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comparison venn.xml @ 1:a5b314f7fa9e draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit ea40e3d84e7850eb4226d6c85f709dcad18d4ba9
author iuc
date Thu, 18 May 2017 18:11:33 -0400
parents 3977ec624bc8
children cf4bae168475
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0:3977ec624bc8 1:a5b314f7fa9e
2 <description>Generate Venn diagrams for groups </description> 2 <description>Generate Venn diagrams for groups </description>
3 <macros> 3 <macros>
4 <import>macros.xml</import> 4 <import>macros.xml</import>
5 </macros> 5 </macros>
6 <expand macro="requirements"/> 6 <expand macro="requirements"/>
7 <expand macro="stdio"/>
7 <expand macro="version_command"/> 8 <expand macro="version_command"/>
8 <command detect_errors="aggressive"><![CDATA[ 9 <command><![CDATA[
10 @SHELL_OPTIONS@
11
9 ## create symlinks to input datasets 12 ## create symlinks to input datasets
10 ln -s "$input.otu" input_otu.dat && 13 ln -s "$input.otu" input_otu.dat &&
11 14
12 echo 'venn( 15 echo 'venn(
13 #if $input.source == "shared": 16 #if $input.source == "shared":
30 fontsize=$fontsize, 33 fontsize=$fontsize,
31 sharedotus=$sharedotus 34 sharedotus=$sharedotus
32 )' 35 )'
33 | sed 's/ //g' ## mothur trips over whitespace 36 | sed 's/ //g' ## mothur trips over whitespace
34 | mothur 37 | mothur
38 | tee mothur.out.log
35 ]]></command> 39 ]]></command>
36 <inputs> 40 <inputs>
37 <conditional name="input"> 41 <conditional name="input">
38 <param name="source" type="select" label="Generate Heatmap for"> 42 <param name="source" type="select" label="Generate Heatmap for">
39 <option value="shared">OTU Shared</option> 43 <option value="shared">OTU Shared</option>
117 <help> 121 <help>
118 <![CDATA[ 122 <![CDATA[
119 123
120 @MOTHUR_OVERVIEW@ 124 @MOTHUR_OVERVIEW@
121 125
122 **Command Documenation** 126 **Command Documentation**
123 127
124 The venn_ command generates Venn diagrams to compare the richness shared among 2, 3, or 4 groups. For calc parameter choices see: http://www.mothur.org/wiki/Calculators 128 The venn_ command generates Venn diagrams to compare the richness shared among 2, 3, or 4 groups. For calc parameter choices see: https://www.mothur.org/wiki/Calculators
125 129
126 .. _venn: http://www.mothur.org/wiki/Venn 130 .. _venn: https://www.mothur.org/wiki/Venn
127 131
128 ]]> 132 ]]>
129 </help> 133 </help>
130 <expand macro="citations"/> 134 <expand macro="citations"/>
131 </tool> 135 </tool>