Mercurial > repos > crs4 > edge_pro
annotate get_edge_data.xml @ 6:e6e6f5f9b9c4 draft default tip
planemo upload for repository https://bitbucket.org/crs4/orione-tools/src/bb-orione-tools/custom/edge_pro/ commit 02541df6373bc61be0cdc0617c8549cf8b49b832
| author | crs4 |
|---|---|
| date | Thu, 31 Aug 2017 12:54:08 -0400 |
| parents | ddcbf8732706 |
| children |
| rev | line source |
|---|---|
| 0 | 1 <tool id="get_edge_data" name="Get EDGE-pro files" version="1.0.1"> |
| 2 <description></description> | |
| 3 <command interpreter="python">get_edge_data.py -i "$gbkid" --fna $fnafile --ptt $pttfile --rnt $rntfile --gff $gfffile</command> | |
| 4 | |
| 5 <inputs> | |
| 6 <param name="gbkid" type="text" value="NC_" label="RefSeq Genomic Accession ID"> | |
| 7 <validator type="empty_field" /> | |
| 8 </param> | |
| 9 </inputs> | |
| 10 <outputs> | |
| 11 <data name="fnafile" format="fasta" label="${tool.name} on ${on_string}: FASTA" /> | |
| 12 <data name="pttfile" format="ptt" label="${tool.name} on ${on_string}: PTT" /> | |
| 13 <data name="rntfile" format="rnt" label="${tool.name} on ${on_string}: RNT" /> | |
| 14 <data name="gfffile" format="gff" label="${tool.name} on ${on_string}: GFF" /> | |
| 15 </outputs> | |
| 16 <tests> | |
| 17 | |
| 18 </tests> | |
| 19 <help> | |
| 20 **What it does** | |
| 21 | |
| 22 This tool retrieves from NCBI the files required by `EDGE-pro`_. | |
| 23 | |
| 24 .. _EDGE-pro: http://ccb.jhu.edu/software/EDGE-pro/ | |
| 25 | |
| 26 **License and citation** | |
| 27 | |
|
3
ddcbf8732706
Fix edge-pro tool dependency (uninstall and install again the tool dependency if you were encountering errors like 'Can't exec "./bowtie2-build": No such file or directory'). Update Orione citation.
crs4
parents:
2
diff
changeset
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28 This Galaxy tool is Copyright © 2012-2014 `CRS4 Srl.`_ and is released under the `MIT license`_. |
| 0 | 29 |
| 30 .. _CRS4 Srl.: http://www.crs4.it/ | |
| 31 .. _MIT license: http://opensource.org/licenses/MIT | |
| 32 | |
|
3
ddcbf8732706
Fix edge-pro tool dependency (uninstall and install again the tool dependency if you were encountering errors like 'Can't exec "./bowtie2-build": No such file or directory'). Update Orione citation.
crs4
parents:
2
diff
changeset
|
33 If you use this tool, please cite |Cuccuru2014|_. |
| 0 | 34 |
|
3
ddcbf8732706
Fix edge-pro tool dependency (uninstall and install again the tool dependency if you were encountering errors like 'Can't exec "./bowtie2-build": No such file or directory'). Update Orione citation.
crs4
parents:
2
diff
changeset
|
35 .. |Cuccuru2014| replace:: Cuccuru, G., Orsini, M., Pinna, A., Sbardellati, A., Soranzo, N., Travaglione, A., Uva, P., Zanetti, G., Fotia, G. (2014) Orione, a web-based framework for NGS analysis in microbiology. *Bioinformatics* 30(13), 1928-1929 |
|
ddcbf8732706
Fix edge-pro tool dependency (uninstall and install again the tool dependency if you were encountering errors like 'Can't exec "./bowtie2-build": No such file or directory'). Update Orione citation.
crs4
parents:
2
diff
changeset
|
36 .. _Cuccuru2014: http://bioinformatics.oxfordjournals.org/content/30/13/1928 |
| 0 | 37 </help> |
| 38 </tool> |