Mercurial > repos > iuc > fasttree
annotate fasttree.xml @ 0:c7e73acfa3eb draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasttree commit e47dfac91821500d0fcfc43750d036662c7c43ca
author | iuc |
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date | Mon, 19 Feb 2018 11:36:31 -0500 |
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children | ef46a404db96 |
rev | line source |
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0
c7e73acfa3eb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasttree commit e47dfac91821500d0fcfc43750d036662c7c43ca
iuc
parents:
diff
changeset
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1 <?xml version="1.0"?> |
c7e73acfa3eb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasttree commit e47dfac91821500d0fcfc43750d036662c7c43ca
iuc
parents:
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changeset
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2 <tool id="fasttree" name="FASTTREE" version="@VERSION@"> |
c7e73acfa3eb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasttree commit e47dfac91821500d0fcfc43750d036662c7c43ca
iuc
parents:
diff
changeset
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3 <description>adjust short reads</description> |
c7e73acfa3eb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasttree commit e47dfac91821500d0fcfc43750d036662c7c43ca
iuc
parents:
diff
changeset
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4 <macros> |
c7e73acfa3eb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasttree commit e47dfac91821500d0fcfc43750d036662c7c43ca
iuc
parents:
diff
changeset
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5 <token name="@VERSION@">2.1.10</token> |
c7e73acfa3eb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasttree commit e47dfac91821500d0fcfc43750d036662c7c43ca
iuc
parents:
diff
changeset
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6 </macros> |
c7e73acfa3eb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasttree commit e47dfac91821500d0fcfc43750d036662c7c43ca
iuc
parents:
diff
changeset
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7 <requirements> |
c7e73acfa3eb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasttree commit e47dfac91821500d0fcfc43750d036662c7c43ca
iuc
parents:
diff
changeset
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8 <requirement type="package" version="@VERSION@">FastTree</requirement> |
c7e73acfa3eb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasttree commit e47dfac91821500d0fcfc43750d036662c7c43ca
iuc
parents:
diff
changeset
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9 </requirements> |
c7e73acfa3eb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasttree commit e47dfac91821500d0fcfc43750d036662c7c43ca
iuc
parents:
diff
changeset
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10 <version_command>FastTree</version_command> |
c7e73acfa3eb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasttree commit e47dfac91821500d0fcfc43750d036662c7c43ca
iuc
parents:
diff
changeset
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11 <command detect_errors="aggressive"> |
c7e73acfa3eb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasttree commit e47dfac91821500d0fcfc43750d036662c7c43ca
iuc
parents:
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changeset
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12 <![CDATA[ |
c7e73acfa3eb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasttree commit e47dfac91821500d0fcfc43750d036662c7c43ca
iuc
parents:
diff
changeset
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13 FastTree |
c7e73acfa3eb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasttree commit e47dfac91821500d0fcfc43750d036662c7c43ca
iuc
parents:
diff
changeset
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14 |
c7e73acfa3eb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasttree commit e47dfac91821500d0fcfc43750d036662c7c43ca
iuc
parents:
diff
changeset
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15 $model_selector.format |
c7e73acfa3eb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasttree commit e47dfac91821500d0fcfc43750d036662c7c43ca
iuc
parents:
diff
changeset
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16 $model_selector.model |
c7e73acfa3eb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasttree commit e47dfac91821500d0fcfc43750d036662c7c43ca
iuc
parents:
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changeset
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17 -nopr |
c7e73acfa3eb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasttree commit e47dfac91821500d0fcfc43750d036662c7c43ca
iuc
parents:
diff
changeset
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18 #if $input_selector.select_format == 'fasta': |
c7e73acfa3eb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasttree commit e47dfac91821500d0fcfc43750d036662c7c43ca
iuc
parents:
diff
changeset
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19 $input_selector.quote |
c7e73acfa3eb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasttree commit e47dfac91821500d0fcfc43750d036662c7c43ca
iuc
parents:
diff
changeset
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20 #else if $input_selector.select_format == 'phylip': |
c7e73acfa3eb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasttree commit e47dfac91821500d0fcfc43750d036662c7c43ca
iuc
parents:
diff
changeset
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21 -n $input_selector.num |
c7e73acfa3eb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasttree commit e47dfac91821500d0fcfc43750d036662c7c43ca
iuc
parents:
diff
changeset
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22 #end if |
c7e73acfa3eb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasttree commit e47dfac91821500d0fcfc43750d036662c7c43ca
iuc
parents:
diff
changeset
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23 #set $inform = $input_selector.intree_selector.intree_format |
c7e73acfa3eb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasttree commit e47dfac91821500d0fcfc43750d036662c7c43ca
iuc
parents:
diff
changeset
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24 #if $inform == 'one': |
c7e73acfa3eb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasttree commit e47dfac91821500d0fcfc43750d036662c7c43ca
iuc
parents:
diff
changeset
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25 -intree1 '$input_selector.intree_selector.start_tree' |
c7e73acfa3eb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasttree commit e47dfac91821500d0fcfc43750d036662c7c43ca
iuc
parents:
diff
changeset
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26 #else if $inform == 'many': |
c7e73acfa3eb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasttree commit e47dfac91821500d0fcfc43750d036662c7c43ca
iuc
parents:
diff
changeset
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27 -intree '$input_selector.intree_selector.start_tree' |
c7e73acfa3eb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasttree commit e47dfac91821500d0fcfc43750d036662c7c43ca
iuc
parents:
diff
changeset
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28 #end if |
c7e73acfa3eb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasttree commit e47dfac91821500d0fcfc43750d036662c7c43ca
iuc
parents:
diff
changeset
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29 #if $advanced_selector.maximize == 'max': |
c7e73acfa3eb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasttree commit e47dfac91821500d0fcfc43750d036662c7c43ca
iuc
parents:
diff
changeset
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30 #if $advanced_selector.cat_selector.conrate == 'no': |
c7e73acfa3eb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasttree commit e47dfac91821500d0fcfc43750d036662c7c43ca
iuc
parents:
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changeset
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31 -cat $advanced_selector.cat_selector.ratecat |
c7e73acfa3eb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasttree commit e47dfac91821500d0fcfc43750d036662c7c43ca
iuc
parents:
diff
changeset
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32 #else if $advanced_selector.cat_selector.conrate == 'yes': |
c7e73acfa3eb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasttree commit e47dfac91821500d0fcfc43750d036662c7c43ca
iuc
parents:
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changeset
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33 -nocat |
c7e73acfa3eb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasttree commit e47dfac91821500d0fcfc43750d036662c7c43ca
iuc
parents:
diff
changeset
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34 #end if |
c7e73acfa3eb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasttree commit e47dfac91821500d0fcfc43750d036662c7c43ca
iuc
parents:
diff
changeset
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35 $advanced_selector.gamma |
c7e73acfa3eb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasttree commit e47dfac91821500d0fcfc43750d036662c7c43ca
iuc
parents:
diff
changeset
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36 $advanced_selector.nosupport |
c7e73acfa3eb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasttree commit e47dfac91821500d0fcfc43750d036662c7c43ca
iuc
parents:
diff
changeset
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37 $advanced_selector.mllen |
c7e73acfa3eb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasttree commit e47dfac91821500d0fcfc43750d036662c7c43ca
iuc
parents:
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changeset
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38 $advanced_selector.likelihood |
c7e73acfa3eb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasttree commit e47dfac91821500d0fcfc43750d036662c7c43ca
iuc
parents:
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changeset
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39 $advanced_selector.fastest |
c7e73acfa3eb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasttree commit e47dfac91821500d0fcfc43750d036662c7c43ca
iuc
parents:
diff
changeset
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40 $advanced_selector.pseudo |
c7e73acfa3eb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasttree commit e47dfac91821500d0fcfc43750d036662c7c43ca
iuc
parents:
diff
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41 #end if |
c7e73acfa3eb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasttree commit e47dfac91821500d0fcfc43750d036662c7c43ca
iuc
parents:
diff
changeset
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42 |
c7e73acfa3eb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasttree commit e47dfac91821500d0fcfc43750d036662c7c43ca
iuc
parents:
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43 < '$input' > '$output' |
c7e73acfa3eb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasttree commit e47dfac91821500d0fcfc43750d036662c7c43ca
iuc
parents:
diff
changeset
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44 |
c7e73acfa3eb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasttree commit e47dfac91821500d0fcfc43750d036662c7c43ca
iuc
parents:
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45 #if $save_logfile: |
c7e73acfa3eb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasttree commit e47dfac91821500d0fcfc43750d036662c7c43ca
iuc
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46 2> '$log' |
c7e73acfa3eb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasttree commit e47dfac91821500d0fcfc43750d036662c7c43ca
iuc
parents:
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47 #end if |
c7e73acfa3eb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasttree commit e47dfac91821500d0fcfc43750d036662c7c43ca
iuc
parents:
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changeset
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48 |
c7e73acfa3eb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasttree commit e47dfac91821500d0fcfc43750d036662c7c43ca
iuc
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49 ]]> |
c7e73acfa3eb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasttree commit e47dfac91821500d0fcfc43750d036662c7c43ca
iuc
parents:
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50 </command> |
c7e73acfa3eb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasttree commit e47dfac91821500d0fcfc43750d036662c7c43ca
iuc
parents:
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51 <inputs> |
c7e73acfa3eb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasttree commit e47dfac91821500d0fcfc43750d036662c7c43ca
iuc
parents:
diff
changeset
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52 <conditional name="input_selector"> |
c7e73acfa3eb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasttree commit e47dfac91821500d0fcfc43750d036662c7c43ca
iuc
parents:
diff
changeset
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53 <param name="select_format" type="select" label="Aligned sequences file (FASTA or Phylip format)"> |
c7e73acfa3eb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasttree commit e47dfac91821500d0fcfc43750d036662c7c43ca
iuc
parents:
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changeset
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54 <option value="fasta" selected="true">fasta</option> |
c7e73acfa3eb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasttree commit e47dfac91821500d0fcfc43750d036662c7c43ca
iuc
parents:
diff
changeset
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55 <option value="phylip">phylip</option> |
c7e73acfa3eb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasttree commit e47dfac91821500d0fcfc43750d036662c7c43ca
iuc
parents:
diff
changeset
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56 </param> |
c7e73acfa3eb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasttree commit e47dfac91821500d0fcfc43750d036662c7c43ca
iuc
parents:
diff
changeset
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57 <when value="fasta"> |
c7e73acfa3eb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasttree commit e47dfac91821500d0fcfc43750d036662c7c43ca
iuc
parents:
diff
changeset
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58 <param format="fasta" name="input" type="data" multiple="false" label="FASTA file"/> |
c7e73acfa3eb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasttree commit e47dfac91821500d0fcfc43750d036662c7c43ca
iuc
parents:
diff
changeset
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59 <param name="quote" argument="-quote" type="boolean" truevalue="-quote" falsevalue="" checked="false" label="Allow spaces and other restricted characters (but not ') in sequence and quote names in the output tree." help="This tool is only available for fasta input only; FastTree will not be able to read these trees back in." /> |
c7e73acfa3eb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasttree commit e47dfac91821500d0fcfc43750d036662c7c43ca
iuc
parents:
diff
changeset
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60 <conditional name="intree_selector"> |
c7e73acfa3eb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasttree commit e47dfac91821500d0fcfc43750d036662c7c43ca
iuc
parents:
diff
changeset
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61 <param name="intree_format" type="select" label="Set starting tree(s)"> |
c7e73acfa3eb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasttree commit e47dfac91821500d0fcfc43750d036662c7c43ca
iuc
parents:
diff
changeset
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62 <option value="none" selected="true">No starting trees</option> |
c7e73acfa3eb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasttree commit e47dfac91821500d0fcfc43750d036662c7c43ca
iuc
parents:
diff
changeset
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63 <option value="one">Use starting tree</option> |
c7e73acfa3eb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasttree commit e47dfac91821500d0fcfc43750d036662c7c43ca
iuc
parents:
diff
changeset
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64 </param> |
c7e73acfa3eb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasttree commit e47dfac91821500d0fcfc43750d036662c7c43ca
iuc
parents:
diff
changeset
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65 <when value="none"> |
c7e73acfa3eb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasttree commit e47dfac91821500d0fcfc43750d036662c7c43ca
iuc
parents:
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changeset
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66 </when> |
c7e73acfa3eb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasttree commit e47dfac91821500d0fcfc43750d036662c7c43ca
iuc
parents:
diff
changeset
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67 <when value="one"> |
c7e73acfa3eb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasttree commit e47dfac91821500d0fcfc43750d036662c7c43ca
iuc
parents:
diff
changeset
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68 <param format="nhx" name="start_tree" type="data" label="Newick file" /> |
c7e73acfa3eb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasttree commit e47dfac91821500d0fcfc43750d036662c7c43ca
iuc
parents:
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changeset
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69 </when> |
c7e73acfa3eb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasttree commit e47dfac91821500d0fcfc43750d036662c7c43ca
iuc
parents:
diff
changeset
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70 </conditional> |
c7e73acfa3eb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasttree commit e47dfac91821500d0fcfc43750d036662c7c43ca
iuc
parents:
diff
changeset
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71 </when> |
c7e73acfa3eb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasttree commit e47dfac91821500d0fcfc43750d036662c7c43ca
iuc
parents:
diff
changeset
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72 <when value="phylip"> |
c7e73acfa3eb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasttree commit e47dfac91821500d0fcfc43750d036662c7c43ca
iuc
parents:
diff
changeset
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73 <param format="phylip" name="input" type="data" label="PHYLIP file" /> |
c7e73acfa3eb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasttree commit e47dfac91821500d0fcfc43750d036662c7c43ca
iuc
parents:
diff
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74 <param name="num" type="integer" value="1" optional="true" label="Number of multiple alignments" /> |
c7e73acfa3eb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasttree commit e47dfac91821500d0fcfc43750d036662c7c43ca
iuc
parents:
diff
changeset
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75 <conditional name="intree_selector"> |
c7e73acfa3eb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasttree commit e47dfac91821500d0fcfc43750d036662c7c43ca
iuc
parents:
diff
changeset
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76 <param name="intree_format" type="select" label="Set starting tree(s)"> |
c7e73acfa3eb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasttree commit e47dfac91821500d0fcfc43750d036662c7c43ca
iuc
parents:
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77 <option value="none" selected="true">No starting trees</option> |
c7e73acfa3eb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasttree commit e47dfac91821500d0fcfc43750d036662c7c43ca
iuc
parents:
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changeset
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78 <option value="one">One tree for multiple alignments</option> |
c7e73acfa3eb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasttree commit e47dfac91821500d0fcfc43750d036662c7c43ca
iuc
parents:
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79 <option value="many">Multiple trees for multiple alignments</option> |
c7e73acfa3eb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasttree commit e47dfac91821500d0fcfc43750d036662c7c43ca
iuc
parents:
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changeset
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80 </param> |
c7e73acfa3eb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasttree commit e47dfac91821500d0fcfc43750d036662c7c43ca
iuc
parents:
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81 <when value="none"> |
c7e73acfa3eb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasttree commit e47dfac91821500d0fcfc43750d036662c7c43ca
iuc
parents:
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82 </when> |
c7e73acfa3eb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasttree commit e47dfac91821500d0fcfc43750d036662c7c43ca
iuc
parents:
diff
changeset
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83 <when value="one"> |
c7e73acfa3eb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasttree commit e47dfac91821500d0fcfc43750d036662c7c43ca
iuc
parents:
diff
changeset
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84 <param format="nhx" name="start_tree" type="data" multiple="false" label="Newick file" /> |
c7e73acfa3eb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasttree commit e47dfac91821500d0fcfc43750d036662c7c43ca
iuc
parents:
diff
changeset
|
85 </when> |
c7e73acfa3eb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasttree commit e47dfac91821500d0fcfc43750d036662c7c43ca
iuc
parents:
diff
changeset
|
86 <when value="many"> |
c7e73acfa3eb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasttree commit e47dfac91821500d0fcfc43750d036662c7c43ca
iuc
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diff
changeset
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87 <param format="nhx" name="start_tree" type="data" label="Newick file" multiple="false" help="The tree produced by the full alignment to be used as a starting point for each bootstrapping replicate. This will save considerable computation time." /> |
c7e73acfa3eb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasttree commit e47dfac91821500d0fcfc43750d036662c7c43ca
iuc
parents:
diff
changeset
|
88 </when> |
c7e73acfa3eb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasttree commit e47dfac91821500d0fcfc43750d036662c7c43ca
iuc
parents:
diff
changeset
|
89 </conditional> |
c7e73acfa3eb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasttree commit e47dfac91821500d0fcfc43750d036662c7c43ca
iuc
parents:
diff
changeset
|
90 </when> |
c7e73acfa3eb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasttree commit e47dfac91821500d0fcfc43750d036662c7c43ca
iuc
parents:
diff
changeset
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91 </conditional> |
c7e73acfa3eb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasttree commit e47dfac91821500d0fcfc43750d036662c7c43ca
iuc
parents:
diff
changeset
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92 <param name="save_logfile" type="boolean" truevalue="" falsevalue="" checked="false" label="Save log file output" /> |
c7e73acfa3eb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasttree commit e47dfac91821500d0fcfc43750d036662c7c43ca
iuc
parents:
diff
changeset
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93 <conditional name="model_selector"> |
c7e73acfa3eb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasttree commit e47dfac91821500d0fcfc43750d036662c7c43ca
iuc
parents:
diff
changeset
|
94 <param name="format" type="select" label="Protein or nucleotide alignment" help="Specify if the aligned sequences are nucleotide or protein sequences"> |
c7e73acfa3eb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasttree commit e47dfac91821500d0fcfc43750d036662c7c43ca
iuc
parents:
diff
changeset
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95 <option value="-nt">Nucleotide</option> |
c7e73acfa3eb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasttree commit e47dfac91821500d0fcfc43750d036662c7c43ca
iuc
parents:
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changeset
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96 <option value="" selected="true">Protein</option> |
c7e73acfa3eb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasttree commit e47dfac91821500d0fcfc43750d036662c7c43ca
iuc
parents:
diff
changeset
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97 </param> |
c7e73acfa3eb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasttree commit e47dfac91821500d0fcfc43750d036662c7c43ca
iuc
parents:
diff
changeset
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98 <when value="-nt"> |
c7e73acfa3eb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasttree commit e47dfac91821500d0fcfc43750d036662c7c43ca
iuc
parents:
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changeset
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99 <param name="model" type="select" label="Nucleotide evolution model"> |
c7e73acfa3eb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasttree commit e47dfac91821500d0fcfc43750d036662c7c43ca
iuc
parents:
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changeset
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100 <option value="-gtr" selected="true">GTR+CAT</option> |
c7e73acfa3eb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasttree commit e47dfac91821500d0fcfc43750d036662c7c43ca
iuc
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changeset
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101 <option value="">Jukes-Cantor + CAT</option> |
c7e73acfa3eb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasttree commit e47dfac91821500d0fcfc43750d036662c7c43ca
iuc
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changeset
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102 </param> |
c7e73acfa3eb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasttree commit e47dfac91821500d0fcfc43750d036662c7c43ca
iuc
parents:
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changeset
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103 </when> |
c7e73acfa3eb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasttree commit e47dfac91821500d0fcfc43750d036662c7c43ca
iuc
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changeset
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104 <when value=""> |
c7e73acfa3eb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasttree commit e47dfac91821500d0fcfc43750d036662c7c43ca
iuc
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changeset
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105 <param name="model" type="select" label="Protein evolution model"> |
c7e73acfa3eb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasttree commit e47dfac91821500d0fcfc43750d036662c7c43ca
iuc
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106 <option value="" selected="true">JTT + CAT</option> |
c7e73acfa3eb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasttree commit e47dfac91821500d0fcfc43750d036662c7c43ca
iuc
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107 <option value="-wag">WAG + CAT</option> |
c7e73acfa3eb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasttree commit e47dfac91821500d0fcfc43750d036662c7c43ca
iuc
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108 <option value="-lg">LG + CAT</option> |
c7e73acfa3eb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasttree commit e47dfac91821500d0fcfc43750d036662c7c43ca
iuc
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109 </param> |
c7e73acfa3eb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasttree commit e47dfac91821500d0fcfc43750d036662c7c43ca
iuc
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changeset
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110 </when> |
c7e73acfa3eb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasttree commit e47dfac91821500d0fcfc43750d036662c7c43ca
iuc
parents:
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changeset
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111 </conditional> |
c7e73acfa3eb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasttree commit e47dfac91821500d0fcfc43750d036662c7c43ca
iuc
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112 <conditional name="advanced_selector"> |
c7e73acfa3eb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasttree commit e47dfac91821500d0fcfc43750d036662c7c43ca
iuc
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113 <param name="maximize" type="select" label="Show advanced options"> |
c7e73acfa3eb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasttree commit e47dfac91821500d0fcfc43750d036662c7c43ca
iuc
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114 <option value="min" selected="true">No</option> |
c7e73acfa3eb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasttree commit e47dfac91821500d0fcfc43750d036662c7c43ca
iuc
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115 <option value="max">Yes</option> |
c7e73acfa3eb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasttree commit e47dfac91821500d0fcfc43750d036662c7c43ca
iuc
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116 </param> |
c7e73acfa3eb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasttree commit e47dfac91821500d0fcfc43750d036662c7c43ca
iuc
parents:
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changeset
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117 <when value="min"> |
c7e73acfa3eb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasttree commit e47dfac91821500d0fcfc43750d036662c7c43ca
iuc
parents:
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changeset
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118 </when> |
c7e73acfa3eb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasttree commit e47dfac91821500d0fcfc43750d036662c7c43ca
iuc
parents:
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119 <when value="max"> |
c7e73acfa3eb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasttree commit e47dfac91821500d0fcfc43750d036662c7c43ca
iuc
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120 <conditional name="cat_selector"> |
c7e73acfa3eb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasttree commit e47dfac91821500d0fcfc43750d036662c7c43ca
iuc
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121 <param name="conrate" type="select" label="Use constant rates?"> |
c7e73acfa3eb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasttree commit e47dfac91821500d0fcfc43750d036662c7c43ca
iuc
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122 <option value="no" selected="true">Do not use constant rates.</option> |
c7e73acfa3eb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasttree commit e47dfac91821500d0fcfc43750d036662c7c43ca
iuc
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123 <option value="yes">Use constant rates.</option> |
c7e73acfa3eb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasttree commit e47dfac91821500d0fcfc43750d036662c7c43ca
iuc
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124 </param> |
c7e73acfa3eb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasttree commit e47dfac91821500d0fcfc43750d036662c7c43ca
iuc
parents:
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125 <when value="no"> |
c7e73acfa3eb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasttree commit e47dfac91821500d0fcfc43750d036662c7c43ca
iuc
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126 <param name="ratecat" type="integer" value="20" label="Specify the number of rate categories of sites (default 20)" /> |
c7e73acfa3eb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasttree commit e47dfac91821500d0fcfc43750d036662c7c43ca
iuc
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127 </when> |
c7e73acfa3eb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasttree commit e47dfac91821500d0fcfc43750d036662c7c43ca
iuc
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128 <when value="yes"> |
c7e73acfa3eb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasttree commit e47dfac91821500d0fcfc43750d036662c7c43ca
iuc
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129 </when> |
c7e73acfa3eb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasttree commit e47dfac91821500d0fcfc43750d036662c7c43ca
iuc
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130 </conditional> |
c7e73acfa3eb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasttree commit e47dfac91821500d0fcfc43750d036662c7c43ca
iuc
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131 <param value="gamma" argument="-gamma" type="boolean" truevalue="-gamma" falsevalue="" checked="false" label="Use Gamma20" help="After optimizing the tree under the CAT approximation, rescale the lengths to optimize the Gamma20 likelihood." /> |
c7e73acfa3eb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasttree commit e47dfac91821500d0fcfc43750d036662c7c43ca
iuc
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132 <param value="nosupport" argument="-nosupport" type="boolean" truevalue="-nosupport" falsevalue="" checked="false" label="Eliminates the support value computation. Support value computation is not recommended for wide alignments."/> |
c7e73acfa3eb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasttree commit e47dfac91821500d0fcfc43750d036662c7c43ca
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133 <param name="likelihood" argument="-noml" type="boolean" truevalue="-noml" falsevalue="" checked="false" label = "Turn off maximum-likelihood." /> |
c7e73acfa3eb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasttree commit e47dfac91821500d0fcfc43750d036662c7c43ca
iuc
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134 <param name="fastest" argument="-fastest" type="boolean" truevalue="-fastest" falsevalue="" checked="false" label="Speed up the neighbor joining phase and reduce memory usage (recommended for >50,000 sequences)" /> |
c7e73acfa3eb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasttree commit e47dfac91821500d0fcfc43750d036662c7c43ca
iuc
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135 <param name="pseudo" argument="-pseudo" type="boolean" truevalue="-pseudo" falsevalue="" checked="false" label="Use pseudocounts" help="Recommended for highly gapped/fragmentary sequences." /> |
c7e73acfa3eb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasttree commit e47dfac91821500d0fcfc43750d036662c7c43ca
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136 <param name="mllen" argument="-mllen" type="boolean" truevalue="-mllen" falsevalue="" checked="false" label="Optimize branch lengths without ML NNIs." /> |
c7e73acfa3eb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasttree commit e47dfac91821500d0fcfc43750d036662c7c43ca
iuc
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137 </when> |
c7e73acfa3eb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasttree commit e47dfac91821500d0fcfc43750d036662c7c43ca
iuc
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138 </conditional> |
c7e73acfa3eb
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iuc
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139 </inputs> |
c7e73acfa3eb
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iuc
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140 <outputs> |
c7e73acfa3eb
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iuc
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141 <data name="output" format="nhx" label="${tool.name} on ${on_string}:tree.nhx" /> |
c7e73acfa3eb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasttree commit e47dfac91821500d0fcfc43750d036662c7c43ca
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142 <data name="log" format="txt" label="${tool.name} on ${on_string}:log_FastTree_run.txt"> |
c7e73acfa3eb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasttree commit e47dfac91821500d0fcfc43750d036662c7c43ca
iuc
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143 <filter>save_logfile</filter> |
c7e73acfa3eb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasttree commit e47dfac91821500d0fcfc43750d036662c7c43ca
iuc
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144 </data> |
c7e73acfa3eb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasttree commit e47dfac91821500d0fcfc43750d036662c7c43ca
iuc
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145 </outputs> |
c7e73acfa3eb
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iuc
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146 <tests> |
c7e73acfa3eb
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iuc
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147 <test> |
c7e73acfa3eb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasttree commit e47dfac91821500d0fcfc43750d036662c7c43ca
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148 <param name="select_format" value="fasta" /> |
c7e73acfa3eb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasttree commit e47dfac91821500d0fcfc43750d036662c7c43ca
iuc
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149 <param name="model" value="" /> |
c7e73acfa3eb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasttree commit e47dfac91821500d0fcfc43750d036662c7c43ca
iuc
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150 <param name="input" value="aligned.fasta" /> |
c7e73acfa3eb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasttree commit e47dfac91821500d0fcfc43750d036662c7c43ca
iuc
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151 <param name="format" value="-nt" /> |
c7e73acfa3eb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasttree commit e47dfac91821500d0fcfc43750d036662c7c43ca
iuc
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152 <param name="save_logfile" value="true" /> |
c7e73acfa3eb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasttree commit e47dfac91821500d0fcfc43750d036662c7c43ca
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153 <output name="output" file="tree.nhx" ftype="nhx" lines_diff="2" /> |
c7e73acfa3eb
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iuc
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154 <output name="log" file="log.txt" ftype="txt" compare="contains" /> |
c7e73acfa3eb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasttree commit e47dfac91821500d0fcfc43750d036662c7c43ca
iuc
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155 </test> |
c7e73acfa3eb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasttree commit e47dfac91821500d0fcfc43750d036662c7c43ca
iuc
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156 </tests> |
c7e73acfa3eb
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iuc
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157 <help> |
c7e73acfa3eb
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158 <![CDATA[ |
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159 |
c7e73acfa3eb
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160 =========== |
c7e73acfa3eb
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iuc
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161 Description |
c7e73acfa3eb
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162 =========== |
c7e73acfa3eb
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163 |
c7e73acfa3eb
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164 .. class:: infomark |
c7e73acfa3eb
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165 |
c7e73acfa3eb
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166 FastTree_ infers approximately-maximum-likelihood phylogenetic trees from alignments of nucleotide or protein sequences. FastTree can handle alignments with up to a million of sequences in a reasonable amount of time and memory. For large alignments, FastTree is 100-1,000 times faster than PhyML 3.0 or RAxML 7. FastTree is open-source software. |
c7e73acfa3eb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasttree commit e47dfac91821500d0fcfc43750d036662c7c43ca
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167 |
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168 .. _FastTree: http://meta.microbesonline.org/fasttree |
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169 |
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170 ----- |
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171 |
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172 ----- |
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173 Input |
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174 ----- |
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175 |
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176 A) Aligned sequences file in FASTA format (e.g. the alignment from the 'PyNAST' tool) or PHYLIP format. |
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177 B) Newick file to set the starting tree(s) (optional) |
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178 |
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179 ---------- |
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180 Parameters |
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181 ---------- |
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182 |
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183 Nucleotide or protein alignment |
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184 To specify the type of sequence alignment (nucleotide or protein) you are providing. |
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185 |
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186 Nucleotide evolution model |
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187 Specify GTR+CAT (Generalized Time Reversable Model) or Jukes-Cantor + CAT. |
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188 |
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189 Protein evolution model |
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190 Specify JTT (Jones-Taylor-Thornton 1992 model) + CAT, WAG (Whelan-And-Goldman 2001 model) + CAT, or LG (Le-Gascuel 2008 model) + CAT. |
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191 |
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192 Allow spaces and other restricted characters (but not ') in sequence and quote names in the output tree. (fasta only) |
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193 FastTree will not be able to read these trees back in. (-quote) |
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194 |
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195 Number of multiple alignments (phylip only) |
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196 (-n) |
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197 |
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198 ------------------- |
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199 Advanced Parameters |
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200 ------------------- |
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201 |
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202 Number of rates of sites |
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203 Defaults to 20. Specify whether you wish to choose constant rates. (-cat/-nocat) |
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204 |
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205 Use Gamma20 |
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206 After optimizing the tree under the CAT approximation, rescale the lengths to optimize the Gamma20 likelihood. (-gamma) |
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207 |
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208 Eliminates the support value computation. Support value computation is not recommended for wide alignments. |
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209 (-nosupport) |
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210 |
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211 Turn off maximum-likelihood. |
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212 (-noml) |
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213 |
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214 Speed up the neighbor joining phase and reduce memory usage |
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215 Recommended for >50,000 sequences. (-fastest) |
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216 |
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217 Use pseudocounts |
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218 Recommended if you have many fragmentary sequences. (-pseudo) |
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219 |
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220 Optimize branch lengths without ML NNIs. |
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221 (-mllen) |
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222 |
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223 ------ |
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224 Output |
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225 ------ |
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226 |
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227 This tool produces two output files, one of which is optional (the log file). |
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228 |
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229 (A) The phylogenetic tree in Newick_ format (nhx). |
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230 |
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231 (B) *(optional)* The log file, containing information of the FastTree run to build the phylogenetic tree. |
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232 |
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233 .. class:: infomark |
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234 |
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235 The placement of the root is not biologically meaningful. The local support values are given as names for the internal nodes, and range from 0 to 1, not from 0 to 100 or 0 to 1,000. If all sequences are unique, then the tree will be fully resolved (the root will have three children and other internal nodes will have two children). If there are multiple sequences that are identical to each other, then there will be a multifurcation. Also, there are no support values for the parent nodes of redundant sequences. |
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236 |
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237 .. _Newick: http://en.wikipedia.org/wiki/Newick_format |
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238 |
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239 ----- |
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240 |
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241 |
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242 ========= |
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243 Resources |
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244 ========= |
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245 |
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246 FastTree_v2.1.10_ |
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247 |
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248 .. _FastTree_v2.1.10: http://meta.microbesonline.org/fasttree/#Install |
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249 ]]> |
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250 </help> |
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251 <citations> |
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252 <citation type="doi">10.1371/journal.pone.0009490</citation> |
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253 </citations> |
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254 </tool> |