Mercurial > repos > peterjc > tmhmm_and_signalp
annotate tools/protein_analysis/psortb.xml @ 16:7de64c8b258d draft
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author | peterjc |
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date | Wed, 18 Sep 2013 06:16:58 -0400 |
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1 <tool id="Psortb" name="psortb" version="0.0.3"> |
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2 <description>Determines sub-cellular localisation of bacterial/archaeal protein sequences</description> |
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3 <!-- If job splitting is enabled, break up the query file into parts --> |
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4 <!-- Using 2000 chunks meaning 4 threads doing 500 each is ideal --> |
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5 <parallelism method="basic" split_inputs="fasta_file" split_mode="to_size" split_size="2000" merge_outputs="tabular_file"></parallelism> |
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6 <version_command interpreter="python">psortb.py --version</version_command> |
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7 <command interpreter="python"> |
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8 psortb.py "\$NSLOTS" "$type" "$long" "$cutoff" "$divergent" "$sequence" "$outfile" |
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9 ##I want the number of threads to be a Galaxy config option... |
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10 ##Set the number of threads in the runner entry in universe_wsgi.ini |
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11 ##which (on SGE at least) will set the $NSLOTS environment variable. |
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12 ##If the environment variable isn't set, get "", and python wrapper |
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13 ##defaults to four threads. |
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14 </command> |
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15 <stdio> |
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16 <!-- Anything other than zero is an error --> |
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17 <exit_code range="1:" /> |
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18 <exit_code range=":-1" /> |
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19 </stdio> |
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20 <inputs> |
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21 <param format="fasta" name="sequence" type="data" |
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22 label="Input sequences for which to predict localisation (protein FASTA format)" /> |
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23 <param name="type" type="select" |
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24 label="Organism type (N.B. all sequences in the above file must be of the same type)" > |
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25 <option value="-p">Gram positive bacteria</option> |
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26 <option value="-n">Gram negative bacteria</option> |
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27 <option value="-a">Archaea</option> |
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28 </param> |
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29 <param name="long" type="select" label="Output type"> |
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30 <option value="terse">Short (terse, tabular with 3 columns)</option> |
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31 <!-- The normal output is text, not tabular - worth offering? |
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32 <option value="normal">Normal</option> |
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33 --> |
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34 <option value="long">Long (verbose, tabular with about 30 columns, depending on organism type)</option> |
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35 </param> |
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36 <param name="cutoff" size="10" type="float" optional="true" value="" |
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37 label="Sets a cutoff value for reported results (e.g. 7.5)" |
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38 help="Leave blank or use zero for no cutoff." /> |
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39 <param name="divergent" size="10" type="float" optional="true" value="" |
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40 label="Sets a cutoff value for the multiple localization flag (e.g. 4.5)" |
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41 help="Leave blank or use zero for no cutoff." /> |
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42 </inputs> |
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43 <outputs> |
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44 <data format="tabular" name="outfile" /> |
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45 </outputs> |
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46 <requirements> |
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47 <requirement type="binary">psort</requirement> |
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48 </requirements> |
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49 <tests> |
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50 <test> |
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51 <param name="sequence" value="empty.fasta" ftype="fasta"/> |
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52 <param name="long" value="terse"/> |
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53 <output name="outfile" file="empty_psortb_terse.tabular" ftype="tabular"/> |
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54 </test> |
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55 <test> |
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56 <param name="sequence" value="k12_ten_proteins.fasta" ftype="fasta"/> |
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57 <param name="long" value="terse"/> |
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58 <output name="outfile" file="k12_ten_proteins_psortb_p_terse.tabular" ftype="tabular"/> |
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59 </test> |
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60 </tests> |
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61 <help> |
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62 |
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63 **What it does** |
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64 |
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65 This calls the command line tool PSORTb v3.0 for prediction of prokaryotic |
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66 localization sites. The input dataset needs to be protein FASTA sequences. |
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67 The default output is a simple tabular file with three columns, one row |
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68 per query sequence: |
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69 |
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70 ====== ============================== |
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71 Column Description |
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72 ------ ------------------------------ |
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73 1 Sequence identifier |
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74 2 Localisation, e.g. Cytoplasmic |
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75 3 Score |
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76 ====== ============================== |
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77 |
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78 The long output is also tabular with one row per query sequence, but has |
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79 lots more columns (a different set for each supported organism type). In |
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80 both cases, a simple header line is included (starting with a hash, #, |
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81 so that Galaxy treats it as a comment) giving the column names. |
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82 |
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83 |
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84 **References** |
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85 |
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86 If you use this Galaxy tool in work leading to a scientific publication please |
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87 cite the following papers: |
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88 |
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89 Peter J.A. Cock, Björn A. Grüning, Konrad Paszkiewicz and Leighton Pritchard (2013). |
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90 Galaxy tools and workflows for sequence analysis with applications |
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91 in molecular plant pathology. PeerJ 1:e167 |
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92 http://dx.doi.org/10.7717/peerj.167 |
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93 |
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94 N.Y. Yu, J.R. Wagner, M.R. Laird, G. Melli, S. Rey, R. Lo, P. Dao, |
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95 S.C. Sahinalp, M. Ester, L.J. Foster, F.S.L. Brinkman (2010) |
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96 PSORTb 3.0: Improved protein subcellular localization prediction with |
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97 refined localization subcategories and predictive capabilities for all |
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98 prokaryotes, Bioinformatics 26(13):1608-1615 |
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99 http://dx.doi.org/10.1093/bioinformatics/btq249 |
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100 |
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101 See also http://www.psort.org/documentation/index.html |
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102 |
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103 This wrapper is available to install into other Galaxy Instances via the Galaxy |
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104 Tool Shed at http://toolshed.g2.bx.psu.edu/view/peterjc/tmhmm_and_signalp |
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105 </help> |
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106 </tool> |