Mercurial > repos > peterjc > tmhmm_and_signalp
annotate tools/protein_analysis/psortb.xml @ 25:41a42022f815 draft
Uploaded v0.2.6, embedded citations
| author | peterjc |
|---|---|
| date | Fri, 21 Nov 2014 08:17:36 -0500 |
| parents | 90e3d02f8013 |
| children | 20139cb4c844 |
| rev | line source |
|---|---|
| 25 | 1 <tool id="Psortb" name="psortb" version="0.0.5"> |
| 8 | 2 <description>Determines sub-cellular localisation of bacterial/archaeal protein sequences</description> |
| 3 <!-- If job splitting is enabled, break up the query file into parts --> | |
| 4 <!-- Using 2000 chunks meaning 4 threads doing 500 each is ideal --> | |
| 5 <parallelism method="basic" split_inputs="fasta_file" split_mode="to_size" split_size="2000" merge_outputs="tabular_file"></parallelism> | |
| 6 <version_command interpreter="python">psortb.py --version</version_command> | |
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7 <command interpreter="python"> |
| 25 | 8 psortb.py "\$GALAXY_SLOTS" "$type" "$long" "$cutoff" "$divergent" "$sequence" "$outfile" |
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9 ##If the environment variable isn't set, get "", and python wrapper |
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10 ##defaults to four threads. |
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11 </command> |
| 8 | 12 <stdio> |
| 13 <!-- Anything other than zero is an error --> | |
| 14 <exit_code range="1:" /> | |
| 15 <exit_code range=":-1" /> | |
| 16 </stdio> | |
| 17 <inputs> | |
| 18 <param format="fasta" name="sequence" type="data" | |
| 25 | 19 label="Input sequences for which to predict localisation (protein FASTA format)" /> |
| 8 | 20 <param name="type" type="select" |
| 25 | 21 label="Organism type (N.B. all sequences in the above file must be of the same type)" > |
| 8 | 22 <option value="-p">Gram positive bacteria</option> |
| 23 <option value="-n">Gram negative bacteria</option> | |
| 24 <option value="-a">Archaea</option> | |
| 25 </param> | |
| 26 <param name="long" type="select" label="Output type"> | |
| 27 <option value="terse">Short (terse, tabular with 3 columns)</option> | |
| 28 <!-- The normal output is text, not tabular - worth offering? | |
| 29 <option value="normal">Normal</option> | |
| 30 --> | |
| 31 <option value="long">Long (verbose, tabular with about 30 columns, depending on organism type)</option> | |
| 32 </param> | |
| 33 <param name="cutoff" size="10" type="float" optional="true" value="" | |
| 25 | 34 label="Sets a cutoff value for reported results (e.g. 7.5)" |
| 35 help="Leave blank or use zero for no cutoff." /> | |
| 8 | 36 <param name="divergent" size="10" type="float" optional="true" value="" |
| 25 | 37 label="Sets a cutoff value for the multiple localization flag (e.g. 4.5)" |
| 38 help="Leave blank or use zero for no cutoff." /> | |
| 8 | 39 </inputs> |
| 40 <outputs> | |
| 41 <data format="tabular" name="outfile" /> | |
| 42 </outputs> | |
| 43 <requirements> | |
| 44 <requirement type="binary">psort</requirement> | |
| 45 </requirements> | |
| 46 <tests> | |
| 47 <test> | |
| 11 | 48 <param name="sequence" value="empty.fasta" ftype="fasta"/> |
| 49 <param name="long" value="terse"/> | |
| 50 <output name="outfile" file="empty_psortb_terse.tabular" ftype="tabular"/> | |
| 51 </test> | |
| 52 <test> | |
| 8 | 53 <param name="sequence" value="k12_ten_proteins.fasta" ftype="fasta"/> |
| 54 <param name="long" value="terse"/> | |
| 55 <output name="outfile" file="k12_ten_proteins_psortb_p_terse.tabular" ftype="tabular"/> | |
| 56 </test> | |
| 57 </tests> | |
| 58 <help> | |
| 59 | |
| 60 **What it does** | |
| 61 | |
| 62 This calls the command line tool PSORTb v3.0 for prediction of prokaryotic | |
| 63 localization sites. The input dataset needs to be protein FASTA sequences. | |
| 64 The default output is a simple tabular file with three columns, one row | |
| 65 per query sequence: | |
| 66 | |
| 67 ====== ============================== | |
| 68 Column Description | |
| 69 ------ ------------------------------ | |
| 70 1 Sequence identifier | |
| 71 2 Localisation, e.g. Cytoplasmic | |
| 72 3 Score | |
| 73 ====== ============================== | |
| 74 | |
| 75 The long output is also tabular with one row per query sequence, but has | |
| 76 lots more columns (a different set for each supported organism type). In | |
| 77 both cases, a simple header line is included (starting with a hash, #, | |
| 78 so that Galaxy treats it as a comment) giving the column names. | |
| 79 | |
| 80 | |
| 81 **References** | |
| 82 | |
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83 If you use this Galaxy tool in work leading to a scientific publication please |
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84 cite the following papers: |
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85 |
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86 Peter J.A. Cock, Björn A. Grüning, Konrad Paszkiewicz and Leighton Pritchard (2013). |
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87 Galaxy tools and workflows for sequence analysis with applications |
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88 in molecular plant pathology. PeerJ 1:e167 |
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89 http://dx.doi.org/10.7717/peerj.167 |
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90 |
| 8 | 91 N.Y. Yu, J.R. Wagner, M.R. Laird, G. Melli, S. Rey, R. Lo, P. Dao, |
| 92 S.C. Sahinalp, M. Ester, L.J. Foster, F.S.L. Brinkman (2010) | |
| 93 PSORTb 3.0: Improved protein subcellular localization prediction with | |
| 94 refined localization subcategories and predictive capabilities for all | |
| 95 prokaryotes, Bioinformatics 26(13):1608-1615 | |
| 96 http://dx.doi.org/10.1093/bioinformatics/btq249 | |
| 97 | |
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98 See also http://www.psort.org/documentation/index.html |
| 8 | 99 |
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100 This wrapper is available to install into other Galaxy Instances via the Galaxy |
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101 Tool Shed at http://toolshed.g2.bx.psu.edu/view/peterjc/tmhmm_and_signalp |
| 25 | 102 <citations> |
| 103 <citation type="doi">10.7717/peerj.167</citation> | |
| 104 <citation type="doi">10.1093/bioinformatics/btq249</citation> | |
| 105 </citations> | |
| 8 | 106 </help> |
| 107 </tool> |