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comparison create.database.xml @ 0:6efb9d6ab2b1 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 16:28:52 -0400
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-1:000000000000 0:6efb9d6ab2b1
1 <tool profile="16.07" id="mothur_create_database" name="Create.database" version="@WRAPPER_VERSION@.0">
2 <description>creates a database file from a list, repnames, repfasta and contaxonomy file</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 ## create symlinks to input datasets
10 ln -s "$otu" otu.dat &&
11 ln -s "$group" group.dat &&
12 ln -s "$count" count.dat &&
13 ln -s "$repfasta" repfasta.dat &&
14 ln -s "$repname" repname.dat &&
15 ln -s "$constaxonomy" constaxonomy.dat &&
16
17 echo 'create.database(
18 #if $otu.is_of_type("mothur.list"):
19 list=otu.dat
20 #else
21 shared=otu.dat
22 #end if
23 ,repfasta=repfasta.dat
24 ,repname=repname.dat
25 ,constaxonomy=constaxonomy.dat
26 #if $label:
27 ,label=$label
28 #end if
29 #if $group:
30 ,group=group.dat
31 #end if
32 #if $count:
33 ,count=count.dat
34 #end if
35 )'
36 | sed 's/ //g' ## mothur trips over whitespace
37 | mothur
38 ]]></command>
39 <inputs>
40 <param name="otu" type="data" format="mothur.list,mothur.shared" label="list or shared - OTU List of Shared"/>
41 <param name="repfasta" type="data" format="fasta" label="repfasta - rep.fasta" help="rep.fasta file output by get.oturep"/>
42 <param name="repname" type="data" format="mothur.names" label="repname - rep.names" help="rep.names file output by get.oturep"/>
43 <param name="constaxonomy" type="data" format="mothur.cons.taxonomy" label="constaxonomy - Consensus Taxonomy" help="consensus taxonomy file output by classify.otu"/>
44 <param name="count" type="data" format="mothur.count_table" optional="true" label="count file - count_table"/>
45 <param name="group" type="data" format="mothur.groups" optional="true" label="group - Groups for summary file"/>
46 <param name="label" type="select" label="label - OTU Labels" optional="true" help="Select exactly one label. If none selected, first label in your list or shared file will be used">
47 <expand macro="labeloptions"/>
48 </param>
49 </inputs>
50 <outputs>
51 <expand macro="logfile-output"/>
52 <data name="database" format="tabular" from_work_dir="otu*.database" label="${tool.name} on ${on_string}: database"/>
53 </outputs>
54 <tests>
55 <test>
56 <param name="otu" value="cd-test.list" ftype="mothur.list"/>
57 <param name="repfasta" value="cd-test.repfasta" ftype="fasta"/>
58 <param name="repname" value="cd-test.repname" ftype="mothur.names"/>
59 <param name="label" value="unique"/>
60 <param name="constaxonomy" value="cd-test.constaxonomy" ftype="mothur.cons.taxonomy"/>
61 <output name="database" file="cd-test.database" ftype="tabular"/>
62 <expand macro="logfile-test"/>
63 </test>
64 </tests>
65 <help>
66 <![CDATA[
67
68 @MOTHUR_OVERVIEW@
69
70 **Command Documenation**
71
72 The create.database_ command reads a list_ or shared_ file, .cons.taxonomy, .rep.fasta, .rep.names and optional group file, and creates a database file.
73
74 .. _list: http://www.mothur.org/wiki/List_file
75 .. _shared: http://www.mothur.org/wiki/Shared_file
76 .. _create.database: http://www.mothur.org/wiki/Create.database
77
78 v.1.28.0: Updated to Mothur 1.33, added count paramter.
79
80 ]]>
81 </help>
82 <expand macro="citations"/>
83 </tool>