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annotate alignment/phytab_mview.xml @ 0:5b9a38ec4a39 draft default tip

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author osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
date Tue, 11 Mar 2014 12:19:13 -0700
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1 <tool id="mview_phytab_python" name="phytab_MView" version="1.0">
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2 <description>View multiple phytab sequence alignments in HTML</description>
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3 <requirements><requirement type="package">mview</requirement></requirements>
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4 <command interpreter="python">phytab_mview.py $phytabinput $dna $output "$output.extra_files_path"
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5 </command>
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6
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7 <inputs>
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8 <param format="tabular" name="phytabinput" type="data" label="Phytab file of aligned genes to visualize" />
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9 <param name="dna" type="select" label="Data type">
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10 <option value="dna">DNA</option>
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11 <option value="protein">Protein</option>
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12 </param>
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13 </inputs>
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14
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15 <outputs>
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16 <data format="html" name="output" label="${tool.name} on ${on_string}: Alignment"/>
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17 </outputs>
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18 <help>
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19 **What it does**
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20
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21 This tool uses the MVIEW package to convert an aligned sequences file in phytab format (ie, phytab_PRANK or phytab_MUSCLE output) to HTML for visualizing each gene's alignment directly in Galaxy.
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22
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23 ------
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24
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25 **Input**
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26
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27 ALIGNED phytab example input (fields are tab-delimited)::
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28
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29 Species_1 GeneA UniqueID AAAATGCCTA-GTC
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30 Species_2 GeneA UniqueID AAATTGCCTA-GTG
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31 Species_3 GeneA UniqueID AAAATGGCTAGGAC
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32 Species_1 GeneB UniqueID TACGTAG-CTTGATCCTATAA
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33 Species_2 GeneB UniqueID TACGTAGTCTAGATCCTATAA
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34 Species_3 GeneB UniqueID TACGTAGTCTTGATGGTATAA
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35
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36 ------
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37
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38 **Output**
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39
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40 links to html files for viewing multiple sequence alignments
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41
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42 ------
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43
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44 **Additional Information**
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45
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46 For large datasets, this tool can be slow, as this version runs serially. For a
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47 parallel version that sends different genes to different processors, contact
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48 ucsb_phylogenetics@lifesci.ucsb.edu
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49
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50 Please direct questions or comments to ucsb_phylogenetics@lifesci.ucsb.edu or, if you can, enter them on the osiris_phylogenetics site at
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51 bitbucket.org
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52
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53 ------
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54
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55 **Citations**
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56
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57 This tool is part of the Osiris Phylogenetics Tool Package for Galaxy. If you make extensive use of this tool in a publication, please consider citing the following.
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58
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59 Current Osiris Citation is here
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60
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61 http://osiris-phylogenetics.blogspot.com/2012/10/citation.html
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62
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63 Additional Citations for this tool
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64
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65 Citation for MView:
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66 Brown, N.P., Leroy C., Sander C. (1998). MView: A Web compatible database search or multiple alignment viewer. Bioinformatics. 14(4):380-381.
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67
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68 </help>
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69 </tool>