data format="tsv" name="summary" from_work_dir="Results_Integron_Finder/*.summary" label="Summary from [$tool.name] on $[on_string]"/> 76 <data format="tsv" name="summary" from_work_dir="Results_Integron_Finder/*.summary" label="${tool.name} on ${on_string}: Summary"/>
77 <collection type="list" label="Graphic from [$tool.name] on $[on_string]" name="pdf_out"> 77 <collection name="pdf_out" type="list" label="${tool.name} on ${on_string}: Graphic">
78 <discover_datasets pattern="(?P&lt;designation&gt;.+)\.pdf" format="pdf" visible="false" directory="Results_Integron_Finder/" /> 78 <discover_datasets pattern="(?P&lt;designation&gt;.+)\.pdf" format="pdf" visible="false" directory="Results_Integron_Finder/" />
79 <filter>pdf</filter> 79 <filter>pdf</filter>
80 </collection> 80 </collection>
81 </outputs> 81 </outputs>
82 <tests> 82 <tests>
144 <section name="attc_settings"> 144 <section name="attc_settings">
145 <param name="dist_thresh" value="2000"/> 145 <param name="dist_thresh" value="2000"/>
146 <param name="calin_threshold" value="3"/> 146 <param name="calin_threshold" value="3"/>
147 <param name="max_attc_size" value="188"/> 147 <param name="max_attc_size" value="188"/>
148 <param name="min_attc_size" value="30"/> 148 <param name="min_attc_size" value="30"/>
149 <param name="keep_palindromes" value=""/> 149 <param name="keep_palindromes" value="false"/>
150 </section> 150 </section>
151 </section> 151 </section>
152 <output name="integrons_table" value="test7_integrons_table.tsv" lines_diff="3" /> 152 <output name="integrons_table" value="test7_integrons_table.tsv" lines_diff="3" />
153 <output name="summary" value="summary.tsv" lines_diff="3" /> 153 <output name="summary" value="summary.tsv" lines_diff="3" />
154 </test> 154 </test>