Mercurial > repos > iuc > mothur_create_database

comparison create.database.xml @ 3:0ec0e6261ee6 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 09:24:19 -0500
parents 122c47c8dad6
children 5577a44a7b42
comparison
equal deleted inserted replaced
2:90dd909d4bc5 3:0ec0e6261ee6
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 ## create symlinks to input datasets 12 ## create symlinks to input datasets
13 ln -s "$otu" otu.dat && 13 ln -s '$otu' otu.dat &&
14 ln -s "$repfasta" repfasta.dat && 14 ln -s '$repfasta' repfasta.dat &&
15 ln -s "$nameOrCount" nameOrCount.dat && 15 ln -s '$nameOrCount' nameOrCount.dat &&
16 ln -s "$constaxonomy" constaxonomy.dat && 16 ln -s '$constaxonomy' constaxonomy.dat &&
17 ln -s "$group" group.dat && 17 ln -s '$group' group.dat &&
18 18
19 echo 'create.database( 19 echo 'create.database(
20 #if $otu.is_of_type("mothur.list"): 20 #if $otu.is_of_type("mothur.list"):
21 list=otu.dat 21 list=otu.dat
22 #elif $otu.is_of_type("mothur.shared"): 22 #elif $otu.is_of_type("mothur.shared"):
23 shared=otu.dat 23 shared=otu.dat
24 #end if 24 #end if
25 ,repfasta=repfasta.dat 25 ,repfasta=repfasta.dat
26 #if $nameOrCount.is_of_type("mothur.names"): 26 #if $nameOrCount.is_of_type("mothur.names"):
27 ,repname=nameOrCount.dat 27 ,repname=nameOrCount.dat
28 #elif $nameOrCount.is_of_type("mothur.count_table"): 28 #elif $nameOrCount.is_of_type("mothur.count_table"):
29 ,count=nameOrCount.dat 29 ,count=nameOrCount.dat
30 #end if 30 #end if
31 ,constaxonomy=constaxonomy.dat 31 ,constaxonomy=constaxonomy.dat
32 #if $group: 32 #if $group:
33 ,group=group.dat 33 ,group=group.dat
34 #end if 34 #end if
35 #if $label: 35 #if $label:
36 ,label=$label 36 ,label=$label
37 #end if 37 #end if
38 )' 38 )'
39 | sed 's/ //g' ## mothur trips over whitespace 39 | sed 's/ //g' ## mothur trips over whitespace
40 | mothur 40 | mothur
41 | tee mothur.out.log 41 | tee mothur.out.log
42 ]]></command> 42 ]]></command>
43 <inputs> 43 <inputs>
44 <param name="otu" type="data" format="mothur.list,mothur.shared" label="list or shared - OTU List of Shared"/> 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"/> 45 <param name="repfasta" type="data" format="fasta" optional="true" 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"/> 46 <param name="nameOrCount" type="data" format="mothur.names,mothur.count_table" optional="true" label="repname/count - Representative sequences"
47 <param name="constaxonomy" type="data" format="mothur.cons.taxonomy" label="constaxonomy - Consensus Taxonomy" help="consensus taxonomy file output by classify.otu"/> 47 help="rep.name file or rep.count_table file generated by get.oturep"/>
48 <param name="constaxonomy" type="data" format="mothur.cons.taxonomy" label="constaxonomy - Consensus Taxonomy"
49 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"/> 50 <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"> 51 <param name="label" type="select" label="label - OTU Labels" optional="true"
52 help="Select exactly one label. If none selected, first label in your list or shared file will be used">
50 <expand macro="labeloptions"/> 53 <expand macro="labeloptions"/>
51 </param> 54 </param>
52 </inputs> 55 </inputs>
53 <outputs> 56 <outputs>
54 <expand macro="logfile-output"/> 57 <expand macro="logfile-output"/>
74 <param name="label" value="unique"/> 77 <param name="label" value="unique"/>
75 <output name="database" file="cd-test.database" ftype="tabular"/> 78 <output name="database" file="cd-test.database" ftype="tabular"/>
76 <expand macro="logfile-test"/> 79 <expand macro="logfile-test"/>
77 </test> 80 </test>
78 </tests> 81 </tests>
79 <help> 82 <help><![CDATA[
80 <![CDATA[
81 83
82 @MOTHUR_OVERVIEW@ 84 @MOTHUR_OVERVIEW@
83 85
84 **Command Documentation** 86 **Command Documentation**
85 87
89 .. _shared: https://www.mothur.org/wiki/Shared_file 91 .. _shared: https://www.mothur.org/wiki/Shared_file
90 .. _create.database: https://www.mothur.org/wiki/Create.database 92 .. _create.database: https://www.mothur.org/wiki/Create.database
91 93
92 v.1.28.0: Updated to Mothur 1.33, added count paramter. 94 v.1.28.0: Updated to Mothur 1.33, added count paramter.
93 95
94 ]]> 96 ]]></help>
95 </help>
96 <expand macro="citations"/> 97 <expand macro="citations"/>
97 </tool> 98 </tool>