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annotate tools/protein_analysis/psortb.xml @ 20:a19b3ded8f33 draft

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v0.2.11 Job splitting fast-fail; RXLR tools supports HMMER2 from BioConda; Capture more version information; misc internal changes
author peterjc
date Thu, 21 Sep 2017 11:35:20 -0400
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1 <tool id="Psortb" name="psortb" version="0.0.9">
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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 <requirements>
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7 <requirement type="package">psort</requirement>
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8 </requirements>
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9 <version_command>
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10 python $__tool_directory__/psortb.py --version
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11 </version_command>
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12 <command detect_errors="aggressive">
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13 python $__tool_directory__/psortb.py "\$GALAXY_SLOTS" '$type' '$long' '$cutoff' '$divergent' '$sequence' '$outfile'
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14 </command>
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15 <inputs>
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16 <param format="fasta" name="sequence" type="data"
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17 label="Input sequences for which to predict localisation (protein FASTA format)" />
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18 <param name="type" type="select"
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19 label="Organism type (N.B. all sequences in the above file must be of the same type)" >
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20 <option value="-p">Gram positive bacteria</option>
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21 <option value="-n">Gram negative bacteria</option>
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22 <option value="-a">Archaea</option>
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23 </param>
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24 <param name="long" type="select" label="Output type">
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25 <option value="terse">Short (terse, tabular with 3 columns)</option>
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26 <!-- The normal output is text, not tabular - worth offering?
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27 <option value="normal">Normal</option>
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28 -->
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29 <option value="long">Long (verbose, tabular with about 30 columns, depending on organism type)</option>
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30 </param>
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31 <param name="cutoff" size="10" type="float" optional="true" value=""
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32 label="Sets a cutoff value for reported results (e.g. 7.5)"
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33 help="Leave blank or use zero for no cutoff." />
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34 <param name="divergent" size="10" type="float" optional="true" value=""
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35 label="Sets a cutoff value for the multiple localization flag (e.g. 4.5)"
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36 help="Leave blank or use zero for no cutoff." />
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37 </inputs>
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38 <outputs>
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39 <data format="tabular" name="outfile" />
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40 </outputs>
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41 <tests>
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42 <test>
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43 <param name="sequence" value="empty.fasta" ftype="fasta"/>
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44 <param name="long" value="terse"/>
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45 <output name="outfile" file="empty_psortb_terse.tabular" ftype="tabular"/>
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46 </test>
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47 <test>
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48 <param name="sequence" value="k12_ten_proteins.fasta" ftype="fasta"/>
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49 <param name="long" value="terse"/>
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50 <output name="outfile" file="k12_ten_proteins_psortb_p_terse.tabular" ftype="tabular"/>
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51 </test>
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52 </tests>
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53 <help>
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54
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55 **What it does**
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56
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57 This calls the command line tool PSORTb v3.0 for prediction of prokaryotic
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58 localization sites. The input dataset needs to be protein FASTA sequences.
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59 The default output is a simple tabular file with three columns, one row
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60 per query sequence:
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61
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62 ====== ==============================
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63 Column Description
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64 ------ ------------------------------
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65 1 Sequence identifier
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66 2 Localisation, e.g. Cytoplasmic
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67 3 Score
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68 ====== ==============================
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69
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70 The long output is also tabular with one row per query sequence, but has
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71 lots more columns (a different set for each supported organism type). In
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72 both cases, a simple header line is included (starting with a hash, #,
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73 so that Galaxy treats it as a comment) giving the column names.
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74
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75
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76 **References**
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77
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78 If you use this Galaxy tool in work leading to a scientific publication please
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79 cite the following papers:
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80
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81 Peter J.A. Cock, Björn A. Grüning, Konrad Paszkiewicz and Leighton Pritchard (2013).
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82 Galaxy tools and workflows for sequence analysis with applications
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83 in molecular plant pathology. PeerJ 1:e167
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84 http://dx.doi.org/10.7717/peerj.167
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85
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86 N.Y. Yu, J.R. Wagner, M.R. Laird, G. Melli, S. Rey, R. Lo, P. Dao,
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87 S.C. Sahinalp, M. Ester, L.J. Foster, F.S.L. Brinkman (2010)
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88 PSORTb 3.0: Improved protein subcellular localization prediction with
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89 refined localization subcategories and predictive capabilities for all
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90 prokaryotes, Bioinformatics 26(13):1608-1615
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91 http://dx.doi.org/10.1093/bioinformatics/btq249
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92
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93 See also http://www.psort.org/documentation/index.html
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94
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95 This wrapper is available to install into other Galaxy Instances via the Galaxy
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96 Tool Shed at http://toolshed.g2.bx.psu.edu/view/peterjc/tmhmm_and_signalp
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97 </help>
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98 <citations>
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99 <citation type="doi">10.7717/peerj.167</citation>
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100 <citation type="doi">10.1093/bioinformatics/btq249</citation>
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101 </citations>
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102 </tool>