Mercurial > repos > peterjc > clinod
annotate tools/clinod/clinod.xml @ 6:77cfe958b5ea draft
v0.0.9 record clinod version
| author | peterjc |
|---|---|
| date | Tue, 01 Sep 2015 06:54:03 -0400 |
| parents | 9485cdfca57e |
| children | f61366a4a14e |
| rev | line source |
|---|---|
| 6 | 1 <tool id="clinod" name="Nucleolar localization sequence Detector (NoD)" version="0.0.9"> |
| 2 | 2 <description>Find nucleolar localization signals (NoLSs) in protein sequences</description> |
| 3 <requirements> | |
| 4 <requirement type="binary">java</requirement> | |
| 5 <requirement type="package" version="1.3">clinod</requirement> | |
| 6 </requirements> | |
| 5 | 7 <stdio> |
| 8 <!-- Assume anything other than zero is an error --> | |
| 9 <exit_code range="1:" /> | |
| 10 <exit_code range=":-1" /> | |
| 11 </stdio> | |
| 6 | 12 <version_command> |
| 13 ##The first non-blank line contains the version information, e.g. | |
| 14 ##NucleOlar localization sequence Detector v. 1.3b (13 May 2011) | |
| 15 ##Question: Why don't we have to escape the dollar here? | |
| 16 java -jar $CLINOD/clinod-1.3.jar | grep -i "^NucleOlar localization sequence Detector" | |
| 17 </version_command> | |
| 2 | 18 <command> |
| 19 ##The Galaxy Tool Shed installation should define $CLINOD to point at folder | |
| 20 ##containing both clinod-1.3.jar and the batchman binary: | |
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21 java -jar \$CLINOD/clinod-1.3.jar -in="$fasta_file" -out="$tabular_file" -t="\$GALAXY_SLOTS" -f=MEDIUM_TAB -nonols -clean_sequence |
| 2 | 22 ##TODO - Make the -clean_sequence argument a parameter? |
| 23 </command> | |
| 24 <inputs> | |
| 25 <param name="fasta_file" type="data" format="fasta" label="FASTA file of protein sequences"/> | |
| 26 </inputs> | |
| 27 <outputs> | |
| 28 <data name="tabular_file" format="tabular" label="NoD results" /> | |
| 29 </outputs> | |
| 30 <tests> | |
| 31 <test> | |
| 32 <param name="fasta_file" value="four_human_proteins.fasta" ftype="fasta" /> | |
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4d9a4a43861b
Uploaded v0.0.7, uses $GALAXY_SLOTS and embeds citation in tool XML.
peterjc
parents:
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33 <output name="tabular_file" file="four_human_proteins.clinod-1.3.tabular" ftype="tabular" /> |
| 2 | 34 </test> |
| 35 </tests> | |
| 36 <help> | |
| 37 | |
| 38 **What it does** | |
| 39 | |
| 40 This calls the command line version of the NoD tool from the Barton Group for | |
| 41 prediction of nucleolar localization sequences (NoLSs). The NoD tool uses an | |
| 42 artificial neural network trained on a set of human NoLSs. | |
| 43 | |
| 44 The nucleolus is a sub-compartmentof the nucleus, thus an NoLS can be regarded | |
| 45 as a special nuclear localization sequence (NLS). | |
| 46 | |
| 47 The input is a FASTA file of protein sequences, and the output is tabular with | |
| 48 four columns (multiple rows per protein): | |
| 49 | |
| 50 ====== =================== | |
| 51 Column Description | |
| 52 ------ ------------------- | |
| 53 1 Sequence identifier | |
| 54 2 Start of NoLS | |
| 55 3 End of NoLS | |
| 56 4 NoLS sequence | |
| 57 ====== =================== | |
| 58 | |
| 59 If a sequence has no predicted NoLS, then there is no line in the output file | |
| 60 for it. | |
| 61 | |
| 62 ----- | |
| 63 | |
| 64 **References** | |
| 65 | |
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66 If you use this Galaxy tool in work leading to a scientific publication please |
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67 cite the following papers: |
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68 |
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69 Peter J.A. Cock, Björn A. Grüning, Konrad Paszkiewicz and Leighton Pritchard (2013). |
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70 Galaxy tools and workflows for sequence analysis with applications |
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71 in molecular plant pathology. PeerJ 1:e167 |
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72 http://dx.doi.org/10.7717/peerj.167 |
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73 |
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74 M. S. Scott, F. M. Boisvert, M. D. McDowall, A. I. Lamond and G. J. Barton (2010). |
| 2 | 75 Characterization and prediction of protein nucleolar localization sequences. |
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76 Nucleic Acids Research 38(21), 7388-7399. |
| 2 | 77 http://dx.doi.org/10.1093/nar/gkq653 |
| 78 | |
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79 M. S. Scott, P. V. Troshin and G. J. Barton (2011). |
| 2 | 80 NoD: a Nucleolar localization sequence detector for eukaryotic and viral proteins. |
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81 BMC Bioinformatics, 12:317. |
| 2 | 82 http://dx.doi.org/10.1186/1471-2105-12-317 |
| 83 | |
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84 See also http://www.compbio.dundee.ac.uk/www-nod/ |
| 2 | 85 |
| 86 This wrapper is available to install into other Galaxy Instances via the Galaxy | |
| 87 Tool Shed at http://toolshed.g2.bx.psu.edu/view/peterjc/clinod | |
| 88 | |
| 89 </help> | |
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4
4d9a4a43861b
Uploaded v0.0.7, uses $GALAXY_SLOTS and embeds citation in tool XML.
peterjc
parents:
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90 <citations> |
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4d9a4a43861b
Uploaded v0.0.7, uses $GALAXY_SLOTS and embeds citation in tool XML.
peterjc
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91 <citation type="doi">10.7717/peerj.167</citation> |
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4d9a4a43861b
Uploaded v0.0.7, uses $GALAXY_SLOTS and embeds citation in tool XML.
peterjc
parents:
3
diff
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|
92 <citation type="doi">10.1093/nar/gkq653</citation> |
|
4d9a4a43861b
Uploaded v0.0.7, uses $GALAXY_SLOTS and embeds citation in tool XML.
peterjc
parents:
3
diff
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|
93 <citation type="doi">10.1186/1471-2105-12-317</citation> |
|
4d9a4a43861b
Uploaded v0.0.7, uses $GALAXY_SLOTS and embeds citation in tool XML.
peterjc
parents:
3
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|
94 </citations> |
| 2 | 95 </tool> |