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comparison summary.seqs.xml @ 1:03bc0aa0f9d2 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 18:20:19 -0400
parents a8637d3ac14a
children b7c0b62e024a
comparison
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0:a8637d3ac14a 1:03bc0aa0f9d2
2 <description>Summarize the quality of sequences</description> 2 <description>Summarize the quality of 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 "$fasta" fasta.dat && 13 ln -s "$fasta" fasta.dat &&
11 ln -s "$name" name.dat && 14 ln -s "$name" name.dat &&
12 ln -s "$count" count.dat && 15 ln -s "$count" count.dat &&
13 16
21 #end if 24 #end if
22 processors='\${GALAXY_SLOTS:-8}' 25 processors='\${GALAXY_SLOTS:-8}'
23 )' 26 )'
24 | sed 's/ //g' ## mothur trips over whitespace 27 | sed 's/ //g' ## mothur trips over whitespace
25 | mothur 28 | mothur
29 | tee mothur.out.log
26 ]]></command> 30 ]]></command>
27 <inputs> 31 <inputs>
28 <param name="fasta" type="data" format="fasta,mothur.align" label="fasta - Dataset"/> 32 <param name="fasta" type="data" format="fasta,mothur.align" label="fasta - Dataset"/>
29 <param name="name" type="data" format="mothur.names" label="name - Names" optional="true"/> 33 <param name="name" type="data" format="mothur.names" label="name - Names" optional="true"/>
30 <param name="count" type="data" format="mothur.count_table" optional="true" label="count - a count_table" help="The count file is similar to the name file in that it is used to represent the number of duplicate sequences for a given representative sequence. "/> 34 <param name="count" type="data" format="mothur.count_table" optional="true" label="count - a count_table" help="The count file is similar to the name file in that it is used to represent the number of duplicate sequences for a given representative sequence. "/>
55 <help> 59 <help>
56 <![CDATA[ 60 <![CDATA[
57 61
58 @MOTHUR_OVERVIEW@ 62 @MOTHUR_OVERVIEW@
59 63
60 **Command Documenation** 64 **Command Documentation**
61 65
62 The summary.seqs_ command will summarize the quality of sequences in an unaligned or aligned fasta-formatted sequence file. 66 The summary.seqs_ command will summarize the quality of sequences in an unaligned or aligned fasta-formatted sequence file.
63 67
64 68
65 .. _summary.seqs: http://www.mothur.org/wiki/Summary.seqs 69 .. _summary.seqs: https://www.mothur.org/wiki/Summary.seqs
66 ]]> 70 ]]>
67 </help> 71 </help>
68 <expand macro="citations"/> 72 <expand macro="citations"/>
69 </tool> 73 </tool>