Mercurial > repos > iuc > mothur_unique_seqs

comparison unique.seqs.xml @ 2:837f454548b8 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
author iuc
date Tue, 20 Mar 2018 21:58:25 -0400
parents 0468cb2dd83e
children a033f325ad8d
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1:1f72d9a3d09f 2:837f454548b8
5 </macros> 5 </macros>
6 <expand macro="requirements"/> 6 <expand macro="requirements"/>
7 <expand macro="stdio"/> 7 <expand macro="stdio"/>
8 <expand macro="version_command"/> 8 <expand macro="version_command"/>
9 <command><![CDATA[ 9 <command><![CDATA[
10 @SHELL_OPTIONS@ 10 @SHELL_OPTIONS@
11 11
12 ## create symlinks to input datasets 12 ## create symlinks to input datasets
13 ln -s "$names" names.dat && 13 ln -s '$names' names.dat &&
14 ln -s "$fasta" fasta.dat && 14 ln -s '$fasta' fasta.dat &&
15 15
16 echo 'unique.seqs( 16 echo 'unique.seqs(
17 #if $names.is_of_type('mothur.names'): 17 #if $names.is_of_type('mothur.names'):
18 name=names.dat, 18 name=names.dat,
19 #elif $names.is_of_type('mothur.count_table'): 19 #elif $names.is_of_type('mothur.count_table'):
20 count=names.dat, 20 count=names.dat,
21 #end if 21 #end if
22 fasta=fasta.dat 22 fasta=fasta.dat,
23 )' 23 format=$format
24 | sed 's/ //g' ## mothur trips over whitespace 24 )'
25 | mothur 25 | sed 's/ //g' ## mothur trips over whitespace
26 | tee mothur.out.log 26 | mothur
27 | tee mothur.out.log
27 ]]></command> 28 ]]></command>
28 <inputs> 29 <inputs>
29 <param name="fasta" type="data" format="fasta" label="fasta - Sequences to filter"/> 30 <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 <param name="names" type="data" format="mothur.names,mothur.count_table" optional="true" label="name file or count table - Sequences Names"/>
32 <param name="format" type="select" label="output format">
33 <option value="count" selected="true"> Count table </option>
34 <option value="name"> Name file </option>
35 </param>
36 <expand macro="param-savelog"/>
31 </inputs> 37 </inputs>
32 <outputs> 38 <outputs>
33 <expand macro="logfile-output"/> 39 <expand macro="logfile-output"/>
34 <data name="out_fasta" format_source="fasta" from_work_dir="fasta*.unique.*" label="${tool.name} on ${on_string}: fasta"/> 40 <data name="out_fasta" format_source="fasta" from_work_dir="fasta*.unique.*" label="${tool.name} on ${on_string}: fasta"/>
35 <data name="out_names" format="mothur.names" from_work_dir="fasta*.names" label="${tool.name} on ${on_string}: names"> 41 <data name="out_names" format="mothur.names" from_work_dir="fasta*.names" label="${tool.name} on ${on_string}: names">
36 <filter>names.ext != "mothur.count_table"</filter> 42 <filter> format == "name" </filter>
37 </data> 43 </data>
38 <data name="out_count" format="mothur.count_table" from_work_dir="fasta*.count_table" label="${tool.name} on ${on_string}: count_table"> 44 <data name="out_count" format="mothur.count_table" from_work_dir="fasta*.count_table" label="${tool.name} on ${on_string}: count_table">
39 <filter>names and names.ext == "mothur.count_table"</filter> 45 <filter> format == "count" </filter>
40 </data> 46 </data>
41 </outputs> 47 </outputs>
42 <tests> 48 <tests>
43 <test><!-- test with names file --> 49 <test><!-- test with names file -->
44 <param name="fasta" value="amazon.fasta"/> 50 <param name="fasta" value="amazon.fasta"/>
45 <param name="names" value="amazon1.names" ftype="mothur.names"/> 51 <param name="names" value="amazon1.names" ftype="mothur.names"/>
52 <param name="format" value="name"/>
46 <output name="out_fasta" file="amazon.unique.fasta" ftype="fasta"/> 53 <output name="out_fasta" file="amazon.unique.fasta" ftype="fasta"/>
47 <output name="out_names" file="amazon.unique.names" ftype="mothur.names"/> 54 <output name="out_names" file="amazon.unique.names" ftype="mothur.names"/>
55 <param name="savelog" value="true"/>
48 <expand macro="logfile-test"/> 56 <expand macro="logfile-test"/>
49 </test> 57 </test>
50 <test><!-- test with count file --> 58 <test><!-- test with count file -->
51 <param name="fasta" value="amazon.unique.fasta"/> 59 <param name="fasta" value="amazon.unique.fasta"/>
52 <param name="names" value="amazon.count_table" ftype="mothur.count_table"/> 60 <param name="names" value="amazon.count_table" ftype="mothur.count_table"/>
53 <output name="out_fasta" file="amazon.unique.fasta" ftype="fasta"/> 61 <output name="out_fasta" file="amazon.unique.fasta" ftype="fasta"/>
54 <output name="out_count" md5="2024cbb895f79346606ab196dd130639" ftype="mothur.count_table"/> 62 <output name="out_count" md5="2024cbb895f79346606ab196dd130639" ftype="mothur.count_table"/>
63 <param name="savelog" value="true"/>
55 <expand macro="logfile-test"/> 64 <expand macro="logfile-test"/>
56 </test> 65 </test>
57 <test><!-- test wth fasta only --> 66 <test><!-- test wth fasta only -->
58 <param name="fasta" value="amazon.fasta"/> 67 <param name="fasta" value="amazon.fasta"/>
68 <param name="format" value="name"/>
59 <output name="out_fasta" file="amazon.unique.fasta" ftype="fasta"/> 69 <output name="out_fasta" file="amazon.unique.fasta" ftype="fasta"/>
60 <output name="out_names" file="amazon.unique.names" ftype="mothur.names"/> 70 <output name="out_names" file="amazon.unique.names" ftype="mothur.names"/>
71 <param name="savelog" value="true"/>
61 <expand macro="logfile-test"/> 72 <expand macro="logfile-test"/>
62 </test> 73 </test>
63 </tests> 74 </tests>
64 <help> 75 <help><![CDATA[
65 <![CDATA[
66 76
67 @MOTHUR_OVERVIEW@ 77 @MOTHUR_OVERVIEW@
68 78
69 **Command Documentation** 79 **Command Documentation**
70 80
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. 81 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 82
73 .. _name: https://www.mothur.org/wiki/Name_file 83 .. _name: https://www.mothur.org/wiki/Name_file
74 .. _unique.seqs: https://www.mothur.org/wiki/Unique.seqs 84 .. _unique.seqs: https://www.mothur.org/wiki/Unique.seqs
75 85
76 ]]> 86 ]]></help>
77 </help>
78 <expand macro="citations"/> 87 <expand macro="citations"/>
79 </tool> 88 </tool>