Mercurial > repos > earlhaminst > ete

annotate ete_species_tree_generator.xml @ 14:d40b9a7debe5 draft default tip

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author earlhaminst
date Thu, 07 Mar 2024 19:39:30 +0000
parents f1eca1158f21
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1 <tool id="ete_species_tree_generator" name="ETE species tree generator" version="@VERSION@">
1
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2 <description>from a list of species using the ETE Toolkit</description>
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3 <macros>
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4 <import>ete_macros.xml</import>
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5 </macros>
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6 <expand macro="bio_tools"/>
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7 <expand macro="requirements" />
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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 </stdio>
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12 <command><![CDATA[
2
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13 python '$__tool_directory__/ete_species_tree_generator.py'
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14 -s '$speciesFile'
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15 -d $database
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16 -o '$outputFile'
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17 #if $output_format.treebest == 'yes'
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18 -f 8
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19 #else
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20 -f ${output_format.format_selector}
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21 #end if
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22 -t $output_format.treebest
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23 ]]></command>
1
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24 <inputs>
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25 <param name="speciesFile" type="data" format="txt" label="Species file" help="List with one species per line" />
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26 <param name="database" type="data" format="sqlite" label="(ETE3) Taxonomy Database" help="The sqlite formatted Taxonomy used by ETE3 (which is derived from NCBI taxonomy)" />
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27 <conditional name="output_format">
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28 <param name="treebest" type="select" label="Use in TreeBest" help="Select yes if specie tree to be used in TreeBest">
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29 <option value="yes">Yes</option>
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30 <option value="no" selected="true">No</option>
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31 </param>
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32 <when value="yes" />
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33 <when value="no">
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34 <param name="format_selector" type="select" label="Output format" help="See table below">
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35 <option value="0" selected="true">Flexible with support values (0)</option>
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36 <option value="1">Flexible with internal node names (1)</option>
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37 <option value="2">All branches + leaf names + internal supports (2)</option>
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38 <option value="3">All branches + all names (3)</option>
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39 <option value="4">Leaf branches + leaf names (4)</option>
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40 <option value="5">Internal and leaf branches + leaf names (5)</option>
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41 <option value="6">Internal branches + leaf names (6)</option>
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42 <option value="7">Leaf branches + all names (7)</option>
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43 <option value="8">All names (8)</option>
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44 <option value="9">Leaf names (9)</option>
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45 <option value="100">Topology only (100)</option>
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46 </param>
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47 </when>
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48 </conditional>
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49 </inputs>
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50 <outputs>
2
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51 <data format="nhx" name="outputFile" label="${tool.name} on ${on_string}"/>
1
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52 </outputs>
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53 <tests>
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54 <test>
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55 <param name="speciesFile" ftype="txt" value="species.txt" />
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56 <param name="database" ftype="sqlite" value="taxdump.sqlite" />
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57 <param name="treebest" value="yes" />
2
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58 <output name="outputFile">
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59 <assert_contents>
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60 <has_text text="(Homosapiens*,Pantroglodytes*,Gorillagorillagorilla*)" />
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61 <has_text text=")root;" />
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62 </assert_contents>
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63 </output>
1
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64 </test>
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65 </tests>
3
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66 <help><![CDATA[
1
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67 Generate a species tree from a list of species using the `ETE Toolkit`_.
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68
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69 .. _ETE Toolkit: http://etetoolkit.org/
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70
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71 **Output format:**
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72
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73 ======= ============================================= ========================================================================================
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74 FORMAT DESCRIPTION SAMPLE
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75 ------- --------------------------------------------- ----------------------------------------------------------------------------------------
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76 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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77 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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78 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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79 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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80 4 leaf branches + leaf names ((D:0.723274,F:0.567784),(B:0.279326,H:0.756049));
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81 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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82 6 internal branches + leaf names ((D,F):0.067192,(B,H):0.807788);
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83 7 leaf branches + all names ((D:0.723274,F:0.567784)E,(B:0.279326,H:0.756049)B);
a4ba317fc713 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete commit df73a2add6dba8550867034e157ed0699b3b2f53
earlhaminst
parents:
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84 8 all names ((D,F)E,(B,H)B);
a4ba317fc713 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete commit df73a2add6dba8550867034e157ed0699b3b2f53
earlhaminst
parents:
diff changeset
85 9 leaf names ((D,F),(B,H));
a4ba317fc713 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete commit df73a2add6dba8550867034e157ed0699b3b2f53
earlhaminst
parents:
diff changeset
86 100 topology only ((,),(,));
a4ba317fc713 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete commit df73a2add6dba8550867034e157ed0699b3b2f53
earlhaminst
parents:
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87 ======= ============================================= ========================================================================================
3
077021c45b96 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete commit a22e605b871c2185e98d89598aebb2fa3a82bb8f
earlhaminst
parents: 2
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88 ]]></help>
2
03c10736e497 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete commit 91b634b8f9b131045bbbbf43cc8edbea59ac686b-dirty
earlhaminst
parents: 1
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89 <expand macro="citations" />
1
a4ba317fc713 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete commit df73a2add6dba8550867034e157ed0699b3b2f53
earlhaminst
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90 </tool>