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comparison indicator.xml @ 1:95175e14cc16 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 18:45:13 -0400
parents 10ae17108e85
children 7064503531b8
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0:10ae17108e85 1:95175e14cc16
2 <description>Identify indicator "species" for nodes on a tree</description> 2 <description>Identify indicator "species" for nodes on a tree</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 "$otu" otu.dat && 13 ln -s "$otu" otu.dat &&
11 #if $withdesign.tree: 14 #if $withdesign.tree:
12 ln -s "$withdesign.tree" withdesign.tree.dat && 15 ln -s "$withdesign.tree" withdesign.tree.dat &&
13 #end if 16 #end if
35 #end if 38 #end if
36 processors='\${GALAXY_SLOTS:-8}' 39 processors='\${GALAXY_SLOTS:-8}'
37 )' 40 )'
38 | sed 's/ //g' ## mothur trips over whitespace 41 | sed 's/ //g' ## mothur trips over whitespace
39 | mothur 42 | mothur
43 | tee mothur.out.log
40 ]]></command> 44 ]]></command>
41 <inputs> 45 <inputs>
42 <param name="otu" type="data" format="mothur.shared,mothur.relabund" label="shared/relabund - OTU dataset"/> 46 <param name="otu" type="data" format="mothur.shared,mothur.relabund" label="shared/relabund - OTU dataset"/>
43 <param name="label" type="select" optional="true" multiple="false" label="label - OTU Labels"> 47 <param name="label" type="select" optional="true" multiple="false" label="label - OTU Labels">
44 <expand macro="labeloptions"/> 48 <expand macro="labeloptions"/>
136 <help> 140 <help>
137 <![CDATA[ 141 <![CDATA[
138 142
139 @MOTHUR_OVERVIEW@ 143 @MOTHUR_OVERVIEW@
140 144
141 **Command Documenation** 145 **Command Documentation**
142 146
143 The indicator_ command reads a shared_ or relabund_ file and a tree file, and outputs a .indicator.summary file and when a tree file is given a .indicator.tre file. The summary file lists the indicator value for each OTU for each node. The new tree contains labels at each internal node. The label is the node number so you can relate the tree to the summary file. 147 The indicator_ command reads a shared_ or relabund_ file and a tree file, and outputs a .indicator.summary file and when a tree file is given a .indicator.tre file. The summary file lists the indicator value for each OTU for each node. The new tree contains labels at each internal node. The label is the node number so you can relate the tree to the summary file.
144 148
145 .. _shared: http://www.mothur.org/wiki/Shared_file 149 .. _shared: https://www.mothur.org/wiki/Shared_file
146 .. _relabund: http://www.mothur.org/wiki/Get.relabund 150 .. _relabund: https://www.mothur.org/wiki/Get.relabund
147 .. _indicator: http://www.mothur.org/wiki/Indicator 151 .. _indicator: https://www.mothur.org/wiki/Indicator
148 152
149 v.1.22.0: Updated to Mothur 1.33 153 v.1.22.0: Updated to Mothur 1.33
150 ]]> 154 ]]>
151 </help> 155 </help>
152 <expand macro="citations"/> 156 <expand macro="citations"/>