Mercurial > repos > iuc > mothur_make_lookup

comparison make.lookup.xml @ 3:91652222f7b4 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
author iuc
date Tue, 20 Mar 2018 22:15:22 -0400
parents f338c64b09c1
children d56e5a7a9cef
comparison
equal deleted inserted replaced
2:f338c64b09c1 3:91652222f7b4
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>
51 <option value="I">I</option> 51 <option value="I">I</option>
52 </param> 52 </param>
53 <param name="barcode" type="text" value="AACCGTGTC" label="barcode - provide the barcode sequence"/> 53 <param name="barcode" type="text" value="AACCGTGTC" label="barcode - provide the barcode sequence"/>
54 <param name="key" type="text" value="TCAG" label="key - provide the key sequence"/> 54 <param name="key" type="text" value="TCAG" label="key - provide the key sequence"/>
55 <param name="threshold" type="integer" value="10000" min="0" label="threshold - " help=""/> 55 <param name="threshold" type="integer" value="10000" min="0" label="threshold - " help=""/>
56 <expand macro="param-savelog"/>
56 </inputs> 57 </inputs>
57 <outputs> 58 <outputs>
58 <expand macro="logfile-output"/> 59 <expand macro="logfile-output"/>
59 <data name="lookup_out" format="txt" from_work_dir="flow*.lookup" label="${tool.name} on ${on_string}: lookup"/> 60 <data name="lookup_out" format="txt" from_work_dir="flow*.lookup" label="${tool.name} on ${on_string}: lookup"/>
60 </outputs> 61 </outputs>
67 <output name="lookup_out" ftype="txt"> 68 <output name="lookup_out" ftype="txt">
68 <assert_contents> 69 <assert_contents>
69 <has_line_matching expression="^(-?[(\d\.|nan)]+\t?)+$"/> 70 <has_line_matching expression="^(-?[(\d\.|nan)]+\t?)+$"/>
70 </assert_contents> 71 </assert_contents>
71 </output> 72 </output>
73 <param name="savelog" value="true"/>
72 <expand macro="logfile-test"/> 74 <expand macro="logfile-test"/>
73 </test> 75 </test>
74 <test><!-- test sanitizers --> 76 <test><!-- test sanitizers -->
75 <param name="source" value="hist"/> 77 <param name="source" value="hist"/>
76 <param name="template" value="HMP_MOCK.v35.align" ftype="mothur.align"/> 78 <param name="template" value="HMP_MOCK.v35.align" ftype="mothur.align"/>
81 <output name="lookup_out" ftype="txt"> 83 <output name="lookup_out" ftype="txt">
82 <assert_contents> 84 <assert_contents>
83 <has_line_matching expression="^(-?[(\d\.|nan)]+\t?)+$"/> 85 <has_line_matching expression="^(-?[(\d\.|nan)]+\t?)+$"/>
84 </assert_contents> 86 </assert_contents>
85 </output> 87 </output>
88 <param name="savelog" value="true"/>
86 <expand macro="logfile-test"/> 89 <expand macro="logfile-test"/>
87 </test> 90 </test>
88 </tests> 91 </tests>
89 <help> 92 <help><![CDATA[
90 <![CDATA[
91 93
92 @MOTHUR_OVERVIEW@ 94 @MOTHUR_OVERVIEW@
93 95
94 **Command Documentation** 96 **Command Documentation**
95 97
96 The make.lookup_ allows you to create custom lookup files for use with shhh.flows. 98 The make.lookup_ allows you to create custom lookup files for use with shhh.flows.
97 99
98 .. _make.lookup: https://www.mothur.org/wiki/Make.lookup 100 .. _make.lookup: https://www.mothur.org/wiki/Make.lookup
99 101
100 ]]> 102 ]]></help>
101 </help>
102 <citations> 103 <citations>
103 <citation type="doi">10.1128/AEM.01541-09</citation> 104 <citation type="doi">10.1128/AEM.01541-09</citation>
104 </citations> 105 </citations>
105 </tool> 106 </tool>