Mercurial > repos > brinkmanlab > islandpath

annotate IslandPath.xml @ 0:d798a01c4c16 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/islandpath-dimob commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e-dirty"
author brinkmanlab
date Fri, 24 Jan 2020 18:01:06 -0500
parents
children a56b2acd567b
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
d798a01c4c16 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/islandpath-dimob commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e-dirty"
brinkmanlab
parents:
diff changeset
1 <tool id="islandpath" name="IslandPath" version="1.0.4" profile="16.04">
d798a01c4c16 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/islandpath-dimob commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e-dirty"
brinkmanlab
parents:
diff changeset
2 <description>predict genomic islands in bacterial and archaeal genomes based on the presence of dinucleotide biases and mobility genes</description>
d798a01c4c16 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/islandpath-dimob commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e-dirty"
brinkmanlab
parents:
diff changeset
3 <edam_topics>
d798a01c4c16 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/islandpath-dimob commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e-dirty"
brinkmanlab
parents:
diff changeset
4 <edam_topic>topic_0194</edam_topic>
d798a01c4c16 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/islandpath-dimob commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e-dirty"
brinkmanlab
parents:
diff changeset
5 <edam_topic>topic_0091</edam_topic>
d798a01c4c16 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/islandpath-dimob commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e-dirty"
brinkmanlab
parents:
diff changeset
6 </edam_topics>
d798a01c4c16 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/islandpath-dimob commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e-dirty"
brinkmanlab
parents:
diff changeset
7 <edam_operations>
d798a01c4c16 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/islandpath-dimob commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e-dirty"
brinkmanlab
parents:
diff changeset
8 <edam_operation>operation_0362</edam_operation>
d798a01c4c16 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/islandpath-dimob commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e-dirty"
brinkmanlab
parents:
diff changeset
9 </edam_operations>
d798a01c4c16 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/islandpath-dimob commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e-dirty"
brinkmanlab
parents:
diff changeset
10 <requirements>
d798a01c4c16 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/islandpath-dimob commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e-dirty"
brinkmanlab
parents:
diff changeset
11 <requirement type="package" version="1.0.4">islandpath</requirement>
d798a01c4c16 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/islandpath-dimob commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e-dirty"
brinkmanlab
parents:
diff changeset
12 </requirements>
d798a01c4c16 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/islandpath-dimob commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e-dirty"
brinkmanlab
parents:
diff changeset
13 <version_command><![CDATA[ echo "1.0.4" ]]></version_command>
d798a01c4c16 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/islandpath-dimob commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e-dirty"
brinkmanlab
parents:
diff changeset
14 <command detect_errors="aggressive"><![CDATA[
d798a01c4c16 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/islandpath-dimob commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e-dirty"
brinkmanlab
parents:
diff changeset
15 #import os
d798a01c4c16 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/islandpath-dimob commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e-dirty"
brinkmanlab
parents:
diff changeset
16 #if $input.is_of_type("embl")
d798a01c4c16 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/islandpath-dimob commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e-dirty"
brinkmanlab
parents:
diff changeset
17 #set inp=$os.path.basename(str($input))+".embl"
d798a01c4c16 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/islandpath-dimob commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e-dirty"
brinkmanlab
parents:
diff changeset
18 #else
d798a01c4c16 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/islandpath-dimob commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e-dirty"
brinkmanlab
parents:
diff changeset
19 #set inp=$os.path.basename(str($input))+".gbk"
d798a01c4c16 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/islandpath-dimob commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e-dirty"
brinkmanlab
parents:
diff changeset
20 #end if
d798a01c4c16 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/islandpath-dimob commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e-dirty"
brinkmanlab
parents:
diff changeset
21 ln -s "$input" "$inp"
d798a01c4c16 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/islandpath-dimob commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e-dirty"
brinkmanlab
parents:
diff changeset
22 && islandpath "$inp" "$output"
d798a01c4c16 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/islandpath-dimob commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e-dirty"
brinkmanlab
parents:
diff changeset
23 ]]></command>
d798a01c4c16 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/islandpath-dimob commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e-dirty"
brinkmanlab
parents:
diff changeset
24 <inputs>
d798a01c4c16 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/islandpath-dimob commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e-dirty"
brinkmanlab
parents:
diff changeset
25 <param type="data" format="genbank,embl" name="input" argument="input" label="Input" optional="false"/>
d798a01c4c16 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/islandpath-dimob commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e-dirty"
brinkmanlab
parents:
diff changeset
26 </inputs>
d798a01c4c16 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/islandpath-dimob commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e-dirty"
brinkmanlab
parents:
diff changeset
27 <outputs>
d798a01c4c16 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/islandpath-dimob commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e-dirty"
brinkmanlab
parents:
diff changeset
28 <data format="gff" name="output" />
d798a01c4c16 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/islandpath-dimob commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e-dirty"
brinkmanlab
parents:
diff changeset
29 </outputs>
d798a01c4c16 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/islandpath-dimob commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e-dirty"
brinkmanlab
parents:
diff changeset
30 <tests>
d798a01c4c16 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/islandpath-dimob commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e-dirty"
brinkmanlab
parents:
diff changeset
31 <test expect_num_outputs="1">
d798a01c4c16 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/islandpath-dimob commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e-dirty"
brinkmanlab
parents:
diff changeset
32 <param name="input" value="test-data/test.embl" ftype="embl" />
d798a01c4c16 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/islandpath-dimob commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e-dirty"
brinkmanlab
parents:
diff changeset
33 <output name="output" checksum="sha256:36d25184326c3415001675921bf76be588edce9fe3313b8082c3eeac83dcf958" ftype="gff" />
d798a01c4c16 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/islandpath-dimob commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e-dirty"
brinkmanlab
parents:
diff changeset
34 </test>
d798a01c4c16 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/islandpath-dimob commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e-dirty"
brinkmanlab
parents:
diff changeset
35 </tests>
d798a01c4c16 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/islandpath-dimob commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e-dirty"
brinkmanlab
parents:
diff changeset
36 <help><![CDATA[
d798a01c4c16 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/islandpath-dimob commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e-dirty"
brinkmanlab
parents:
diff changeset
37 [IslandPath](http://www.pathogenomics.sfu.ca/islandpath/) was originally designed to aid to the identification of prokaryotic genomics islands (GIs),
d798a01c4c16 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/islandpath-dimob commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e-dirty"
brinkmanlab
parents:
diff changeset
38 including pathogenicity islands, of potentially horizontally transferred genes by visualizing several common characteristics of GIs such as abnormal
d798a01c4c16 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/islandpath-dimob commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e-dirty"
brinkmanlab
parents:
diff changeset
39 sequence composition or the presence of genes that functionally related to mobile elements (termed mobility genes).
d798a01c4c16 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/islandpath-dimob commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e-dirty"
brinkmanlab
parents:
diff changeset
40
d798a01c4c16 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/islandpath-dimob commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e-dirty"
brinkmanlab
parents:
diff changeset
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
d798a01c4c16 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/islandpath-dimob commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e-dirty"
brinkmanlab
parents:
diff changeset
42 mobility genes to develop a dataset of GIs (IslandPath DIMOB) for multiple organisms and revealed that these genomic regions contain higher
d798a01c4c16 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/islandpath-dimob commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e-dirty"
brinkmanlab
parents:
diff changeset
43 proportions of novel genes.
d798a01c4c16 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/islandpath-dimob commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e-dirty"
brinkmanlab
parents:
diff changeset
44
d798a01c4c16 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/islandpath-dimob commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e-dirty"
brinkmanlab
parents:
diff changeset
45 A recent study (see Langille et al 2008 (submitted)), developed a new method called [IslandPick](http://www.pathogenomics.sfu.ca/islandpick/)
d798a01c4c16 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/islandpath-dimob commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e-dirty"
brinkmanlab
parents:
diff changeset
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
d798a01c4c16 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/islandpath-dimob commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e-dirty"
brinkmanlab
parents:
diff changeset
47 sequence composition bias allowed for an independent review of several previously published GI predictors. Although the overall accuracy of
d798a01c4c16 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/islandpath-dimob commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e-dirty"
brinkmanlab
parents:
diff changeset
48 several of the tools were similar, IslandPath DIMOB was shown to have the highest accuracy.
d798a01c4c16 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/islandpath-dimob commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e-dirty"
brinkmanlab
parents:
diff changeset
49 ]]></help>
d798a01c4c16 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/islandpath-dimob commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e-dirty"
brinkmanlab
parents:
diff changeset
50 <citations>
d798a01c4c16 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/islandpath-dimob commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e-dirty"
brinkmanlab
parents:
diff changeset
51 <citation type="doi">10.5281/zenodo.3364789</citation>
d798a01c4c16 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/islandpath-dimob commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e-dirty"
brinkmanlab
parents:
diff changeset
52 <citation type="doi">10.1093/bioinformatics/bty095</citation>
d798a01c4c16 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/islandpath-dimob commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e-dirty"
brinkmanlab
parents:
diff changeset
53 </citations>
d798a01c4c16 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/islandpath-dimob commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e-dirty"
brinkmanlab
parents:
diff changeset
54 </tool>