Mercurial > repos > iuc > mothur_split_groups

comparison split.groups.xml @ 3:883a95e17395 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
author iuc
date Wed, 14 Feb 2018 10:10:40 -0500
parents 87bee516388b
children 7b20827f8e8f
comparison
equal deleted inserted replaced
2:ce407814d4de 3:883a95e17395
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 "$name" name.dat && 13 ln -s '$name' name.dat &&
14 ln -s "$count" count.dat && 14 ln -s '$count' count.dat &&
15 ln -s "$fasta" fasta.dat && 15 ln -s '$fasta' fasta.dat &&
16 ln -s "$group" group.dat && 16 ln -s '$group' group.dat &&
17 17
18 echo 'split.groups( 18 echo 'split.groups(
19 #if $name: 19 #if $name:
20 name=name.dat, 20 name=name.dat,
21 #end if 21 #end if
22 #if $groups: 22 #if $groups:
23 groups=${ str($groups).replace(",","-") }, 23 groups=${ str($groups).replace(",","-") },
24 #end if 24 #end if
25 #if $count: 25 #if $count:
26 count=count.dat, 26 count=count.dat,
27 #end if 27 #end if
28 fasta=fasta.dat, 28 fasta=fasta.dat,
29 group=group.dat 29 group=group.dat
30 )' 30 )'
31 | sed 's/ //g' ## mothur trips over whitespace 31 | sed 's/ //g' ## mothur trips over whitespace
32 | mothur 32 | mothur
33 | tee mothur.out.log 33 | tee mothur.out.log
34 ]]></command> 34 ]]></command>
35 <inputs> 35 <inputs>
36 <param name="fasta" type="data" format="fasta" label="fasta - Fasta to split by group"/> 36 <param name="fasta" type="data" format="fasta" label="fasta - Fasta to split by group"/>
37 <param name="name" type="data" format="mothur.names" label="name - Names to split by group" optional="true"/> 37 <param name="name" type="data" format="mothur.names" label="name - Names to split by group" optional="true"/>
38 <param name="group" type="data" format="mothur.groups" label="group - Groups"/> 38 <param name="group" type="data" format="mothur.groups" label="group - Groups"/>
59 <element name="forest" md5="f0e662d1d82e96b4977864925493dbf5" ftype="fasta"/> 59 <element name="forest" md5="f0e662d1d82e96b4977864925493dbf5" ftype="fasta"/>
60 </output_collection> 60 </output_collection>
61 <expand macro="logfile-test"/> 61 <expand macro="logfile-test"/>
62 </test> 62 </test>
63 </tests> 63 </tests>
64 <help> 64 <help><![CDATA[
65 <![CDATA[
66 65
67 @MOTHUR_OVERVIEW@ 66 @MOTHUR_OVERVIEW@
68 67
69 **Command Documentation** 68 **Command Documentation**
70 69
71 The split.groups_ command reads a fasta file and group_ file and generates a fasta file for each group in the groupfile. A name_ file can also be split into groups. 70 The split.groups_ command reads a fasta file and group_ file and generates a fasta file for each group in the groupfile. A name_ file can also be split into groups.
72 71
73 .. _group: https://www.mothur.org/wiki/Group_file 72 .. _group: https://www.mothur.org/wiki/Group_file
74 .. _name: https://www.mothur.org/wiki/Name_file 73 .. _name: https://www.mothur.org/wiki/Name_file
75 .. _split.groups: https://www.mothur.org/wiki/Split.groups 74 .. _split.groups: https://www.mothur.org/wiki/Split.groups
76 ]]> 75
77 </help> 76 ]]></help>
78 <expand macro="citations"/> 77 <expand macro="citations"/>
79 </tool> 78 </tool>