Mercurial > repos > iuc > mothur_parsimony
annotate parsimony.xml @ 7:fd6cebeaa143 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit debdcdbb89f9bf3e2c3eed05cb078eddb27d4684"
author | iuc |
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date | Mon, 02 Dec 2019 06:08:45 -0500 |
parents | 65955ae23f29 |
children | fbb78e1bc3a3 |
rev | line source |
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0
5b184e7eebaa
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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1 <tool profile="16.07" id="mothur_parsimony" name="Parsimony" version="@WRAPPER_VERSION@.0"> |
5b184e7eebaa
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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2 <description>Describes whether two or more communities have the same structure</description> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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3 <macros> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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4 <import>macros.xml</import> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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5 </macros> |
5b184e7eebaa
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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6 <expand macro="requirements"/> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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7 <expand macro="stdio"/> |
5b184e7eebaa
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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8 <expand macro="version_command"/> |
5b184e7eebaa
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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9 <command><![CDATA[ |
2
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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10 @SHELL_OPTIONS@ |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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11 |
2
4e3816a6462a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
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12 ## create symlinks to input datasets |
4e3816a6462a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
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13 ln -s '$tree' tree.dat && |
4e3816a6462a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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14 ln -s '$group' group.dat && |
4e3816a6462a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
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15 ln -s '$count' count.dat && |
4e3816a6462a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
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16 ln -s '$name' name.dat && |
0
5b184e7eebaa
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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17 |
2
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
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18 echo 'parsimony( |
4e3816a6462a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
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19 tree=tree.dat, |
4e3816a6462a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
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20 iters=$iters, |
4e3816a6462a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
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21 group=group.dat, |
4e3816a6462a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
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22 #if $groups: |
4e3816a6462a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
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23 groups=${ str($groups).replace(",","-") }, |
4e3816a6462a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
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24 #end if |
4e3816a6462a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
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25 #if $name: |
4e3816a6462a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
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26 name=name.dat, |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
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27 #end if |
4e3816a6462a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
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28 #if $count: |
4e3816a6462a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
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29 count=count.dat, |
4e3816a6462a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
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30 #end if |
4e3816a6462a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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31 processors='\${GALAXY_SLOTS:-8}' |
4e3816a6462a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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32 )' |
4e3816a6462a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
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33 | sed 's/ //g' ## mothur trips over whitespace |
4e3816a6462a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
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34 | mothur |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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35 | tee mothur.out.log |
0
5b184e7eebaa
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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36 ]]></command> |
5b184e7eebaa
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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37 <inputs> |
2
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
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38 <param argument="tree" type="data" format="mothur.tre" label="tree - Phylogenetic Tree"/> |
4e3816a6462a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
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39 <param argument="group" type="data" format="mothur.groups" label="group - Group file for the tree"/> |
4e3816a6462a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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40 <param argument="groups" type="select" multiple="true" label="groups - Groups to display" help="By default all are included if no selection is made."> |
0
5b184e7eebaa
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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41 <options> |
5b184e7eebaa
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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42 <filter type="data_meta" ref="group" key="groups"/> |
5b184e7eebaa
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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43 </options> |
5b184e7eebaa
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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44 </param> |
2
4e3816a6462a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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45 <param argument="name" type="data" format="mothur.names" optional="true" label="name - Sequences Name reference file for the tree"/> |
4e3816a6462a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
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46 <param argument="iters" type="integer" min="1" value="1000" label="iters - Number of bootstrap iterations to try (default 1000)"/> |
4e3816a6462a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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47 <param argument="count" type="data" format="mothur.count_table" optional="true" label="count - a count_table" help="generated by count.seqs"/> |
4e3816a6462a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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48 <expand macro="param-savelog"/> |
0
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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49 </inputs> |
5b184e7eebaa
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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50 <outputs> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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51 <expand macro="logfile-output"/> |
5b184e7eebaa
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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52 <data name="psummary" format="tabular" from_work_dir="tree*.psummary" label="${tool.name} on ${on_string}: psummary"/> |
5b184e7eebaa
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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53 <data name="parsimony" format="tabular" from_work_dir="tree*.parsimony" label="${tool.name} on ${on_string}: parsimony"/> |
5b184e7eebaa
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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54 </outputs> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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55 <tests> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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56 <test> |
5b184e7eebaa
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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57 <param name="tree" value="treetest.tre" ftype="mothur.tre"/> |
5
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58 <param name="group" value="treetest.groups" ftype="mothur.groups"/> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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59 <param name="groups" value="green,orange"/> |
5b184e7eebaa
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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60 <param name="name" value="treetest.names"/> |
5b184e7eebaa
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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61 <param name="iters" value="1000"/> |
2
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62 <output name="psummary" ftype="tabular"> |
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63 <assert_contents> |
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64 <has_line_matching expression="^Tree#\tGroups\tParsScore\tParsSig$"/> |
4e3816a6462a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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65 </assert_contents> |
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66 </output> |
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67 <output name="parsimony" ftype="tabular"> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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68 <assert_contents> |
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69 <has_text text="green-orangeScore"/> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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70 </assert_contents> |
4e3816a6462a
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71 </output> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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72 <param name="savelog" value="true"/> |
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73 <expand macro="logfile-test"/> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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74 </test> |
5b184e7eebaa
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75 </tests> |
2
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76 <help><![CDATA[ |
0
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77 |
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78 @MOTHUR_OVERVIEW@ |
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79 |
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80 **Command Documentation** |
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81 |
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82 The parsimony_ command implements the parsimony method (aka P-test), which was previously implemented in TreeClimber |
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83 and is also available in MacClade and on the UniFrac website. The parsimony method is a generic test that describes |
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84 whether two or more communities have the same structure. The significance of the test statistic can only indicate the |
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85 probability that the communities have the same structure by chance. The value does not indicate a level of similarity. |
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86 |
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87 .. _parsimony: https://www.mothur.org/wiki/Parsimony |
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88 |
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89 v.1.20.0: Added count parameter |
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90 |
2
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91 ]]></help> |
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92 <expand macro="citations"> |
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93 <citation type="bibtex"> |
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94 @article{slatkin1989cladistic, |
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95 title={A cladistic measure of gene flow inferred from the phylogenies of alleles.}, |
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96 author={Slatkin, Montgomery and Maddison, Wayne P}, |
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97 journal={Genetics}, |
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98 volume={123}, |
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99 number={3}, |
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100 pages={603--613}, |
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101 year={1989}, |
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102 publisher={Genetics Soc America} |
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103 } |
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104 </citation> |
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105 <citation type="bibtex"> |
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106 @article{slatkin1990detecting, |
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107 title={Detecting isolation by distance using phylogenies of genes.}, |
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108 author={Slatkin, Montgomery and Maddison, Wayne P}, |
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109 journal={Genetics}, |
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110 volume={126}, |
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111 number={1}, |
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112 pages={249--260}, |
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113 year={1990}, |
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114 publisher={Genetics Soc America} |
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115 } |
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116 </citation> |
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117 <citation type="doi">10.1128/AEM.68.8.3673-3682.2002</citation> |
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118 <citation type="doi">10.1128/AEM.72.4.2379-2384.2006</citation> |
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119 </expand> |
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120 </tool> |