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comparison filter.shared.xml @ 1:897ba33ecbdb draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
author iuc
date Fri, 19 May 2017 05:16:28 -0400
parents 4adf107b126e
children d3f5d41208c1
comparison
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0:4adf107b126e 1:897ba33ecbdb
2 <description>remove OTUs based on various critieria</description> 2 <description>remove OTUs based on various critieria</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 14
12 echo 'filter.shared( 15 echo 'filter.shared(
13 shared=otu.dat, 16 shared=otu.dat,
26 mintotal=$mintotal, 29 mintotal=$mintotal,
27 makerare=$makerare 30 makerare=$makerare
28 )' 31 )'
29 | sed 's/ //g' ## mothur trips over whitespace 32 | sed 's/ //g' ## mothur trips over whitespace
30 | mothur 33 | mothur
34 | tee mothur.out.log
31 ]]></command> 35 ]]></command>
32 <inputs> 36 <inputs>
33 <param name="otu" type="data" format="mothur.shared" label="shared - specify your shared file"/> 37 <param name="otu" type="data" format="mothur.shared" label="shared - specify your shared file"/>
34 <param name="label" type="select" optional="true" multiple="true" label="label - OTU Labels" help="If none selected, all labels will be output"> 38 <param name="label" type="select" optional="true" multiple="true" label="label - OTU Labels" help="If none selected, all labels will be output">
35 <expand macro="labeloptions"/> 39 <expand macro="labeloptions"/>
77 <help> 81 <help>
78 <![CDATA[ 82 <![CDATA[
79 83
80 @MOTHUR_OVERVIEW@ 84 @MOTHUR_OVERVIEW@
81 85
82 **Command Documenation** 86 **Command Documentation**
83 87
84 The filter.shared_ is used to remove OTUs based on various critieria. 88 The filter.shared_ is used to remove OTUs based on various critieria.
85 89
86 .. _filter.shared: http://www.mothur.org/wiki/Filter.shared 90 .. _filter.shared: https://www.mothur.org/wiki/Filter.shared
87 91
88 ]]> 92 ]]>
89 </help> 93 </help>
90 <citations> 94 <citations>
91 <citation type="doi">10.1128/AEM.01541-09</citation> 95 <citation type="doi">10.1128/AEM.01541-09</citation>