Mercurial > repos > iuc > mothur_deunique_seqs

comparison deunique.seqs.xml @ 0:57cf9fc6c84a 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 16:29:24 -0400
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1 <tool profile="16.07" id="mothur_deunique_seqs" name="Deunique.seqs" version="@WRAPPER_VERSION@.0">
2 <description>Return all sequences</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 "$fasta" fasta.dat &&
11 ln -s "$names" names.dat &&
12
13 echo 'deunique.seqs(
14 #if $inputtype.intype == "countfile":
15 count=names.dat,
16 #else
17 name=names.dat,
18 #end if
19 fasta=fasta.dat
20 )'
21 | sed 's/ //g' ## mothur trips over whitespace
22 | mothur
23 ]]></command>
24 <inputs>
25 <param name="fasta" type="data" format="fasta" label="fasta - Sequences to filter"/>
26 <conditional name="inputtype">
27 <param name="intype" type="select" label="type of file to provide, may be either a names or a count file" help="">
28 <option value="namesfile">names</option>
29 <option value="countfile">count table</option>
30 </param>
31 <when value="namesfile">
32 <param name="names" type="data" format="mothur.names" label="provide a names file" help="A names file will generate a new faste file containing all the sequences."/>
33 </when>
34 <when value="countfile">
35 <param name="names" type="data" format="mothur.count_table" label="provide a count table" help="A counts table will generate a new faste file containing all the sequences. If the file contains group information, a group file will also be created."/>
36 </when>
37 </conditional>
38 </inputs>
39 <outputs>
40 <expand macro="logfile-output"/>
41 <data name="out_fasta" format_source="fasta" from_work_dir="fasta*.redundant.fasta" label="${tool.name} on ${on_string}: fasta"/>
42 <!-- groups file is created when a count file is used as input, but will be empty if the count file did not contain group information -->
43 <data name="groups_file" format="mothur.groups" from_work_dir="names.redundant.groups" label="${tool.name} on ${on_string}: groups">
44 <filter>inputtype.intype == 'countfile'</filter>
45 </data>
46 </outputs>
47 <tests>
48 <test><!-- test names file input -->
49 <param name="fasta" value="amazon.unique.fasta"/>
50 <param name="intype" value="namesfile"/>
51 <param name="names" value="amazon.unique.names"/>
52 <output name="out_fasta" md5="579698b8037ee939dd730e2cf0dd018d" ftype="fasta"/>
53 <expand macro="logfile-test"/>
54 </test>
55 <test><!-- test count file input with group file output -->
56 <param name="fasta" value="amazon.unique.fasta"/>
57 <param name="intype" value="countfile"/>
58 <param name="names" value="amazon_withgroups.count_table"/>
59 <output name="out_fasta" md5="177f5cf92a84ab3aef0a665e06178bbe" ftype="fasta"/>
60 <output name="groups_file" file="amazon_withgroups.redundant.groups" ftype="mothur.groups"/>
61 <expand macro="logfile-test"/>
62 </test>
63 <test><!-- test count file input without group file output -->
64 <param name="fasta" value="amazon.unique.fasta"/>
65 <param name="intype" value="countfile"/>
66 <param name="names" value="amazon.count_table"/>
67 <output name="out_fasta" md5="177f5cf92a84ab3aef0a665e06178bbe" ftype="fasta"/>
68 <output name="groups_file" md5="d41d8cd98f00b204e9800998ecf8427e" ftype="mothur.groups"/> <!--empty-->
69 <expand macro="logfile-test"/>
70 </test>
71 </tests>
72 <help>
73 <![CDATA[
74
75 @MOTHUR_OVERVIEW@
76
77 **Command Documenation**
78
79 The deunique.seqs_ command is the reverse of the unique.seqs command, and creates a fasta file from a fasta and name_ file.
80
81 .. _name: http://www.mothur.org/wiki/Name_file
82 .. _deunique.seqs: http://www.mothur.org/wiki/Deunique.seqs
83
84 v.1.21.0: Updated to Mothur 1.33, added option to provide count instead of names file, new groups file as output
85
86 ]]>
87 </help>
88 <expand macro="citations"/>
89 </tool>