Mercurial > repos > iuc > mothur_make_lookup

comparison make.lookup.xml @ 1:f1c8a12f90be 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 18:35:11 -0400
parents f4b0766a9082
children ba85750d241d
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0:f4b0766a9082 1:f1c8a12f90be
2 <description>allows you to create custom lookup files for use with shhh.flows</description> 2 <description>allows you to create custom lookup files for use with shhh.flows</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 #import re 12 #import re
10 ## create symlinks to input datasets 13 ## create symlinks to input datasets
11 ln -s "$reference.template" reference.template.dat && 14 ln -s "$reference.template" reference.template.dat &&
12 ln -s "$flow" flow.dat && 15 ln -s "$flow" flow.dat &&
13 ln -s "$error" error.dat && 16 ln -s "$error" error.dat &&
21 key=$re.sub("[^ACTG]","",str($key)), 24 key=$re.sub("[^ACTG]","",str($key)),
22 threshold=$threshold 25 threshold=$threshold
23 )' 26 )'
24 | sed 's/ //g' ## mothur trips over whitespace 27 | sed 's/ //g' ## mothur trips over whitespace
25 | mothur 28 | mothur
29 | tee mothur.out.log
26 ]]></command> 30 ]]></command>
27 <inputs> 31 <inputs>
28 <conditional name="reference"> 32 <conditional name="reference">
29 <param name="source" type="select" label="Select Reference Template from" help=""> 33 <param name="source" type="select" label="Select Reference Template from" help="">
30 <option value="hist">History</option> 34 <option value="hist">History</option>
85 <help> 89 <help>
86 <![CDATA[ 90 <![CDATA[
87 91
88 @MOTHUR_OVERVIEW@ 92 @MOTHUR_OVERVIEW@
89 93
90 **Command Documenation** 94 **Command Documentation**
91 95
92 The make.lookup_ allows you to create custom lookup files for use with shhh.flows. 96 The make.lookup_ allows you to create custom lookup files for use with shhh.flows.
93 97
94 .. _make.lookup: http://www.mothur.org/wiki/Make.lookup 98 .. _make.lookup: https://www.mothur.org/wiki/Make.lookup
95 99
96 ]]> 100 ]]>
97 </help> 101 </help>
98 <citations> 102 <citations>
99 <citation type="doi">10.1128/AEM.01541-09</citation> 103 <citation type="doi">10.1128/AEM.01541-09</citation>