Mercurial > repos > iuc > mothur_phylo_diversity

annotate phylo.diversity.xml @ 2:292c7c4d2789 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
author iuc
date Tue, 20 Mar 2018 22:24:23 -0400
parents 917aa3b39ccd
children e398beade8e7
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917aa3b39ccd 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_phylo_diversity" name="Phylo.diversity" version="@WRAPPER_VERSION@.0">
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2 <description>Alpha Diversity calculates unique branch length</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
292c7c4d2789 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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12 ## create symlinks to input datasets
292c7c4d2789 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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13 ln -s '$tree' tree.dat &&
292c7c4d2789 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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14 ln -s '$name' name.dat &&
292c7c4d2789 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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15 ln -s '$count' count.dat &&
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16 #if $grouping.use == "yes":
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17 ln -s '$grouping.group' grouping.group.dat &&
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18 #end if
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19
2
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20 echo 'phylo.diversity(
292c7c4d2789 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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21 tree=tree.dat,
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22 #if $grouping.use == "yes":
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23 group=grouping.group.dat,
292c7c4d2789 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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24 #if $grouping.groups:
292c7c4d2789 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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25 groups=${ str($grouping.groups).replace(",","-") },
292c7c4d2789 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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26 #end if
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27 #end if
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28 #if $name:
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29 name=name.dat,
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30 #end if
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31 iters=$iters,
292c7c4d2789 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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32 freq=$freq,
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33 scale=$scale,
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34 collect=$collect,
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35 rarefy=$rarefy,
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36 summary=$summary,
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37 #if $count:
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38 count=count.dat,
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39 #end if
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40 processors='\${GALAXY_SLOTS:-8}'
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41 )'
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42 | sed 's/ //g' ## mothur trips over whitespace
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43 | mothur
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44 | tee mothur.out.log
0
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45 ]]></command>
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46 <inputs>
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47 <param name="tree" type="data" format="mothur.tre" label="tree - Phylogenetic Tree"/>
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48 <conditional name="grouping">
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49 <param name="use" type="select" label="Analyze by group using a Group file">
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50 <option value="no" selected="true">no</option>
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51 <option value="yes">yes</option>
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52 </param>
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53 <when value="yes">
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54 <param name="group" type="data" format="mothur.groups" label="group - Group file for the tree"/>
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55 <param name="groups" type="select" multiple="true" label="groups - Groups to display">
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56 <help>All groups displayed if none are selected.</help>
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57 <options>
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58 <filter type="data_meta" ref="group" key="groups"/>
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59 </options>
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60 </param>
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61 </when>
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62 <when value="no"/>
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63 </conditional>
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64 <param name="name" type="data" format="mothur.names" optional="true" label="name - Sequences Name reference file for the tree"/>
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65 <param name="iters" type="integer" value="1000" min="0" label="iters - Number of iterations to try (default 1000)"/>
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66 <param name="freq" type="float" value="100" min="0.0" label="freq - Reporting frequency" help="if between 0 and 100, the percentage of sequences to sample, if greater than one - report every n iterations"/>
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67 <param name="scale" type="boolean" truevalue="true" falsevalue="false" checked="false" label="scale - Scale output to the number of sequences sampled"/>
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68 <param name="rarefy" type="boolean" truevalue="true" falsevalue="false" checked="false" label="rarefy - Calculate the rarefaction data"/>
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69 <param name="summary" type="boolean" truevalue="true" falsevalue="false" checked="true" label="summary - Generate a summary file"/>
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70 <param name="collect" type="boolean" truevalue="true" falsevalue="false" checked="false" label="collect - Create a collectors curve"/>
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71 <param name="count" type="data" format="mothur.count_table" optional="true" label="count - a count_table" help="generated by count.seqs"/>
2
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72 <expand macro="param-savelog"/>
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73 </inputs>
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74 <outputs>
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75 <expand macro="logfile-output"/>
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76 <data name="summary_out" format="tabular" from_work_dir="tree*.phylodiv.summary" label="${tool.name} on ${on_string}: summary">
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77 <filter>summary</filter>
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78 </data>
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79 <data name="rarefaction_out" format="tabular" from_work_dir="tree*.phylodiv.rarefaction" label="${tool.name} on ${on_string}: rarefaction">
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80 <filter>rarefy</filter>
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81 </data>
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82 <data name="collectors_out" format="tabular" from_work_dir="tree*.phylodiv" label="${tool.name} on ${on_string}: collectors">
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83 <filter>collect</filter>
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84 </data>
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85 </outputs>
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86 <tests>
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87 <test><!-- test with tree file only -->
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88 <param name="tree" value="treetest.tre" ftype="mothur.tre"/>
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89 <param name="use" value="no"/>
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90 <output name="summary_out" md5="a9feb4031094b555baf62e0165dd3637" ftype="tabular"/>
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91 <param name="savelog" value="true"/>
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92 <expand macro="logfile-test"/>
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93 </test>
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94 <test><!-- test with tree file and group file and all outputs -->
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95 <param name="tree" value="treetest.tre" ftype="mothur.tre"/>
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96 <param name="use" value="yes"/>
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97 <param name="group" value="treetest.groups"/>
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98 <param name="groups" value="orange,green"/>
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99 <param name="rarefy" value="true"/>
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100 <param name="collect" value="true"/>
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101 <output name="summary_out" md5="27375ea164ad39fb56b9606023cae504" ftype="tabular"/>
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102 <output name="rarefaction_out" ftype="tabular">
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103 <assert_contents>
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104 <has_text text="numSampled"/>
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105 <has_text text="orange"/>
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106 <has_text text="green"/>
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107 </assert_contents>
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108 </output>
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109 <output name="collectors_out" ftype="tabular">
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110 <assert_contents>
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111 <has_text text="numSampled"/>
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112 <has_text text="orange"/>
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113 <has_text text="green"/>
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114 </assert_contents>
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115 </output>
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116 <param name="savelog" value="true"/>
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117 <expand macro="logfile-test"/>
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118 </test>
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119 </tests>
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120 <help><![CDATA[
0
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121
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122 @MOTHUR_OVERVIEW@
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123
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124
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125 **Command Documentation**
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126
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127 The phylo.diversity_ command calculates alpha diversity as the total of the unique branch length.
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128
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129 .. _phylo.diversity: https://www.mothur.org/wiki/Phylo.diversity
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130
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131 v.1.21.0: Updated to Mothur 1.33, added count parameter
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132
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133 ]]></help>
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134 <expand macro="citations"/>
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135 </tool>