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comparison mothur/tools/mothur/indicator.xml @ 25:bfbaf823be4c

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Change metagenomics datatypes to include labels and groups metadata. change Mothur tool configs to get label and group select options from a data_meta filter rather than using the options from_dataset attribute. This grealty decreases memory demand for the galaxy server.
author Jim Johnson <jj@umn.edu>
date Wed, 16 May 2012 12:28:44 -0500
parents 4f797d3eee3a
children 49058b1f8d3f
comparison
equal deleted inserted replaced
24:09740be2bc9c 25:bfbaf823be4c
27 --processors=8 27 --processors=8
28 </command> 28 </command>
29 <inputs> 29 <inputs>
30 <param name="otu" type="data" format="shared,relabund" label="shared/relabund - Otu dataset"/> 30 <param name="otu" type="data" format="shared,relabund" label="shared/relabund - Otu dataset"/>
31 <param name="label" type="select" optional="true" label="label - OTU Labels" > 31 <param name="label" type="select" optional="true" label="label - OTU Labels" >
32 <options from_dataset="otu"> 32 <options>
33 <column name="name" index="0"/> 33 <filter type="data_meta" ref="otu" key="labels" />
34 <column name="value" index="0"/>
35 <filter type="static_value" name="ignore_header" keep="False" column="0" value = "label"/>
36 <filter type="unique_value" name="unq_lbl" column="0" />
37 </options> 34 </options>
38 </param> 35 </param>
39 <param name="groups" type="select" optional="true" label="groups - Pick groups to annalyze" multiple="true"> 36 <param name="groups" type="select" optional="true" label="groups - Pick groups to annalyze" multiple="true">
40 <options from_dataset="otu"> 37 <options>
41 <column name="name" index="1"/> 38 <filter type="data_meta" ref="otu" key="groups" />
42 <column name="value" index="1"/>
43 <filter type="static_value" name="ignore_header" keep="False" column="1" value = "Group"/>
44 <filter type="unique_value" name="unq_grp" column="1" />
45 </options> 39 </options>
46 </param> 40 </param>
47 <param name="tree" type="data" format="tree" optional="true" label="tree - A newick-formatted tree" 41 <param name="tree" type="data" format="tree" optional="true" label="tree - A newick-formatted tree"
48 help="Optional, if a design file is provided."/> 42 help="Optional, if a design file is provided."/>
49 <param name="design" type="data" format="tabular" optional="true" label="design - assign groups to new grouping" 43 <param name="design" type="data" format="tabular" optional="true" label="design - assign groups to new grouping"