Mercurial > repos > iuc > mothur_unique_seqs

comparison unique.seqs.xml @ 0:4098a8c01660 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 16:54:29 -0400
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1 <tool profile="16.07" id="mothur_unique_seqs" name="Unique.seqs" version="@WRAPPER_VERSION@.0">
2 <description>Return unique 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 "$names" names.dat &&
11 ln -s "$fasta" fasta.dat &&
12
13 echo 'unique.seqs(
14 #if $names:
15 name=names.dat,
16 #end if
17 fasta=fasta.dat
18 )'
19 | sed 's/ //g' ## mothur trips over whitespace
20 | mothur
21 ]]></command>
22 <inputs>
23 <param name="fasta" type="data" format="fasta" label="fasta - Sequences to filter"/>
24 <param name="names" type="data" format="mothur.names" optional="true" label="names - Sequences Names"/>
25 </inputs>
26 <outputs>
27 <expand macro="logfile-output"/>
28 <data name="out_fasta" format_source="fasta" from_work_dir="fasta*.unique.*" label="${tool.name} on ${on_string}: fasta"/>
29 <data name="out_names" format="mothur.names" from_work_dir="fasta*.names" label="${tool.name} on ${on_string}: names"/>
30 </outputs>
31 <tests>
32 <test>
33 <param name="fasta" value="amazon.fasta"/>
34 <param name="names" value="amazon.names"/>
35 <output name="out_fasta" file="amazon.unique.fasta" ftype="fasta"/>
36 <output name="out_names" file="amazon.unique.names" ftype="mothur.names"/>
37 <expand macro="logfile-test"/>
38 </test>
39 </tests>
40 <help>
41 <![CDATA[
42
43 @MOTHUR_OVERVIEW@
44
45 **Command Documenation**
46
47 The unique.seqs_ command returns only the unique sequences found in a fasta-formatted sequence file and a name_ file that indicates those sequences that are identical to the reference sequence.
48
49 .. _name: http://www.mothur.org/wiki/Name_file
50 .. _unique.seqs: http://www.mothur.org/wiki/Unique.seqs
51
52 ]]>
53 </help>
54 <expand macro="citations"/>
55 </tool>