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comparison summary.qual.xml @ 1:c6f0d24c9cfe 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 18:49:08 -0400
parents b889c8e70a45
children 30b226ea4888
comparison
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0:b889c8e70a45 1:c6f0d24c9cfe
2 <description>Summarize the quality scores</description> 2 <description>Summarize the quality scores</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 "$qfile" qfile.dat && 13 ln -s "$qfile" qfile.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
20 ,count=count.dat 23 ,count=count.dat
21 #end if 24 #end if
22 )' 25 )'
23 | sed 's/ //g' ## mothur trips over whitespace 26 | sed 's/ //g' ## mothur trips over whitespace
24 | mothur 27 | mothur
28 | tee mothur.out.log
25 ]]></command> 29 ]]></command>
26 <inputs> 30 <inputs>
27 <param name="qfile" type="data" format="qual" label="qfile - Sequence Quality file"/> 31 <param name="qfile" type="data" format="qual" label="qfile - Sequence Quality file"/>
28 <param name="name" type="data" format="mothur.names" optional="true" label="name - Names"/> 32 <param name="name" type="data" format="mothur.names" optional="true" label="name - Names"/>
29 <param name="count" type="data" format="mothur.count_table" optional="true" label="count - a count_table" help="generated by count.seqs"/> 33 <param name="count" type="data" format="mothur.count_table" optional="true" label="count - a count_table" help="generated by count.seqs"/>
42 <help> 46 <help>
43 <![CDATA[ 47 <![CDATA[
44 48
45 @MOTHUR_OVERVIEW@ 49 @MOTHUR_OVERVIEW@
46 50
47 **Command Documenation** 51 **Command Documentation**
48 52
49 The summary.qual_ command reads a quality file and an optional name, and summarizes the quality information. 53 The summary.qual_ command reads a quality file and an optional name, and summarizes the quality information.
50 54
51 .. _summary.qual: http://www.mothur.org/wiki/Summary.qual 55 .. _summary.qual: https://www.mothur.org/wiki/Summary.qual
52 ]]> 56 ]]>
53 </help> 57 </help>
54 <expand macro="citations"/> 58 <expand macro="citations"/>
55 </tool> 59 </tool>