Mercurial > repos > earlhaminst > ete

annotate ete_tree_generator.xml @ 0:276e3ee68c37 draft

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planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete commit 230ae552ddeb1bfdef3a09becaa5c6d373529a05-dirty
author earlhaminst
date Thu, 15 Dec 2016 12:55:02 -0500
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0
276e3ee68c37 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete commit 230ae552ddeb1bfdef3a09becaa5c6d373529a05-dirty
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1 <tool id="species_tree_generator" name="Species tree generator" version="3.0.0b35">
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2 <description>from a list of species using the ETE Toolkit</description>
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3 <requirements>
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4 <requirement type="package" version="3.0.0b35">ete3</requirement>
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5 </requirements>
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6 <stdio>
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7 <!-- Anything other than zero is an error -->
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8 <exit_code range="1:" />
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9 </stdio>
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10 <command>
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11 <![CDATA[
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12 python $__tool_directory__/ete_tree_generator.py
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13 -s '$speciesFile'
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14 #if $output_format.treebest == 'yes'
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15 -f 8
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16 #else
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17 -f ${output_format.format_selector}
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18 #end if
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19 -t $output_format.treebest
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20 -d $database
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21 ]]>
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22 </command>
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23 <inputs>
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24 <param name="speciesFile" type="data" format="txt" label="Species file" help="List with one species per line" />
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25 <conditional name="output_format">
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26 <param name="treebest" type="select" label="Use in TreeBest" help="Select yes if specie tree to be used in TreeBest">
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27 <option value="yes">Yes</option>
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28 <option value="no" selected="true">No</option>
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29 </param>
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30 <when value="yes" />
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31 <when value="no">
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32 <param name="format_selector" type="select" label="Output format" help="See table below">
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33 <option value="0" selected="true">Flexible with support values (0)</option>
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34 <option value="1">Flexible with internal node names (1)</option>
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35 <option value="2">All branches + leaf names + internal supports (2)</option>
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36 <option value="3">All branches + all names (3)</option>
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37 <option value="4">Leaf branches + leaf names (4)</option>
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38 <option value="5">Internal and leaf branches + leaf names (5)</option>
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39 <option value="6">Internal branches + leaf names (6)</option>
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40 <option value="7">Leaf branches + all names (7)</option>
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41 <option value="8">All names (8)</option>
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42 <option value="9">Leaf names (9)</option>
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43 <option value="100">Topology only (100)</option>
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44 </param>
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45 </when>
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46 </conditional>
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47 <param name="database" type="select" label="Update database" help="Update database from NCBI (slower)">
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48 <option value="no" selected="true">No</option>
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49 <option value="yes">Yes</option>
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50 </param>
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51 </inputs>
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52 <outputs>
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53 <data format="nhx" name="outputFile" label="${tool.name} on ${on_string}" from_work_dir="newickTree.nhx"/>
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54 </outputs>
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55 <tests>
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56 <test>
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57 <param name="speciesFile" ftype="txt" value="species.txt" />
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58 <param name="treebest" value="yes" />
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59 <output name="outputFile" file="out.nhx" />
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60 </test>
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61 </tests>
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62 <help>
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63 <![CDATA[
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64 Generate a species tree from a list of species using the `ETE Toolkit`_.
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65
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66 .. _ETE Toolkit: http://etetoolkit.org/
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67
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68 **Output format:**
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69
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70 ======= ============================================= ========================================================================================
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71 FORMAT DESCRIPTION SAMPLE
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72 ------- --------------------------------------------- ----------------------------------------------------------------------------------------
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73 0 flexible with support values ((D:0.723274,F:0.567784)1.000000:0.067192,(B:0.279326,H:0.756049)1.000000:0.807788);
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74 1 flexible with internal node names ((D:0.723274,F:0.567784)E:0.067192,(B:0.279326,H:0.756049)B:0.807788);
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75 2 all branches + leaf names + internal supports ((D:0.723274,F:0.567784)1.000000:0.067192,(B:0.279326,H:0.756049)1.000000:0.807788);
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76 3 all branches + all names ((D:0.723274,F:0.567784)E:0.067192,(B:0.279326,H:0.756049)B:0.807788);
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77 4 leaf branches + leaf names ((D:0.723274,F:0.567784),(B:0.279326,H:0.756049));
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78 5 internal and leaf branches + leaf names ((D:0.723274,F:0.567784):0.067192,(B:0.279326,H:0.756049):0.807788);
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79 6 internal branches + leaf names ((D,F):0.067192,(B,H):0.807788);
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80 7 leaf branches + all names ((D:0.723274,F:0.567784)E,(B:0.279326,H:0.756049)B);
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81 8 all names ((D,F)E,(B,H)B);
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82 9 leaf names ((D,F),(B,H));
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83 100 topology only ((,),(,));
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84 ======= ============================================= ========================================================================================
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85 ]]>
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86 </help>
276e3ee68c37 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete commit 230ae552ddeb1bfdef3a09becaa5c6d373529a05-dirty
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87 <citations>
276e3ee68c37 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete commit 230ae552ddeb1bfdef3a09becaa5c6d373529a05-dirty
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88 <citation type="doi">10.1093/molbev/msw046</citation>
276e3ee68c37 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete commit 230ae552ddeb1bfdef3a09becaa5c6d373529a05-dirty
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89 </citations>
276e3ee68c37 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete commit 230ae552ddeb1bfdef3a09becaa5c6d373529a05-dirty
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90 </tool>