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1 <tool id="Psortb" name="psortb" version="0.0.1">
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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">psortb.py "\$NSLOTS" "$type" "$long" "$cutoff" "$divergent" "$sequence" "$outfile"</command>
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8 <stdio>
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9 <!-- Anything other than zero is an error -->
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10 <exit_code range="1:" />
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11 <exit_code range=":-1" />
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12 </stdio>
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13 <inputs>
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14 <param format="fasta" name="sequence" type="data"
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15 label="Input sequences for which to predict localisation (protein FASTA format)" />
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16 <param name="type" type="select"
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17 label="Organism type (N.B. all sequences in the above file must be of the same type)" >
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18 <option value="-p">Gram positive bacteria</option>
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19 <option value="-n">Gram negative bacteria</option>
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20 <option value="-a">Archaea</option>
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21 </param>
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22 <param name="long" type="select" label="Output type">
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23 <option value="terse">Short (terse, tabular with 3 columns)</option>
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24 <!-- The normal output is text, not tabular - worth offering?
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25 <option value="normal">Normal</option>
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26 -->
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27 <option value="long">Long (verbose, tabular with about 30 columns, depending on organism type)</option>
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28 </param>
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29 <param name="cutoff" size="10" type="float" optional="true" value=""
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30 label="Sets a cutoff value for reported results (e.g. 7.5)"
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31 help="Leave blank or use zero for no cutoff." />
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32 <param name="divergent" size="10" type="float" optional="true" value=""
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33 label="Sets a cutoff value for the multiple localization flag (e.g. 4.5)"
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34 help="Leave blank or use zero for no cutoff." />
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35 </inputs>
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36 <outputs>
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37 <data format="tabular" name="outfile" />
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38 </outputs>
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39 <requirements>
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40 <requirement type="binary">psort</requirement>
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41 </requirements>
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42 <tests>
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43 <test>
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44 <param name="sequence" value="k12_ten_proteins.fasta" ftype="fasta"/>
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45 <param name="long" value="terse"/>
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46 <output name="outfile" file="k12_ten_proteins_psortb_p_terse.tabular" ftype="tabular"/>
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47 </test>
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48 </tests>
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49 <help>
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50
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51 **What it does**
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52
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53 This calls the command line tool PSORTb v3.0 for prediction of prokaryotic
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54 localization sites. The input dataset needs to be protein FASTA sequences.
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55 The default output is a simple tabular file with three columns, one row
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56 per query sequence:
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57
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58 ====== ==============================
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59 Column Description
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60 ------ ------------------------------
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61 1 Sequence identifier
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62 2 Localisation, e.g. Cytoplasmic
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63 3 Score
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64 ====== ==============================
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65
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66 The long output is also tabular with one row per query sequence, but has
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67 lots more columns (a different set for each supported organism type). In
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68 both cases, a simple header line is included (starting with a hash, #,
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69 so that Galaxy treats it as a comment) giving the column names.
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70
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71
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72 **References**
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73
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74 N.Y. Yu, J.R. Wagner, M.R. Laird, G. Melli, S. Rey, R. Lo, P. Dao,
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75 S.C. Sahinalp, M. Ester, L.J. Foster, F.S.L. Brinkman (2010)
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76 PSORTb 3.0: Improved protein subcellular localization prediction with
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77 refined localization subcategories and predictive capabilities for all
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78 prokaryotes, Bioinformatics 26(13):1608-1615
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79 http://dx.doi.org/10.1093/bioinformatics/btq249
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80
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81 http://www.psort.org/documentation/index.html
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82
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83 </help>
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84 </tool>
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