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Migrated tool version 0.1 from old tool shed archive to new tool shed repository
author fubar
date Tue, 07 Jun 2011 17:43:58 -0400
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cec2527697f6 Migrated tool version 0.1 from old tool shed archive to new tool shed repository
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1 <tool id="weblogo3" name="Sequence Logo" version="0.1">
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2 <description>generator for fasta (eg Clustal alignments)</description>
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3 <command>
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4 weblogo -F $outformat -s $size -f $input -o $output -t "$logoname"
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5 </command>
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6 <inputs>
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7 <page>
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8 <param format="fasta" name="input" type="data" label="Fasta File" />
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9 <param name="logoname" label="Name for output logo - will appear on graphics" type="text" size="50" value="Galaxy/Rgenetics weblogo" />
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10 <param name="outformat" type="select" label="Output weblogo format" >
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11 <option value="png" selected="True">PNG screen quality</option>
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12 <option value="png_print">High quality printable PNG</option>
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13 <option value="pdf">PDF</option>
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14 <option value="jpeg">JPG</option>
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15 <option value="eps">EPS</option>
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16 <option value="txt">Text (shows the detailed calculations for each position - no image)</option>
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17 </param>
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18 <param name="size" type="select" label="Output weblogo size" >
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19 <option value="large" selected="True">Large</option>
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20 <option value="medium">Medium</option>
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21 <option value="small">Small</option>
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22 </param>
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23 </page>
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24 </inputs>
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25 <outputs>
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26 <data format="pdf" name="output" label="${logoname}_output.${outformat}">
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27 <change_format>
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28 <when input="outformat" value="png_print" format="png" />
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29 <when input="outformat" value="png" format="png" />
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30 <when input="outformat" value="jpeg" format="jpg" />
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31 <when input="outformat" value="eps" format="eps" />
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32 <when input="outformat" value="txt" format="txt" />
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33 </change_format>
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34 </data>
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35 </outputs>
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36 <tests>
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37 <test>
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38
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39 <param name="input" value="rgClustal_testout.fasta" />
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40 <param name = "logoname" value="Galaxy/Rgenetics weblogo" />
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41 <param name = "outformat" value="jpeg" />
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42 <param name = "size" value="medium" />
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43
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44 <output name="output" file="rgWebLogo3_test.jpg" ftype="jpg" />
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45 </test>
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46
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47 </tests>
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48 <help>
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49
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50 **Note**
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51
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52 This tool uses Weblogo3_ in Galaxy to generate a sequence logo. The input file must be a fasta file in your current history.
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53
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54 A typical output looks like this
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55
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56 .. image:: ./static/images/rgWebLogo3_test.jpg
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57
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58 ----
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59
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60 **Why use WebLogo in Galaxy?**
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61
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62 Weblogo3_ is a good example of an easy to use tool and there are plenty of other web accessible weblogo generator sites available.
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63
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64 However, none of those offer the combination of:
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65
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66 1) persistence of analyses and data in multiple shareable histories, pages and libraries
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67
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68 2) convenient access to shared data libraries, workflows and user controlled pages, and to 3rd party data sources like UCSC tables.
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69
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70 3) analyses integrated with many other applicable generic and specialized tools already available for downstream processing.
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71
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72 that you get for free when you use Galaxy. No muss; no fuss.
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73
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74 ----
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75
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76 **Attribution**
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77
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78 Weblogo attribution and associated documentation are available at Weblogo3_
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79
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80 This wrapper was written by Ross Lazarus for the rgenetics project and the source code is licensed under the LGPL_ like other rgenetics artefacts
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81
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82 .. _Weblogo3: http://weblogo.berkeley.edu/
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83
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84 .. _LGPL: http://www.gnu.org/copyleft/lesser.html
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85
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86 </help>
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87
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88 </tool>
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89
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90