comparison sappDocker/interproscan.xml @ 31:957156367442 draft

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author jjkoehorst
date Wed, 29 Jun 2016 01:36:58 -0400
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30:0a947cb25a3d 31:957156367442
1 <tool id="DInterproscan" name="Interproscan" version="1.0.0">
2 <description>Interproscan annotation for SAPP</description>
3 <requirements>
4 <container type="docker">jjkoehorst/sappdocker:INTERPROSCAN</container>
5 </requirements>
6 <command interpreter="docker">java -jar /interproscan/target/interproscanRDF-0.0.1-SNAPSHOT-jar-with-dependencies.jar
7 '-input' '$input' '-format' 'TURTLE'
8 '-applications' '$appl'
9 '-output'
10 '$outfile' -v '$version' '$disable'
11 </command>
12 <inputs>
13 <param format="ttl" label="genome rdf file with orf prediction" name="input" type="data"/>
14 <param display="checkboxes" help="Select your programm." label="Applications to run" multiple="True" name="appl" type="select">
15 <option selected="true" value="TIGRFAM">TIGRFAM: protein families
16 based on Hidden Markov Models or HMMs
17 </option>
18 <option selected="false" value="PIRSF">PIRSF: non-overlapping
19 clustering of UniProtKB sequences into a hierarchical order
20 (evolutionary relationships)
21 </option>
22 <option selected="true" value="ProDom">ProDom: set of protein domain
23 families generated from the UniProtKB
24 </option>
25 <option selected="true" value="SMART">SMART: identification and
26 analysis of domain architectures based on Hidden Markov Models or
27 HMMs
28 </option>
29 <option selected="false" value="PrositeProfiles">PROSITE Profiles:
30 protein domains, families and functional sites as well as associated
31 profiles to identify them
32 </option>
33 <option selected="true" value="PrositePatterns">PROSITE Pattern:
34 protein domains, families and functional sites as well as associated
35 patterns to identify them
36 </option>
37 <option selected="false" value="HAMAP">HAMAP: High-quality Automated
38 Annotation of Microbial Proteomes
39 </option>
40 <option selected="true" value="PfamA">PfamA: protein families, each
41 represented by multiple sequence alignments and hidden Markov models
42 </option>
43 <option selected="true" value="PRINTS">PRINTS: group of conserved
44 motifs (fingerprints) used to characterise a protein family
45 </option>
46 <option selected="true" value="SuperFamily">SUPERFAMILY: database of
47 structural and functional annotation
48 </option>
49 <option selected="true" value="Coils">Coils: Prediction of Coiled
50 Coil Regions in Proteins
51 </option>
52 <option selected="true" value="Gene3d">Gene3d: Structural assignment
53 for whole genes and genomes using the CATH domain structure database
54 </option>
55 </param>
56 <param label="Version selection" name="version" type="select">
57 <option value="interproscan-5.17-56.0">interproscan-5.17-56.0</option>
58 </param>
59 <param checked="false" falsevalue="-disableprecalc" help="You need to setup your own lookup server as the EBI version can differ. Look at interproscan configuration file for more info" label="Perform lookup of InterPro at defined server address" name="disable" truevalue="" type="boolean"/>
60 </inputs>
61 <outputs>
62 <data format="ttl" label="IPR: ${input.name}" name="outfile"/>
63 </outputs>
64 <help>Interproscan annotation suite. Select your RDF genome with
65 protein annotation.
66 This can be either from a converted GenBank/EMBL
67 file or from a
68 Prodigal prediction.
69 The output will be an RDF file with
70 protein domain annotation from
71 InterPro.
72 </help>
73 <citations>
74 <citation type="bibtex">@article{Mitchell26112014,
75 author = {Mitchell,
76 Alex and Chang, Hsin-Yu and Daugherty, Louise and
77 Fraser, Matthew and
78 Hunter, Sarah and Lopez, Rodrigo and McAnulla,
79 Craig and McMenamin,
80 Conor and Nuka, Gift and Pesseat, Sebastien and
81 Sangrador-Vegas, Amaia
82 and Scheremetjew, Maxim and Rato, Claudia and
83 Yong, Siew-Yit and
84 Bateman, Alex and Punta, Marco and Attwood, Teresa
85 K. and Sigrist,
86 Christian J.A. and Redaschi, Nicole and Rivoire,
87 Catherine and
88 Xenarios, Ioannis and Kahn, Daniel and Guyot, Dominique
89 and Bork, Peer
90 and Letunic, Ivica and Gough, Julian and Oates, Matt
91 and Haft, Daniel
92 and Huang, Hongzhan and Natale, Darren A. and Wu,
93 Cathy H. and Orengo,
94 Christine and Sillitoe, Ian and Mi, Huaiyu and
95 Thomas, Paul D. and
96 Finn, Robert D.},
97 title = {The InterPro protein families database: the
98 classification
99 resource after 15 years},
100 year = {2014},
101 doi =
102 {10.1093/nar/gku1243},
103 abstract ={The InterPro database
104 (http://www.ebi.ac.uk/interpro/) is a freely
105 available resource that
106 can be used to classify sequences into
107 protein families and to predict
108 the presence of important domains and
109 sites. Central to the InterPro
110 database are predictive models, known
111 as signatures, from a range of
112 different protein family databases
113 that have different biological
114 focuses and use different
115 methodological approaches to classify
116 protein families and domains.
117 InterPro integrates these signatures,
118 capitalizing on the respective
119 strengths of the individual databases,
120 to produce a powerful protein
121 classification resource. Here, we report
122 on the status of InterPro as
123 it enters its 15th year of operation, and
124 give an overview of new
125 developments with the database and its
126 associated Web interfaces and
127 software. In particular, the new domain
128 architecture search tool is
129 described and the process of mapping of
130 Gene Ontology terms to
131 InterPro is outlined. We also discuss the
132 challenges faced by the
133 resource given the explosive growth in
134 sequence data in recent years.
135 InterPro (version 48.0) contains 36 766
136 member database signatures
137 integrated into 26 238 InterPro entries, an
138 increase of over 3993
139 entries (5081 signatures), since 2012.},
140 URL =
141 {http://nar.oxfordjournals.org/content/early/2014/11/26/nar.gku1243.abstract},
142 eprint =
143 {http://nar.oxfordjournals.org/content/early/2014/11/26/nar.gku1243.full.pdf+html},
144 journal = {Nucleic Acids Research}
145 }
146 </citation>
147 </citations>
148 </tool>