Mercurial > repos > iuc > mothur_summary_seqs

comparison summary.seqs.xml @ 3:b7c0b62e024a 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 10:04:27 -0500
parents 03bc0aa0f9d2
children 6082f78ea7cb
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2:9918e1425895 3:b7c0b62e024a
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 "$name" name.dat && 14 ln -s '$name' name.dat &&
15 ln -s "$count" count.dat && 15 ln -s '$count' count.dat &&
16 16
17 echo 'summary.seqs( 17 echo 'summary.seqs(
18 fasta=fasta.dat, 18 fasta=fasta.dat,
19 #if $name: 19 #if $name:
20 name=name.dat, 20 name=name.dat,
21 #end if 21 #end if
22 #if $count: 22 #if $count:
23 count=count.dat, 23 count=count.dat,
24 #end if 24 #end if
25 processors='\${GALAXY_SLOTS:-8}' 25 processors='\${GALAXY_SLOTS:-8}'
26 )' 26 )'
27 | sed 's/ //g' ## mothur trips over whitespace 27 | sed 's/ //g' ## mothur trips over whitespace
28 | mothur 28 | mothur
29 | tee mothur.out.log 29 | tee mothur.out.log
30 ]]></command> 30 ]]></command>
31 <inputs> 31 <inputs>
32 <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"/>
33 <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"/>
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. "/> 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. "/>
54 <param name="count" value="amazon.count_table"/> 54 <param name="count" value="amazon.count_table"/>
55 <output name="out_summary" md5="b8a53926f64434291d232d2736da8293" ftype="mothur.summary"/> 55 <output name="out_summary" md5="b8a53926f64434291d232d2736da8293" ftype="mothur.summary"/>
56 <expand macro="logfile-test"/> 56 <expand macro="logfile-test"/>
57 </test> 57 </test>
58 </tests> 58 </tests>
59 <help> 59 <help><![CDATA[
60 <![CDATA[
61 60
62 @MOTHUR_OVERVIEW@ 61 @MOTHUR_OVERVIEW@
63 62
64 **Command Documentation** 63 **Command Documentation**
65 64
66 The summary.seqs_ command will summarize the quality of sequences in an unaligned or aligned fasta-formatted sequence file. 65 The summary.seqs_ command will summarize the quality of sequences in an unaligned or aligned fasta-formatted sequence file.
67 66
68 67
69 .. _summary.seqs: https://www.mothur.org/wiki/Summary.seqs 68 .. _summary.seqs: https://www.mothur.org/wiki/Summary.seqs
70 ]]> 69
71 </help> 70 ]]></help>
72 <expand macro="citations"/> 71 <expand macro="citations"/>
73 </tool> 72 </tool>