Mercurial > repos > iuc > mothur_create_database

comparison create.database.xml @ 0:9ab5ebae3fb2 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 a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
author iuc
date Fri, 19 May 2017 05:56:16 -0400
parents
children 024a52bdf70c
comparison
equal deleted inserted replaced
-1:000000000000 0:9ab5ebae3fb2
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="stdio"/>
8 <expand macro="version_command"/>
9 <command><![CDATA[
10 @SHELL_OPTIONS@
11
12 ## create symlinks to input datasets
13 ln -s "$otu" otu.dat &&
14 ln -s "$repfasta" repfasta.dat &&
15 ln -s "$nameOrCount" nameOrCount.dat &&
16 ln -s "$constaxonomy" constaxonomy.dat &&
17 ln -s "$group" group.dat &&
18
19 echo 'create.database(
20 #if $otu.is_of_type("mothur.list"):
21 list=otu.dat
22 #elif $otu.is_of_type("mothur.shared"):
23 shared=otu.dat
24 #end if
25 ,repfasta=repfasta.dat
26 #if $nameOrCount.is_of_type("mothur.names"):
27 ,repname=nameOrCount.dat
28 #elif $nameOrCount.is_of_type("mothur.count_table"):
29 ,count=nameOrCount.dat
30 #end if
31 ,constaxonomy=constaxonomy.dat
32 #if $group:
33 ,group=group.dat
34 #end if
35 #if $label:
36 ,label=$label
37 #end if
38 )'
39 | sed 's/ //g' ## mothur trips over whitespace
40 | mothur
41 | tee mothur.out.log
42 ]]></command>
43 <inputs>
44 <param name="otu" type="data" format="mothur.list,mothur.shared" label="list or shared - OTU List of Shared"/>
45 <param name="repfasta" type="data" format="fasta" label="repfasta - rep.fasta" help="rep.fasta file generated by get.oturep"/>
46 <param name="nameOrCount" type="data" format="mothur.names,mothur.count_table" label="repname/count - Representative sequences" help="rep.name file or rep.count_table file generated by get.oturep"/>
47 <param name="constaxonomy" type="data" format="mothur.cons.taxonomy" label="constaxonomy - Consensus Taxonomy" help="consensus taxonomy file output by classify.otu"/>
48 <param name="group" type="data" format="mothur.groups" optional="true" label="group - Groups for summary file"/>
49 <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">
50 <expand macro="labeloptions"/>
51 </param>
52 </inputs>
53 <outputs>
54 <expand macro="logfile-output"/>
55 <data name="database" format="tabular" from_work_dir="otu*.database" label="${tool.name} on ${on_string}: database"/>
56 </outputs>
57 <tests>
58 <!-- Test with a mothur.names file -->
59 <test>
60 <param name="otu" value="cd-test.list" ftype="mothur.list"/>
61 <param name="repfasta" value="cd-test.repfasta" ftype="fasta"/>
62 <param name="nameOrCount" value="cd-test.repname" ftype="mothur.names"/>
63 <param name="constaxonomy" value="cd-test.constaxonomy" ftype="mothur.cons.taxonomy"/>
64 <param name="label" value="unique"/>
65 <output name="database" file="cd-test.database" ftype="tabular"/>
66 <expand macro="logfile-test"/>
67 </test>
68 <!-- Test with a mothur.count_table file -->
69 <test>
70 <param name="otu" value="cd-test.list" ftype="mothur.list"/>
71 <param name="repfasta" value="cd-test.repfasta" ftype="fasta"/>
72 <param name="nameOrCount" value="cd-test.count_table" ftype="mothur.count_table"/>
73 <param name="constaxonomy" value="cd-test.constaxonomy" ftype="mothur.cons.taxonomy"/>
74 <param name="label" value="unique"/>
75 <output name="database" file="cd-test.database" ftype="tabular"/>
76 <expand macro="logfile-test"/>
77 </test>
78 </tests>
79 <help>
80 <![CDATA[
81
82 @MOTHUR_OVERVIEW@
83
84 **Command Documentation**
85
86 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.
87
88 .. _list: https://www.mothur.org/wiki/List_file
89 .. _shared: https://www.mothur.org/wiki/Shared_file
90 .. _create.database: https://www.mothur.org/wiki/Create.database
91
92 v.1.28.0: Updated to Mothur 1.33, added count paramter.
93
94 ]]>
95 </help>
96 <expand macro="citations"/>
97 </tool>