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comparison sffinfo.xml @ 1:32a19ce534d1 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 18:13:05 -0400
parents b2c31e79e969
children e65c60fb2e5a
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0:b2c31e79e969 1:32a19ce534d1
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 "$sff" sff.dat && 13 ln -s "$sff" sff.dat &&
11 ln -s "$accnos" accnos.dat && 14 ln -s "$accnos" accnos.dat &&
12 #if $oligo.add == "yes": 15 #if $oligo.add == "yes":
13 ln -s "$oligo.oligos" oligo.oligos.dat && 16 ln -s "$oligo.oligos" oligo.oligos.dat &&
32 ,sdiffs=$oligo.sdiffs 35 ,sdiffs=$oligo.sdiffs
33 #end if 36 #end if
34 )' 37 )'
35 | sed 's/ //g' ## mothur trips over whitespace 38 | sed 's/ //g' ## mothur trips over whitespace
36 | mothur 39 | mothur
40 | tee mothur.out.log
37 ]]></command> 41 ]]></command>
38 <inputs> 42 <inputs>
39 <param name="sff" type="data" format="sff" label="sff - Sff data"/> 43 <param name="sff" type="data" format="sff" label="sff - Sff data"/>
40 <conditional name="oligo"> 44 <conditional name="oligo">
41 <param name="add" type="select" label="Trim with an oligos file?" help="a file that can contain the sequences of the forward and reverse primers and barcodes and their sample identifier. Each line of the oligos file can start with the key words &quot;forward&quot;, &quot;reverse&quot;, and &quot;barcode&quot; or it can start with a &quot;#&quot; to tell mothur to ignore that line of the oligos file."> 45 <param name="add" type="select" label="Trim with an oligos file?" help="a file that can contain the sequences of the forward and reverse primers and barcodes and their sample identifier. Each line of the oligos file can start with the key words &quot;forward&quot;, &quot;reverse&quot;, and &quot;barcode&quot; or it can start with a &quot;#&quot; to tell mothur to ignore that line of the oligos file.">
101 <help> 105 <help>
102 <![CDATA[ 106 <![CDATA[
103 107
104 @MOTHUR_OVERVIEW@ 108 @MOTHUR_OVERVIEW@
105 109
106 **Command Documenation** 110 **Command Documentation**
107 111
108 The sffinfo_ command will summarize the quality of sequences in an unaligned or aligned fasta-formatted sequence file. 112 The sffinfo_ command will summarize the quality of sequences in an unaligned or aligned fasta-formatted sequence file.
109 113
110 114
111 .. _sffinfo: http://www.mothur.org/wiki/Sffinfo 115 .. _sffinfo: https://www.mothur.org/wiki/Sffinfo
112 ]]> 116 ]]>
113 </help> 117 </help>
114 <expand macro="citations"/> 118 <expand macro="citations"/>
115 </tool> 119 </tool>