Mercurial > repos > iuc > mothur_deunique_seqs

comparison deunique.seqs.xml @ 0:4b2dabf45996 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
author iuc
date Fri, 19 May 2017 04:56:44 -0400
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children 3291237294fe
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-1:000000000000 0:4b2dabf45996
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="stdio"/>
8 <expand macro="version_command"/>
9 <command><![CDATA[
10 @SHELL_OPTIONS@
11
12 ## create symlinks to input datasets
13 ln -s "$fasta" fasta.dat &&
14 ln -s "$names" names.dat &&
15
16 echo 'deunique.seqs(
17 #if $inputtype.intype == "countfile":
18 count=names.dat,
19 #else
20 name=names.dat,
21 #end if
22 fasta=fasta.dat
23 )'
24 | sed 's/ //g' ## mothur trips over whitespace
25 | mothur
26 | tee mothur.out.log
27 ]]></command>
28 <inputs>
29 <param name="fasta" type="data" format="fasta" label="fasta - Sequences to filter"/>
30 <conditional name="inputtype">
31 <param name="intype" type="select" label="type of file to provide, may be either a names or a count file" help="">
32 <option value="namesfile">names</option>
33 <option value="countfile">count table</option>
34 </param>
35 <when value="namesfile">
36 <param name="names" type="data" format="mothur.names" label="provide a names file" help="A names file will generate a new faste file containing all the sequences."/>
37 </when>
38 <when value="countfile">
39 <param name="names" type="data" format="mothur.count_table" label="provide a count table" help="A counts table will generate a new faste file containing all the sequences. If the file contains group information, a group file will also be created."/>
40 </when>
41 </conditional>
42 </inputs>
43 <outputs>
44 <expand macro="logfile-output"/>
45 <data name="out_fasta" format_source="fasta" from_work_dir="fasta*.redundant.fasta" label="${tool.name} on ${on_string}: fasta"/>
46 <!-- groups file is created when a count file is used as input, but will be empty if the count file did not contain group information -->
47 <data name="groups_file" format="mothur.groups" from_work_dir="names.redundant.groups" label="${tool.name} on ${on_string}: groups">
48 <filter>inputtype.intype == 'countfile'</filter>
49 </data>
50 </outputs>
51 <tests>
52 <test><!-- test names file input -->
53 <param name="fasta" value="amazon.unique.fasta"/>
54 <param name="intype" value="namesfile"/>
55 <param name="names" value="amazon.unique.names"/>
56 <output name="out_fasta" md5="579698b8037ee939dd730e2cf0dd018d" ftype="fasta"/>
57 <expand macro="logfile-test"/>
58 </test>
59 <test><!-- test count file input with group file output -->
60 <param name="fasta" value="amazon.unique.fasta"/>
61 <param name="intype" value="countfile"/>
62 <param name="names" value="amazon_withgroups.count_table"/>
63 <output name="out_fasta" md5="177f5cf92a84ab3aef0a665e06178bbe" ftype="fasta"/>
64 <output name="groups_file" file="amazon_withgroups.redundant.groups" ftype="mothur.groups"/>
65 <expand macro="logfile-test"/>
66 </test>
67 <test><!-- test count file input without group file output -->
68 <param name="fasta" value="amazon.unique.fasta"/>
69 <param name="intype" value="countfile"/>
70 <param name="names" value="amazon.count_table"/>
71 <output name="out_fasta" md5="177f5cf92a84ab3aef0a665e06178bbe" ftype="fasta"/>
72 <output name="groups_file" md5="d41d8cd98f00b204e9800998ecf8427e" ftype="mothur.groups"/> <!--empty-->
73 <expand macro="logfile-test"/>
74 </test>
75 </tests>
76 <help>
77 <![CDATA[
78
79 @MOTHUR_OVERVIEW@
80
81 **Command Documentation**
82
83 The deunique.seqs_ command is the reverse of the unique.seqs command, and creates a fasta file from a fasta and name_ file.
84
85 .. _name: https://www.mothur.org/wiki/Name_file
86 .. _deunique.seqs: https://www.mothur.org/wiki/Deunique.seqs
87
88 v.1.21.0: Updated to Mothur 1.33, added option to provide count instead of names file, new groups file as output
89
90 ]]>
91 </help>
92 <expand macro="citations"/>
93 </tool>