Mercurial > repos > iuc > mothur_get_coremicrobiome

comparison get.coremicrobiome.xml @ 1:af8e6f1110b3 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 18:29:48 -0400
parents 1dd4d752f823
children 5e29cbb2fdef
comparison
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0:1dd4d752f823 1:af8e6f1110b3
2 <description>fraction of OTUs for samples or abundances</description> 2 <description>fraction of OTUs for samples or abundances</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 'get.coremicrobiome( 15 echo 'get.coremicrobiome(
13 #if $otu.is_of_type("mothur.relabund"): 16 #if $otu.is_of_type("mothur.relabund"):
28 ,samples=$samples 31 ,samples=$samples
29 #end if 32 #end if
30 )' 33 )'
31 | sed 's/ //g' ## mothur trips over whitespace 34 | sed 's/ //g' ## mothur trips over whitespace
32 | mothur 35 | mothur
36 | tee mothur.out.log
33 ]]></command> 37 ]]></command>
34 <inputs> 38 <inputs>
35 <param name="otu" type="data" format="mothur.shared,mothur.relabund" label="shared or relabund - OTU Shared or Relabund"/> 39 <param name="otu" type="data" format="mothur.shared,mothur.relabund" label="shared or relabund - OTU Shared or Relabund"/>
36 <param name="label" type="select" optional="true" label="label - OTU Labels" multiple="true"> 40 <param name="label" type="select" optional="true" label="label - OTU Labels" multiple="true">
37 <expand macro="labeloptions"/> 41 <expand macro="labeloptions"/>
83 <help> 87 <help>
84 <![CDATA[ 88 <![CDATA[
85 89
86 @MOTHUR_OVERVIEW@ 90 @MOTHUR_OVERVIEW@
87 91
88 **Command Documenation** 92 **Command Documentation**
89 93
90 The get.coremicrobiome_ command determines the fraction of OTUs that are found in varying numbers of samples for different minimum relative abundances. 94 The get.coremicrobiome_ command determines the fraction of OTUs that are found in varying numbers of samples for different minimum relative abundances.
91 95
92 .. _get.coremicrobiome: http://www.mothur.org/wiki/Get.coremicrobiome 96 .. _get.coremicrobiome: https://www.mothur.org/wiki/Get.coremicrobiome
93 97
94 v1.27.0: Updated to Mothur 1.33 98 v1.27.0: Updated to Mothur 1.33
95 99
96 ]]> 100 ]]>
97 </help> 101 </help>