Mercurial > repos > iuc > mothur_unique_seqs

comparison unique.seqs.xml @ 0:0468cb2dd83e 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 05:51:37 -0400
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children 837f454548b8
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-1:000000000000 0:0468cb2dd83e
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="stdio"/>
8 <expand macro="version_command"/>
9 <command><![CDATA[
10 @SHELL_OPTIONS@
11
12 ## create symlinks to input datasets
13 ln -s "$names" names.dat &&
14 ln -s "$fasta" fasta.dat &&
15
16 echo 'unique.seqs(
17 #if $names.is_of_type('mothur.names'):
18 name=names.dat,
19 #elif $names.is_of_type('mothur.count_table'):
20 count=names.dat,
21 #end if
22 fasta=fasta.dat
23 )'
24 | sed 's/ //g' ## mothur trips over whitespace
25 | mothur
26 | tee mothur.out.log
27 ]]></command>
28 <inputs>
29 <param name="fasta" type="data" format="fasta" label="fasta - Sequences to filter"/>
30 <param name="names" type="data" format="mothur.names,mothur.count_table" optional="true" label="name file or count table - Sequences Names"/>
31 </inputs>
32 <outputs>
33 <expand macro="logfile-output"/>
34 <data name="out_fasta" format_source="fasta" from_work_dir="fasta*.unique.*" label="${tool.name} on ${on_string}: fasta"/>
35 <data name="out_names" format="mothur.names" from_work_dir="fasta*.names" label="${tool.name} on ${on_string}: names">
36 <filter>names.ext != "mothur.count_table"</filter>
37 </data>
38 <data name="out_count" format="mothur.count_table" from_work_dir="fasta*.count_table" label="${tool.name} on ${on_string}: count_table">
39 <filter>names and names.ext == "mothur.count_table"</filter>
40 </data>
41 </outputs>
42 <tests>
43 <test><!-- test with names file -->
44 <param name="fasta" value="amazon.fasta"/>
45 <param name="names" value="amazon1.names" ftype="mothur.names"/>
46 <output name="out_fasta" file="amazon.unique.fasta" ftype="fasta"/>
47 <output name="out_names" file="amazon.unique.names" ftype="mothur.names"/>
48 <expand macro="logfile-test"/>
49 </test>
50 <test><!-- test with count file -->
51 <param name="fasta" value="amazon.unique.fasta"/>
52 <param name="names" value="amazon.count_table" ftype="mothur.count_table"/>
53 <output name="out_fasta" file="amazon.unique.fasta" ftype="fasta"/>
54 <output name="out_count" md5="2024cbb895f79346606ab196dd130639" ftype="mothur.count_table"/>
55 <expand macro="logfile-test"/>
56 </test>
57 <test><!-- test wth fasta only -->
58 <param name="fasta" value="amazon.fasta"/>
59 <output name="out_fasta" file="amazon.unique.fasta" ftype="fasta"/>
60 <output name="out_names" file="amazon.unique.names" ftype="mothur.names"/>
61 <expand macro="logfile-test"/>
62 </test>
63 </tests>
64 <help>
65 <![CDATA[
66
67 @MOTHUR_OVERVIEW@
68
69 **Command Documentation**
70
71 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.
72
73 .. _name: https://www.mothur.org/wiki/Name_file
74 .. _unique.seqs: https://www.mothur.org/wiki/Unique.seqs
75
76 ]]>
77 </help>
78 <expand macro="citations"/>
79 </tool>