Mercurial > repos > iuc > mothur_parsimony

annotate parsimony.xml @ 6:65955ae23f29 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 7f7605c2c8d8e92f3369dfdc290e5d8d06fa409a
author iuc
date Fri, 03 Aug 2018 14:29:55 -0400
parents da7f70ebfb4c
children fbb78e1bc3a3
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1 <tool profile="16.07" id="mothur_parsimony" name="Parsimony" version="@WRAPPER_VERSION@.0">
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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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6 <expand macro="requirements"/>
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7 <expand macro="stdio"/>
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8 <expand macro="version_command"/>
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9 <command><![CDATA[
2
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10 @SHELL_OPTIONS@
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11
2
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12 ## create symlinks to input datasets
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13 ln -s '$tree' tree.dat &&
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14 ln -s '$group' group.dat &&
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15 ln -s '$count' count.dat &&
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16 ln -s '$name' name.dat &&
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17
2
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18 echo 'parsimony(
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19 tree=tree.dat,
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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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24 #end if
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25 #if $name:
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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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29 count=count.dat,
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30 #end if
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31 processors='\${GALAXY_SLOTS:-8}'
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32 )'
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33 | sed 's/ //g' ## mothur trips over whitespace
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34 | mothur
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35 | tee mothur.out.log
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36 ]]></command>
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37 <inputs>
2
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38 <param argument="tree" type="data" format="mothur.tre" label="tree - Phylogenetic Tree"/>
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39 <param argument="group" type="data" format="mothur.groups" label="group - Group file for the tree"/>
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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
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41 <options>
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42 <filter type="data_meta" ref="group" key="groups"/>
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43 </options>
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44 </param>
2
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45 <param argument="name" type="data" format="mothur.names" optional="true" label="name - Sequences Name reference file for the tree"/>
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46 <param argument="iters" type="integer" min="1" value="1000" label="iters - Number of bootstrap iterations to try (default 1000)"/>
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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"/>
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48 <expand macro="param-savelog"/>
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49 </inputs>
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50 <outputs>
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51 <expand macro="logfile-output"/>
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52 <data name="psummary" format="tabular" from_work_dir="tree*.psummary" label="${tool.name} on ${on_string}: psummary"/>
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53 <data name="parsimony" format="tabular" from_work_dir="tree*.parsimony" label="${tool.name} on ${on_string}: parsimony"/>
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54 </outputs>
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55 <tests>
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56 <test>
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57 <param name="tree" value="treetest.tre" ftype="mothur.tre"/>
5
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58 <param name="group" value="treetest.groups" ftype="mothur.groups"/>
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59 <param name="groups" value="green,orange"/>
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60 <param name="name" value="treetest.names"/>
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61 <param name="iters" value="1000"/>
2
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62 <output name="psummary" ftype="tabular">
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63 <assert_contents>
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64 <has_line_matching expression="^Tree#\tGroups\tParsScore\tParsSig$"/>
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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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68 <assert_contents>
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69 <has_text text="green-orangeScore"/>
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70 </assert_contents>
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71 </output>
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72 <param name="savelog" value="true"/>
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73 <expand macro="logfile-test"/>
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74 </test>
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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
2
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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>
6
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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>
0
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120 </tool>