Mercurial > repos > iuc > mothur_parsimony
annotate parsimony.xml @ 1:c7a4a69fcc4a draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 721531d2e9fd1e208a3fba8cfbe5dcd572599ca2
author | iuc |
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date | Tue, 05 Sep 2017 17:16:57 -0400 |
parents | 5b184e7eebaa |
children | 4e3816a6462a |
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
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1 <tool profile="16.07" id="mothur_parsimony" name="Parsimony" version="@WRAPPER_VERSION@.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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2 <description>Describes whether two or more communities have the same structure</description> |
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3 <macros> |
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4 <import>macros.xml</import> |
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5 </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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6 <expand macro="requirements"/> |
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7 <expand macro="stdio"/> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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8 <expand macro="version_command"/> |
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9 <command><![CDATA[ |
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10 @SHELL_OPTIONS@ |
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11 |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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12 ## create symlinks to input datasets |
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13 ln -s "$tree" tree.dat && |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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14 ln -s "$group" group.dat && |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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15 ln -s "$count" count.dat && |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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16 ln -s "$name" name.dat && |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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17 |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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18 echo 'parsimony( |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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19 tree=tree.dat, |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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20 iters=$iters, |
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21 group=group.dat, |
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22 #if $groups: |
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23 groups=${ str($groups).replace(",","-") }, |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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24 #end if |
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25 #if $name: |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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26 name=name.dat, |
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27 #end if |
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28 #if $count: |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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29 count=count.dat, |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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30 #end if |
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31 processors='\${GALAXY_SLOTS:-8}' |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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32 )' |
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33 | sed 's/ //g' ## mothur trips over whitespace |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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34 | mothur |
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35 | tee mothur.out.log |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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36 ]]></command> |
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37 <inputs> |
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38 <param name="tree" type="data" format="mothur.tre" label="tree - Phylogenetic Tree"/> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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39 <param name="group" type="data" format="mothur.groups" label="group - Group file for the tree"/> |
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40 <param name="groups" type="select" label="groups - Groups to display" multiple="true" help="By default all are included if no selection is made."> |
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41 <options> |
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42 <filter type="data_meta" ref="group" key="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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43 </options> |
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44 </param> |
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45 <param name="name" type="data" format="mothur.names" optional="true" label="name - Sequences Name reference file for the tree"/> |
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46 <param name="iters" type="integer" min="1" value="1000" label="iters - Number of bootstrap iterations to try (default 1000)"/> |
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47 <param name="count" type="data" format="mothur.count_table" optional="true" label="count - a count_table" help="generated by count.seqs"/> |
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48 </inputs> |
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49 <outputs> |
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50 <expand macro="logfile-output"/> |
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51 <data name="psummary" format="tabular" from_work_dir="tree*.psummary" label="${tool.name} on ${on_string}: psummary"/> |
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52 <data name="parsimony" format="tabular" from_work_dir="tree*.parsimony" label="${tool.name} on ${on_string}: parsimony"/> |
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53 </outputs> |
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54 <tests> |
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55 <test> |
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56 <param name="tree" value="treetest.tre" ftype="mothur.tre"/> |
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57 <param name="group" value="treetest.groups"/> |
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58 <param name="groups" value="green,orange"/> |
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59 <param name="name" value="treetest.names"/> |
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60 <param name="iters" value="1000"/> |
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61 <output name="psummary" md5="011c202c5e5e33cb1af7c742aeb06457"/> |
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62 <output name="parsimony" md5="f49e0d64fd0c5df01abc913f398d428a"/> |
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63 <expand macro="logfile-test"/> |
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64 </test> |
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65 </tests> |
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66 <help> |
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67 <![CDATA[ |
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68 |
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69 @MOTHUR_OVERVIEW@ |
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70 |
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71 **Command Documentation** |
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72 |
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73 The parsimony_ command implements the parsimony method (aka P-test), which was previously implemented in TreeClimber and is also available in MacClade and on the UniFrac website. The parsimony method is a generic test that describes whether two or more communities have the same structure. The significance of the test statistic can only indicate the probability that the communities have the same structure by chance. The value does not indicate a level of similarity. |
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74 |
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75 .. _parsimony: https://www.mothur.org/wiki/Parsimony |
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76 |
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77 v.1.20.0: Added count parameter |
5b184e7eebaa
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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78 |
5b184e7eebaa
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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79 ]]> |
5b184e7eebaa
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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80 </help> |
5b184e7eebaa
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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81 <expand macro="citations"/> |
5b184e7eebaa
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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82 </tool> |