Mercurial > repos > iuc > mothur_phylotype

comparison phylotype.xml @ 1:4f5ecd0c94b3 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 05:27:23 -0400
parents 78de57134315
children 61846dca0ad1
comparison
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0:78de57134315 1:4f5ecd0c94b3
2 <description>Assign sequences to OTUs based on taxonomy</description> 2 <description>Assign sequences to OTUs based on taxonomy</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 "$taxonomy" taxonomy.dat && 13 ln -s "$taxonomy" taxonomy.dat &&
11 ln -s "$name" name.dat && 14 ln -s "$name" name.dat &&
12 15
13 echo 'phylotype( 16 echo 'phylotype(
22 ,label=${ str($label).replace(",","-") } 25 ,label=${ str($label).replace(",","-") }
23 #end if 26 #end if
24 )' 27 )'
25 | sed 's/ //g' ## mothur trips over whitespace 28 | sed 's/ //g' ## mothur trips over whitespace
26 | mothur 29 | mothur
30 | tee mothur.out.log
27 ]]></command> 31 ]]></command>
28 <inputs> 32 <inputs>
29 <param name="taxonomy" type="data" format="mothur.seq.taxonomy" label="taxonomy - Taxonomy"/> 33 <param name="taxonomy" type="data" format="mothur.seq.taxonomy" label="taxonomy - Taxonomy"/>
30 <param name="name" type="data" format="mothur.names" optional="true" label="name - Names reference file for the taxonomy"/> 34 <param name="name" type="data" format="mothur.names" optional="true" label="name - Names reference file for the taxonomy"/>
31 <param name="label" type="select" label="label - Taxonomy Levels to report (All when none are selected)" multiple="true"> 35 <param name="label" type="select" label="label - Taxonomy Levels to report (All when none are selected)" multiple="true">
70 <help> 74 <help>
71 <![CDATA[ 75 <![CDATA[
72 76
73 @MOTHUR_OVERVIEW@ 77 @MOTHUR_OVERVIEW@
74 78
75 **Command Documenation** 79 **Command Documentation**
76 80
77 The phylotype_ command assign sequences to OTUs based on their taxonomy and outputs a a list_, a sabund_ (Species Abundance), and a rabund_ (Relative Abundance) file. 81 The phylotype_ command assign sequences to OTUs based on their taxonomy and outputs a a list_, a sabund_ (Species Abundance), and a rabund_ (Relative Abundance) file.
78 82
79 .. _list: http://www.mothur.org/wiki/List_file 83 .. _list: https://www.mothur.org/wiki/List_file
80 .. _rabund: http://www.mothur.org/wiki/Rabund_file 84 .. _rabund: https://www.mothur.org/wiki/Rabund_file
81 .. _sabund: http://www.mothur.org/wiki/Sabund_file 85 .. _sabund: https://www.mothur.org/wiki/Sabund_file
82 .. _phylotype: http://www.mothur.org/wiki/Phylotype 86 .. _phylotype: https://www.mothur.org/wiki/Phylotype
83 87
84 ]]> 88 ]]>
85 </help> 89 </help>
86 <expand macro="citations"/> 90 <expand macro="citations"/>
87 </tool> 91 </tool>