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comparison make.lookup.xml @ 0:f4b0766a9082 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
author iuc
date Fri, 24 Jun 2016 16:38:35 -0400
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1 <tool profile="16.07" id="mothur_make_lookup" name="Make.lookup" version="@WRAPPER_VERSION@.0">
2 <description>allows you to create custom lookup files for use with shhh.flows</description>
3 <macros>
4 <import>macros.xml</import>
5 </macros>
6 <expand macro="requirements"/>
7 <expand macro="version_command"/>
8 <command detect_errors="aggressive"><![CDATA[
9 #import re
10 ## create symlinks to input datasets
11 ln -s "$reference.template" reference.template.dat &&
12 ln -s "$flow" flow.dat &&
13 ln -s "$error" error.dat &&
14
15 echo 'make.lookup(
16 reference=reference.template.dat,
17 flow=flow.dat,
18 error=error.dat,
19 order=$order,
20 barcode=$re.sub("[^ACTG]","",str($barcode)),
21 key=$re.sub("[^ACTG]","",str($key)),
22 threshold=$threshold
23 )'
24 | sed 's/ //g' ## mothur trips over whitespace
25 | mothur
26 ]]></command>
27 <inputs>
28 <conditional name="reference">
29 <param name="source" type="select" label="Select Reference Template from" help="">
30 <option value="hist">History</option>
31 <option value="ref">Cached Reference</option>
32 </param>
33 <when value="ref">
34 <param name="template" type="select" label="reference - Select an alignment database " help="">
35 <options from_data_table="mothur_aligndb"/>
36 </param>
37 </when>
38 <when value="hist">
39 <param name="template" type="data" format="fasta" label="reference - Reference to align with" help=""/>
40 </when>
41 </conditional>
42 <param name="flow" type="data" format="motur.sff.flow" label="flow - provide file with flow data"/>
43 <param name="error" type="data" format="tabular" label="error - provide the error summary" help="this file is an output of seq.error tool"/>
44 <param name="order" type="select" label="order - flow order for nucleotides in the sequencer" help="default is A, was TACG. Also accepts B or I">
45 <option value="A" selected="true">A (TACG)</option>
46 <option value="B">B</option>
47 <option value="I">I</option>
48 </param>
49 <param name="barcode" type="text" value="AACCGTGTC" label="barcode - provide the barcode sequence"/>
50 <param name="key" type="text" value="TCAG" label="key - provide the key sequence"/>
51 <param name="threshold" type="integer" value="10000" min="0" label="threshold - " help=""/>
52 </inputs>
53 <outputs>
54 <expand macro="logfile-output"/>
55 <data name="lookup_out" format="txt" from_work_dir="flow*.lookup" label="${tool.name} on ${on_string}: lookup"/>
56 </outputs>
57 <tests>
58 <test><!-- test with defaults -->
59 <param name="source" value="hist"/>
60 <param name="template" value="HMP_MOCK.v35.align" ftype="mothur.align"/>
61 <param name="flow" value="testflow.flow" ftype="mothur.sff.flow"/>
62 <param name="error" value="Mock_S280_L001_R1_001_small.trim.contigs.good.error.summary" ftype="tabular"/>
63 <output name="lookup_out" ftype="txt">
64 <assert_contents>
65 <has_line_matching expression="^(-?[(\d\.|nan)]+\t?)+$"/>
66 </assert_contents>
67 </output>
68 <expand macro="logfile-test"/>
69 </test>
70 <test><!-- test sanitizers -->
71 <param name="source" value="hist"/>
72 <param name="template" value="HMP_MOCK.v35.align" ftype="mothur.align"/>
73 <param name="flow" value="testflow.flow" ftype="mothur.sff.flow"/>
74 <param name="error" value="Mock_S280_L001_R1_001_small.trim.contigs.good.error.summary" ftype="tabular"/>
75 <param name="barcode" value="XAXAXCXCXGXTXGXTXC"/><!-- should be converted to default value -->
76 <param name="key" value="XTXCXAXGX"/><!-- should be converted to default value -->
77 <output name="lookup_out" ftype="txt">
78 <assert_contents>
79 <has_line_matching expression="^(-?[(\d\.|nan)]+\t?)+$"/>
80 </assert_contents>
81 </output>
82 <expand macro="logfile-test"/>
83 </test>
84 </tests>
85 <help>
86 <![CDATA[
87
88 @MOTHUR_OVERVIEW@
89
90 **Command Documenation**
91
92 The make.lookup_ allows you to create custom lookup files for use with shhh.flows.
93
94 .. _make.lookup: http://www.mothur.org/wiki/Make.lookup
95
96 ]]>
97 </help>
98 <citations>
99 <citation type="doi">10.1128/AEM.01541-09</citation>
100 </citations>
101 </tool>