Mercurial > repos > iuc > mothur_create_database

comparison create.database.xml @ 1:122c47c8dad6 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit ea40e3d84e7850eb4226d6c85f709dcad18d4ba9
author iuc
date Thu, 18 May 2017 18:10:46 -0400
parents 6efb9d6ab2b1
children 0ec0e6261ee6
comparison
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0:6efb9d6ab2b1 1:122c47c8dad6
2 <description>creates a database file from a list, repnames, repfasta and contaxonomy file</description> 2 <description>creates a database file from a list, repnames, repfasta and contaxonomy file</description>
3 <macros> 3 <macros>
4 <import>macros.xml</import> 4 <import>macros.xml</import>
5 </macros> 5 </macros>
6 <expand macro="requirements"/> 6 <expand macro="requirements"/>
7 <expand macro="stdio"/>
7 <expand macro="version_command"/> 8 <expand macro="version_command"/>
8 <command detect_errors="aggressive"><![CDATA[ 9 <command><![CDATA[
10 @SHELL_OPTIONS@
11
9 ## create symlinks to input datasets 12 ## create symlinks to input datasets
10 ln -s "$otu" otu.dat && 13 ln -s "$otu" otu.dat &&
14 ln -s "$repfasta" repfasta.dat &&
15 ln -s "$nameOrCount" nameOrCount.dat &&
16 ln -s "$constaxonomy" constaxonomy.dat &&
11 ln -s "$group" group.dat && 17 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 18
17 echo 'create.database( 19 echo 'create.database(
18 #if $otu.is_of_type("mothur.list"): 20 #if $otu.is_of_type("mothur.list"):
19 list=otu.dat 21 list=otu.dat
20 #else 22 #elif $otu.is_of_type("mothur.shared"):
21 shared=otu.dat 23 shared=otu.dat
22 #end if 24 #end if
23 ,repfasta=repfasta.dat 25 ,repfasta=repfasta.dat
24 ,repname=repname.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
25 ,constaxonomy=constaxonomy.dat 31 ,constaxonomy=constaxonomy.dat
26 #if $label:
27 ,label=$label
28 #end if
29 #if $group: 32 #if $group:
30 ,group=group.dat 33 ,group=group.dat
31 #end if 34 #end if
32 #if $count: 35 #if $label:
33 ,count=count.dat 36 ,label=$label
34 #end if 37 #end if
35 )' 38 )'
36 | sed 's/ //g' ## mothur trips over whitespace 39 | sed 's/ //g' ## mothur trips over whitespace
37 | mothur 40 | mothur
41 | tee mothur.out.log
38 ]]></command> 42 ]]></command>
39 <inputs> 43 <inputs>
40 <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"/>
41 <param name="repfasta" type="data" format="fasta" label="repfasta - rep.fasta" help="rep.fasta file output by get.oturep"/> 45 <param name="repfasta" type="data" format="fasta" label="repfasta - rep.fasta" help="rep.fasta file generated by get.oturep"/>
42 <param name="repname" type="data" format="mothur.names" label="repname - rep.names" help="rep.names file output 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"/>
43 <param name="constaxonomy" type="data" format="mothur.cons.taxonomy" label="constaxonomy - Consensus Taxonomy" help="consensus taxonomy file output by classify.otu"/> 47 <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"/> 48 <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"> 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">
47 <expand macro="labeloptions"/> 50 <expand macro="labeloptions"/>
48 </param> 51 </param>
49 </inputs> 52 </inputs>
50 <outputs> 53 <outputs>
51 <expand macro="logfile-output"/> 54 <expand macro="logfile-output"/>
52 <data name="database" format="tabular" from_work_dir="otu*.database" label="${tool.name} on ${on_string}: database"/> 55 <data name="database" format="tabular" from_work_dir="otu*.database" label="${tool.name} on ${on_string}: database"/>
53 </outputs> 56 </outputs>
54 <tests> 57 <tests>
58 <!-- Test with a mothur.names file -->
55 <test> 59 <test>
56 <param name="otu" value="cd-test.list" ftype="mothur.list"/> 60 <param name="otu" value="cd-test.list" ftype="mothur.list"/>
57 <param name="repfasta" value="cd-test.repfasta" ftype="fasta"/> 61 <param name="repfasta" value="cd-test.repfasta" ftype="fasta"/>
58 <param name="repname" value="cd-test.repname" ftype="mothur.names"/> 62 <param name="nameOrCount" value="cd-test.repname" ftype="mothur.names"/>
63 <param name="constaxonomy" value="cd-test.constaxonomy" ftype="mothur.cons.taxonomy"/>
59 <param name="label" value="unique"/> 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"/>
60 <param name="constaxonomy" value="cd-test.constaxonomy" ftype="mothur.cons.taxonomy"/> 73 <param name="constaxonomy" value="cd-test.constaxonomy" ftype="mothur.cons.taxonomy"/>
74 <param name="label" value="unique"/>
61 <output name="database" file="cd-test.database" ftype="tabular"/> 75 <output name="database" file="cd-test.database" ftype="tabular"/>
62 <expand macro="logfile-test"/> 76 <expand macro="logfile-test"/>
63 </test> 77 </test>
64 </tests> 78 </tests>
65 <help> 79 <help>
66 <![CDATA[ 80 <![CDATA[
67 81
68 @MOTHUR_OVERVIEW@ 82 @MOTHUR_OVERVIEW@
69 83
70 **Command Documenation** 84 **Command Documentation**
71 85
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. 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.
73 87
74 .. _list: http://www.mothur.org/wiki/List_file 88 .. _list: https://www.mothur.org/wiki/List_file
75 .. _shared: http://www.mothur.org/wiki/Shared_file 89 .. _shared: https://www.mothur.org/wiki/Shared_file
76 .. _create.database: http://www.mothur.org/wiki/Create.database 90 .. _create.database: https://www.mothur.org/wiki/Create.database
77 91
78 v.1.28.0: Updated to Mothur 1.33, added count paramter. 92 v.1.28.0: Updated to Mothur 1.33, added count paramter.
79 93
80 ]]> 94 ]]>
81 </help> 95 </help>