Mercurial > repos > iuc > mothur_make_lookup

comparison make.lookup.xml @ 4:5aab3adcb3a3 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
author iuc
date Wed, 14 Feb 2018 10:03:24 -0500
parents ba85750d241d
children d8bc8984cc49
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3:ba85750d241d 4:5aab3adcb3a3
5 </macros> 5 </macros>
6 <expand macro="requirements"/> 6 <expand macro="requirements"/>
7 <expand macro="stdio"/> 7 <expand macro="stdio"/>
8 <expand macro="version_command"/> 8 <expand macro="version_command"/>
9 <command><![CDATA[ 9 <command><![CDATA[
10 @SHELL_OPTIONS@ 10 @SHELL_OPTIONS@
11 11
12 #import re 12 #import re
13 ## create symlinks to input datasets 13 ## create symlinks to input datasets
14 ln -s "$reference.template" reference.template.dat && 14 ln -s '$reference.template' reference.template.dat &&
15 ln -s "$flow" flow.dat && 15 ln -s '$flow' flow.dat &&
16 ln -s "$error" error.dat && 16 ln -s '$error' error.dat &&
17 17
18 echo 'make.lookup( 18 echo 'make.lookup(
19 reference=reference.template.dat, 19 reference=reference.template.dat,
20 flow=flow.dat, 20 flow=flow.dat,
21 error=error.dat, 21 error=error.dat,
22 order=$order, 22 order=$order,
23 barcode=$re.sub("[^ACTG]","",str($barcode)), 23 barcode=$re.sub("[^ACTG]","",str($barcode)),
24 key=$re.sub("[^ACTG]","",str($key)), 24 key=$re.sub("[^ACTG]","",str($key)),
25 threshold=$threshold 25 threshold=$threshold
26 )' 26 )'
27 | sed 's/ //g' ## mothur trips over whitespace 27 | sed 's/ //g' ## mothur trips over whitespace
28 | mothur 28 | mothur
29 | tee mothur.out.log 29 | tee mothur.out.log
30 ]]></command> 30 ]]></command>
31 <inputs> 31 <inputs>
32 <conditional name="reference"> 32 <conditional name="reference">
33 <param name="source" type="select" label="Select Reference Template from" help=""> 33 <param name="source" type="select" label="Select Reference Template from" help="">
34 <option value="hist">History</option> 34 <option value="hist">History</option>
84 </assert_contents> 84 </assert_contents>
85 </output> 85 </output>
86 <expand macro="logfile-test"/> 86 <expand macro="logfile-test"/>
87 </test> 87 </test>
88 </tests> 88 </tests>
89 <help> 89 <help><![CDATA[
90 <![CDATA[
91 90
92 @MOTHUR_OVERVIEW@ 91 @MOTHUR_OVERVIEW@
93 92
94 **Command Documentation** 93 **Command Documentation**
95 94
96 The make.lookup_ allows you to create custom lookup files for use with shhh.flows. 95 The make.lookup_ allows you to create custom lookup files for use with shhh.flows.
97 96
98 .. _make.lookup: https://www.mothur.org/wiki/Make.lookup 97 .. _make.lookup: https://www.mothur.org/wiki/Make.lookup
99 98
100 ]]> 99 ]]></help>
101 </help>
102 <citations> 100 <citations>
103 <citation type="doi">10.1128/AEM.01541-09</citation> 101 <citation type="doi">10.1128/AEM.01541-09</citation>
104 </citations> 102 </citations>
105 </tool> 103 </tool>