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comparison interproscan.xml @ 1:2d56d3ae499c draft

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author bgruening
date Tue, 08 Oct 2013 09:14:43 -0400
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0:98c6e970cbc1 1:2d56d3ae499c
5 <requirement type="package">phobius</requirement> 5 <requirement type="package">phobius</requirement>
6 <requirement type="package">tmhmm</requirement> 6 <requirement type="package">tmhmm</requirement>
7 <requirement type="set_environment">INTERPROSCAN_SCRIPT_PATH</requirement> 7 <requirement type="set_environment">INTERPROSCAN_SCRIPT_PATH</requirement>
8 </requirements> 8 </requirements>
9 <command> 9 <command>
10
10 #import os 11 #import os
11 interproscan.sh -dp --fasta $infile --seqtype $seqtype -f $oformat --applications $appl --tempdir \$TEMP 12 interproscan.sh
13 ## disables the precalculated lookup service, all calculation will be run locally
14 -dp
15 --input $infile
16 --seqtype $seqtype
17 -f $oformat
18 --applications $appl
19 --tempdir \$TEMP
12 20
13 $pathways 21 $pathways
14 $goterms 22 $goterms
15 $iprlookup 23 $iprlookup
16 24
55 <option value="SignalP-EUK" selected="true">SignalP Eukaryotic Bacteria</option> 63 <option value="SignalP-EUK" selected="true">SignalP Eukaryotic Bacteria</option>
56 <option value="Phobius" selected="true">Phobius: combined transmembrane topology and signal peptide predictor</option> 64 <option value="Phobius" selected="true">Phobius: combined transmembrane topology and signal peptide predictor</option>
57 <option value="TMHMM" selected="true">TMHMM: Prediction of transmembrane helices in proteins</option> 65 <option value="TMHMM" selected="true">TMHMM: Prediction of transmembrane helices in proteins</option>
58 </param> 66 </param>
59 67
60 <param name="pathways" truevalue="--pathways" falsevalue="" checked="True" type="boolean" label="Include pathway information" help="Option that provides mappings from matches to pathway information, which is based on the matched manually curated InterPro entries."/> 68 <param name="pathways" truevalue="--pathways" falsevalue="" checked="True" type="boolean" label="Include pathway information"
61 <param name="goterms" truevalue="--goterms" falsevalue="" checked="True" type="boolean" label="Include Gene Ontology (GO) mappings" /> 69 help="Option that provides mappings from matches to pathway information, which is based on the matched manually curated InterPro entries. (--pathways)"/>
62 <param name="iprlookup" truevalue="--iprlookup" falsevalue="" checked="False" type="boolean" label="Provide mappings from matched member database signatures to the InterPro entries that they are integrated into" /> 70 <param name="goterms" truevalue="--goterms" falsevalue="" checked="True" type="boolean" label="Include Gene Ontology (GO) mappings"
71 help="Look up of corresponding Gene Ontology annotation. Implies -iprlookup option. (--goterms)"/>
72 <param name="iprlookup" truevalue="--iprlookup" falsevalue="" checked="False" type="boolean"
73 label="Provide additional mappings" help="Provide mappings from matched member database signatures to the InterPro entries that they are integrated into (--iprlookup)"/>
63 74
64 <param name="oformat" type="select" label="Output format" help="Please select a output format."> 75 <param name="oformat" type="select" label="Output format" help="Please select a output format.">
65 <option value="TSV" selected="true">Tab-separated values format (TSV)</option> 76 <option value="TSV" selected="true">Tab-separated values format (TSV)</option>
66 <option value="GFF3">GFF3</option> 77 <option value="GFF3">GFF3</option>
67 <option value="SVG">SVG</option> 78 <option value="SVG">SVG</option>
109 * GFF: The `GFF 3.0`_ format 120 * GFF: The `GFF 3.0`_ format
110 * HTML: An HTML representation of the protein matches 121 * HTML: An HTML representation of the protein matches
111 * SVG: An Scalable Vector Graphics representation of the protein matches 122 * SVG: An Scalable Vector Graphics representation of the protein matches
112 123
113 124
114 .. _`GFF3 3.0`: http://gmod.org/wiki/GFF#GFF3_Format 125 .. _`GFF 3.0`: http://gmod.org/wiki/GFF#GFF3_Format
115 .. _here: http://www.ebi.ac.uk/interpro/resources/schemas/interproscan5 126 .. _here: http://www.ebi.ac.uk/interpro/resources/schemas/interproscan5
116 127
117 128
118 Previous versions of InterProScan_ 5 (I5RC1 - I5RC6) could only output data for nucleotide sequences in XML and GFF3. This has now changed and InterProScan_ 5 can output results for nucleotide sequences in all formats. *Please note* you can only trace protein match positions to the original nucleotide sequence with GFF3 and XML.
119
120 You can override the default output formats using the *-f* option, e.g.::
121
122 ./interproscan.sh -f XML -f HTML -i /path/to/sequences.fasta -b /path/to/output_file
123
124 or
125
126 ::
127
128 ./interproscan.sh -f XML, HTML -i /path/to/sequences.fasta -b /path/to/output_file
129
130
131 These two equivalent commands will output the results in XML and HTML format.
132 129
133 Tab-separated values format (TSV) 130 Tab-separated values format (TSV)
134 ================================= 131 =================================
135 132
136 Basic tab delimited format. 133 Basic tab delimited format.
171 168
172 XML representation of the matches - this is the richest form of the data. The XML Schema Definition (XSD) is available [http://www.ebi.ac.uk/interpro/resources/schemas/interproscan5 here]. 169 XML representation of the matches - this is the richest form of the data. The XML Schema Definition (XSD) is available [http://www.ebi.ac.uk/interpro/resources/schemas/interproscan5 here].
173 170
174 Example Output 171 Example Output
175 -------------- 172 --------------
176
177 ::
178 173
179 .. image:: $PATH_TO_IMAGES/example_xml_output.png 174 .. image:: $PATH_TO_IMAGES/example_xml_output.png
180 175
181 176
182 177
218 213
219 214
220 Scalable Vector Graphics (SVG) and HyperText Markup Language (HTML) 215 Scalable Vector Graphics (SVG) and HyperText Markup Language (HTML)
221 ==================================================================== 216 ====================================================================
222 217
223 InterProScan_ 5 outputs a single HTML/SVG file for each protein sequence analysed. The HTML/SVG file(s) are compressed into a single gzipped tar archive (or "tarball") that includes the resources (images, Javascript, style etc) to render the pages/images in a browser or image viewer. (Note that from version 5RC4, the SVG format has no external dependencies.) 218 InterProScan_ 5 outputs a single HTML/SVG file for each protein sequence analysed.
224 219
225 The tarball will be named something similar to::
226
227 base_output_file_name.html.tar.gz OR base_output_file_name.svg.tar.gz
228
229
230 To access the HTML pages/SVG images, unzip the tarball using a command like:
231
232 tar -xvzf base_output_file_name.html(svg).tar.gz
233
234 You can then open the unzipped HTML/SVG files in any browser or image viewer (for SVG).
235 220
236 Example Output 221 Example Output
237 -------------- 222 --------------
238 223
239 .. image:: $PATH_TO_IMAGES/P51587.svg.png 224 .. image:: $PATH_TO_IMAGES/P51587.svg.png
242 227
243 228
244 ---------- 229 ----------
245 References 230 References
246 ---------- 231 ----------
232
233
234 If you use this Galaxy tool in work leading to a scientific publication please
235 cite the following papers:
236
237 Peter J.A. Cock, Björn A. Grüning, Konrad Paszkiewicz and Leighton Pritchard (2013).
238 Galaxy tools and workflows for sequence analysis with applications
239 in molecular plant pathology. PeerJ 1:e167
240 http://dx.doi.org/10.7717/peerj.167
247 241
248 Zdobnov EM, Apweiler R (2001) 242 Zdobnov EM, Apweiler R (2001)
249 InterProScan an integration platform for the signature-recognition methods in InterPro. 243 InterProScan an integration platform for the signature-recognition methods in InterPro.
250 Bioinformatics 17, 847-848. 244 Bioinformatics 17, 847-848.
251 http://dx.doi.org/10.1093/bioinformatics/17.9.847 245 http://dx.doi.org/10.1093/bioinformatics/17.9.847
260 Nucleic Acids Research 37 (Database Issue), D224-228. 254 Nucleic Acids Research 37 (Database Issue), D224-228.
261 http://dx.doi.org/10.1093/nar/gkn785 255 http://dx.doi.org/10.1093/nar/gkn785
262 256
263 257
264 This wrapper is available to install into other Galaxy Instances via the Galaxy Tool Shed at 258 This wrapper is available to install into other Galaxy Instances via the Galaxy Tool Shed at
265 http://toolshed.g2.bx.psu.edu/view/bgruening/interproscan 259 http://toolshed.g2.bx.psu.edu/view/bgruening/interproscan5
266 260
267 261
268 **Galaxy Wrapper Author**:: 262 **Galaxy Wrapper Author**::
269 263
270 * Bjoern Gruening, Pharmaceutical Bioinformatics, University of Freiburg 264 * Bjoern Gruening, University of Freiburg
271 * Konrad Paszkiewicz, Exeter Sequencing Service, University of Exeter 265 * Konrad Paszkiewicz, University of Exeter
272 266
273 </help> 267 </help>
274 </tool> 268 </tool>