Mercurial > repos > iuc > mothur_unique_seqs

comparison unique.seqs.xml @ 1:a8d6c0935377 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit ea40e3d84e7850eb4226d6c85f709dcad18d4ba9
author iuc
date Thu, 18 May 2017 18:19:28 -0400
parents 4098a8c01660
children 84e71b1537f3
comparison
equal deleted inserted replaced
0:4098a8c01660 1:a8d6c0935377
2 <description>Return unique sequences</description> 2 <description>Return unique sequences</description>
3 <macros> 3 <macros>
4 <import>macros.xml</import> 4 <import>macros.xml</import>
5 </macros> 5 </macros>
6 <expand macro="requirements"/> 6 <expand macro="requirements"/>
7 <expand macro="stdio"/>
7 <expand macro="version_command"/> 8 <expand macro="version_command"/>
8 <command detect_errors="aggressive"><![CDATA[ 9 <command><![CDATA[
10 @SHELL_OPTIONS@
11
9 ## create symlinks to input datasets 12 ## create symlinks to input datasets
10 ln -s "$names" names.dat && 13 ln -s "$names" names.dat &&
11 ln -s "$fasta" fasta.dat && 14 ln -s "$fasta" fasta.dat &&
12 15
13 echo 'unique.seqs( 16 echo 'unique.seqs(
14 #if $names: 17 #if $names.is_of_type('mothur.names'):
15 name=names.dat, 18 name=names.dat,
19 #elif $names.is_of_type('mothur.count_table'):
20 count=names.dat,
16 #end if 21 #end if
17 fasta=fasta.dat 22 fasta=fasta.dat
18 )' 23 )'
19 | sed 's/ //g' ## mothur trips over whitespace 24 | sed 's/ //g' ## mothur trips over whitespace
20 | mothur 25 | mothur
26 | tee mothur.out.log
21 ]]></command> 27 ]]></command>
22 <inputs> 28 <inputs>
23 <param name="fasta" type="data" format="fasta" label="fasta - Sequences to filter"/> 29 <param name="fasta" type="data" format="fasta" label="fasta - Sequences to filter"/>
24 <param name="names" type="data" format="mothur.names" optional="true" label="names - Sequences Names"/> 30 <param name="names" type="data" format="mothur.names,mothur.count_table" optional="true" label="name file or count table - Sequences Names"/>
25 </inputs> 31 </inputs>
26 <outputs> 32 <outputs>
27 <expand macro="logfile-output"/> 33 <expand macro="logfile-output"/>
28 <data name="out_fasta" format_source="fasta" from_work_dir="fasta*.unique.*" label="${tool.name} on ${on_string}: fasta"/> 34 <data name="out_fasta" format_source="fasta" from_work_dir="fasta*.unique.*" label="${tool.name} on ${on_string}: fasta"/>
29 <data name="out_names" format="mothur.names" from_work_dir="fasta*.names" label="${tool.name} on ${on_string}: names"/> 35 <data name="out_names" format="mothur.names" from_work_dir="fasta*.names" label="${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>
30 </outputs> 41 </outputs>
31 <tests> 42 <tests>
32 <test> 43 <test><!-- test with names file -->
33 <param name="fasta" value="amazon.fasta"/> 44 <param name="fasta" value="amazon.fasta"/>
34 <param name="names" value="amazon.names"/> 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"/>
35 <output name="out_fasta" file="amazon.unique.fasta" ftype="fasta"/> 59 <output name="out_fasta" file="amazon.unique.fasta" ftype="fasta"/>
36 <output name="out_names" file="amazon.unique.names" ftype="mothur.names"/> 60 <output name="out_names" file="amazon.unique.names" ftype="mothur.names"/>
37 <expand macro="logfile-test"/> 61 <expand macro="logfile-test"/>
38 </test> 62 </test>
39 </tests> 63 </tests>
40 <help> 64 <help>
41 <![CDATA[ 65 <![CDATA[
42 66
43 @MOTHUR_OVERVIEW@ 67 @MOTHUR_OVERVIEW@
44 68
45 **Command Documenation** 69 **Command Documentation**
46 70
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. 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.
48 72
49 .. _name: http://www.mothur.org/wiki/Name_file 73 .. _name: https://www.mothur.org/wiki/Name_file
50 .. _unique.seqs: http://www.mothur.org/wiki/Unique.seqs 74 .. _unique.seqs: https://www.mothur.org/wiki/Unique.seqs
51 75
52 ]]> 76 ]]>
53 </help> 77 </help>
54 <expand macro="citations"/> 78 <expand macro="citations"/>
55 </tool> 79 </tool>