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"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/islandpath-dimob commit 1f5acfa386914e258d99168fe71a7aaa8ec18883"
author brinkmanlab
date Mon, 12 Jul 2021 18:47:36 +0000
parents a56b2acd567b
children
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1 <tool id="islandpath" name="IslandPath" version="1.0.6" profile="16.04">
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2 <description>predict genomic islands in bacterial and archaeal genomes based on the presence of dinucleotide biases and mobility genes</description>
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3 <edam_topics>
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4 <edam_topic>topic_0194</edam_topic>
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5 <edam_topic>topic_0091</edam_topic>
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6 </edam_topics>
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7 <edam_operations>
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8 <edam_operation>operation_0362</edam_operation>
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9 </edam_operations>
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10 <requirements>
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11 <requirement type="package" version="1.0.6">islandpath</requirement>
0
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12 </requirements>
2
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13 <version_command><![CDATA[ echo "1.0.6" ]]></version_command>
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14 <command detect_errors="aggressive"><![CDATA[
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15 #import os
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16 #if $input.is_of_type("embl")
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17 #set inp=$os.path.basename(str($input))+".embl"
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18 #else
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19 #set inp=$os.path.basename(str($input))+".gbk"
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20 #end if
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21 ln -s "$input" "$inp"
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22 && islandpath "$inp" "$output"
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23 ]]></command>
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24 <inputs>
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25 <param type="data" format="genbank,embl" name="input" argument="input" label="Input" optional="false"/>
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26 </inputs>
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27 <outputs>
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28 <data format="gff" name="output" />
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29 </outputs>
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30 <tests>
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31 <test expect_num_outputs="1">
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32 <param name="input" value="test-data/test.embl" ftype="embl" />
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33 <output name="output" checksum="sha256:36d25184326c3415001675921bf76be588edce9fe3313b8082c3eeac83dcf958" ftype="gff" />
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34 </test>
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35 </tests>
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36 <help><![CDATA[
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37 [IslandPath](http://www.pathogenomics.sfu.ca/islandpath/) was originally designed to aid to the identification of prokaryotic genomics islands (GIs),
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38 including pathogenicity islands, of potentially horizontally transferred genes by visualizing several common characteristics of GIs such as abnormal
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39 sequence composition or the presence of genes that functionally related to mobile elements (termed mobility genes).
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40
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41 Further studies (see [Hsiao et al 2005](http://www.ncbi.nlm.nih.gov/pubmed/16299586)) used dinucleotide sequence compostion bias and the presence of
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42 mobility genes to develop a dataset of GIs (IslandPath DIMOB) for multiple organisms and revealed that these genomic regions contain higher
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43 proportions of novel genes.
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44
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45 A recent study (see Langille et al 2008 (submitted)), developed a new method called [IslandPick](http://www.pathogenomics.sfu.ca/islandpick/)
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46 that used comparative genomics to develop stringent data sets of GIs and non-GIs. These positive and negative data sets that were not based on
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47 sequence composition bias allowed for an independent review of several previously published GI predictors. Although the overall accuracy of
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48 several of the tools were similar, IslandPath DIMOB was shown to have the highest accuracy.
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49 ]]></help>
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50 <citations>
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51 <citation type="doi">10.5281/zenodo.3364789</citation>
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52 <citation type="doi">10.1093/bioinformatics/bty095</citation>
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53 </citations>
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54 </tool>