Mercurial > repos > iuc > mothur_make_biom

comparison make.biom.xml @ 1:0eae3db4c7a5 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 04:20:15 -0400
parents 48e4f4dcf0ee
children fe0c38ac3adb
comparison
equal deleted inserted replaced
0:48e4f4dcf0ee 1:0eae3db4c7a5
2 <description>Make biom files from a shared file</description> 2 <description>Make biom files from a shared file</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 ln -s "$constaxonomy" constaxonomy.dat && 14 ln -s "$constaxonomy" constaxonomy.dat &&
12 ln -s "$metadata" metadata.dat && 15 ln -s "$metadata" metadata.dat &&
13 #if $picrustc.use == "yes": 16 #if $picrustc.use == "yes":
35 #end if 38 #end if
36 matrixtype=$matrixtype 39 matrixtype=$matrixtype
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" label="shared - OTU Shared file"/> 46 <param name="otu" type="data" format="mothur.shared" label="shared - OTU Shared file"/>
43 <param name="constaxonomy" type="data" format="mothur.cons.taxonomy" optional="true" label="contaxonomy - consensus taxonomy" help="The contaxonomy file is the taxonomy file outputted by classify.otu"/> 47 <param name="constaxonomy" type="data" format="mothur.cons.taxonomy" optional="true" label="contaxonomy - consensus taxonomy" help="The contaxonomy file is the taxonomy file outputted by classify.otu"/>
44 <param name="metadata" type="data" format="metadata" label="metadata" optional="true" help="You can add sample data support here"/> 48 <param name="metadata" type="data" format="metadata" label="metadata" optional="true" help="You can add sample data support here"/>
123 <help> 127 <help>
124 <![CDATA[ 128 <![CDATA[
125 129
126 @MOTHUR_OVERVIEW@ 130 @MOTHUR_OVERVIEW@
127 131
128 **Command Documenation** 132 **Command Documentation**
129 133
130 The make.biom command converts a shared_ shared file to biom_ files. 134 The make.biom command converts a shared_ shared file to biom_ files.
131 The output can be filtered by groups and labels. 135 The output can be filtered by groups and labels.
132 136
133 137
134 .. _shared: http://www.mothur.org/wiki/Shared_file 138 .. _shared: https://www.mothur.org/wiki/Shared_file
135 .. _biom: http://biom-format.org/documentation/biom_format.html 139 .. _biom: http://biom-format.org/documentation/biom_format.html
136 .. _make.biom: http://www.mothur.org/wiki/Make.biom 140 .. _make.biom: https://www.mothur.org/wiki/Make.biom
137 ]]> 141 ]]>
138 </help> 142 </help>
139 <expand macro="citations"/> 143 <expand macro="citations"/>
140 </tool> 144 </tool>