Mercurial > repos > iuc > integron_finder

comparison integron_finder.xml @ 1:3d4ae4eb3e98 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/integron_finder commit 04aa903b53ba0596d486d2ce4a1b4f1d7125846f
author iuc
date Fri, 17 Feb 2023 18:35:52 +0000
parents 2729629d81db
children
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0:2729629d81db 1:3d4ae4eb3e98
33 $gbk 33 $gbk
34 $pdf 34 $pdf
35 && mv Results_Integron_Finder_* Results_Integron_Finder 35 && mv Results_Integron_Finder_* Results_Integron_Finder
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>
40 </param>
39 <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 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." />
40 <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)">
41 <option value="--linear">linear (--linear)</option> 43 <option value="--linear">linear (--linear)</option>
42 <option value="--circ">circular (--circ)</option> 44 <option value="--circ">circular (--circ)</option>
43 </param> 45 </param>