Mercurial > repos > iuc > mothur_deunique_seqs

comparison deunique.seqs.xml @ 5:09c8815c455b draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
author iuc
date Wed, 14 Feb 2018 10:08:12 -0500
parents 623e22d7cb82
children e301e47b31a5
comparison
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4:60647d93eafc 5:09c8815c455b
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 "$fasta" fasta.dat && 13 ln -s '$fasta' fasta.dat &&
14 ln -s "$names" names.dat && 14 ln -s '$names' names.dat &&
15 15
16 echo 'deunique.seqs( 16 echo 'deunique.seqs(
17 #if $inputtype.intype == "countfile": 17 #if $inputtype.intype == "countfile":
18 count=names.dat, 18 count=names.dat,
19 #else 19 #else
20 name=names.dat, 20 name=names.dat,
21 #end if 21 #end if
22 fasta=fasta.dat 22 fasta=fasta.dat
23 )' 23 )'
24 | sed 's/ //g' ## mothur trips over whitespace 24 | sed 's/ //g' ## mothur trips over whitespace
25 | mothur 25 | mothur
26 | tee mothur.out.log 26 | tee mothur.out.log
27 ]]></command> 27 ]]></command>
28 <inputs> 28 <inputs>
29 <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"/>
30 <conditional name="inputtype"> 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=""> 31 <param name="intype" type="select" label="type of file to provide, may be either a names or a count file" help="">
34 </param> 34 </param>
35 <when value="namesfile"> 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."/> 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> 37 </when>
38 <when value="countfile"> 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."/> 39 <param name="names" type="data" format="mothur.count_table" label="provide a count table"
40 help="A counts table will generate a new faste file containing all the sequences.
41 If the file contains group information, a group file will also be created."/>
40 </when> 42 </when>
41 </conditional> 43 </conditional>
42 </inputs> 44 </inputs>
43 <outputs> 45 <outputs>
44 <expand macro="logfile-output"/> 46 <expand macro="logfile-output"/>
71 <output name="out_fasta" md5="177f5cf92a84ab3aef0a665e06178bbe" ftype="fasta"/> 73 <output name="out_fasta" md5="177f5cf92a84ab3aef0a665e06178bbe" ftype="fasta"/>
72 <output name="groups_file" md5="d41d8cd98f00b204e9800998ecf8427e" ftype="mothur.groups"/> <!--empty--> 74 <output name="groups_file" md5="d41d8cd98f00b204e9800998ecf8427e" ftype="mothur.groups"/> <!--empty-->
73 <expand macro="logfile-test"/> 75 <expand macro="logfile-test"/>
74 </test> 76 </test>
75 </tests> 77 </tests>
76 <help> 78 <help><![CDATA[
77 <![CDATA[
78 79
79 @MOTHUR_OVERVIEW@ 80 @MOTHUR_OVERVIEW@
80 81
81 **Command Documentation** 82 **Command Documentation**
82 83
85 .. _name: https://www.mothur.org/wiki/Name_file 86 .. _name: https://www.mothur.org/wiki/Name_file
86 .. _deunique.seqs: https://www.mothur.org/wiki/Deunique.seqs 87 .. _deunique.seqs: https://www.mothur.org/wiki/Deunique.seqs
87 88
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 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
90 ]]> 91 ]]></help>
91 </help>
92 <expand macro="citations"/> 92 <expand macro="citations"/>
93 </tool> 93 </tool>