Mercurial > repos > iuc > mothur_chop_seqs

comparison chop.seqs.xml @ 1:b0f422397f42 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 04:22:24 -0400
parents f1d0a5a4e30c
children 35eefac6662c
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0:f1d0a5a4e30c 1:b0f422397f42
2 <description>Trim sequences to a specified length</description> 2 <description>Trim sequences to a specified length</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 "$fasta" fasta.dat && 13 ln -s "$fasta" fasta.dat &&
11 ln -s "$name" name.dat && 14 ln -s "$name" name.dat &&
12 ln -s "$group" group.dat && 15 ln -s "$group" group.dat &&
13 ln -s "$count" count.dat && 16 ln -s "$count" count.dat &&
29 #end if 32 #end if
30 processors='\${GALAXY_SLOTS:-8}' 33 processors='\${GALAXY_SLOTS:-8}'
31 )' 34 )'
32 | sed 's/ //g' ## mothur trips over whitespace 35 | sed 's/ //g' ## mothur trips over whitespace
33 | mothur 36 | mothur
37 | tee mothur.out.log
34 ]]></command> 38 ]]></command>
35 <inputs> 39 <inputs>
36 <param name="fasta" type="data" format="fasta,mothur.align" label="fasta - Sequences to be chopped"/> 40 <param name="fasta" type="data" format="fasta,mothur.align" label="fasta - Sequences to be chopped"/>
37 <param name="numbases" type="integer" value="10" label="numbases - Number of bases to keep"/> 41 <param name="numbases" type="integer" value="10" label="numbases - Number of bases to keep"/>
38 <param name="keep" type="select" label="keep - Part of the sequence to keep"> 42 <param name="keep" type="select" label="keep - Part of the sequence to keep">
60 <help> 64 <help>
61 <![CDATA[ 65 <![CDATA[
62 66
63 @MOTHUR_OVERVIEW@ 67 @MOTHUR_OVERVIEW@
64 68
65 **Command Documenation** 69 **Command Documentation**
66 70
67 The chop.seqs_ command reads a fasta file of sequences and outputs a .chop.fasta file containing the trimmed sequences. It works on both aligned and unaligned sequences. 71 The chop.seqs_ command reads a fasta file of sequences and outputs a .chop.fasta file containing the trimmed sequences. It works on both aligned and unaligned sequences.
68 72
69 .. _chop.seqs: http://www.mothur.org/wiki/Chop.seqs 73 .. _chop.seqs: https://www.mothur.org/wiki/Chop.seqs
70 74
71 v1.20.0: Updated to 1.33. Added name, group and count options for mothur version 1.31.0 75 v1.20.0: Updated to 1.33. Added name, group and count options for mothur version 1.31.0
72 ]]> 76 ]]>
73 </help> 77 </help>
74 <expand macro="citations"/> 78 <expand macro="citations"/>