Mercurial > repos > iuc > mothur_normalize_shared

comparison normalize.shared.xml @ 3:6ce70e21be87 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 09:51:13 -0500
parents 00df9f248874
children ad0676e23ef5
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2:a94805e41802 3:6ce70e21be87
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 "$otu" otu.dat && 13 ln -s '$otu' otu.dat &&
14 14
15 echo 'normalize.shared( 15 echo 'normalize.shared(
16 #if $otu.is_of_type("mothur.relabund"): 16 #if $otu.is_of_type("mothur.relabund"):
17 relabund=otu.dat 17 relabund=otu.dat
18 #elif $otu.is_of_type("mothur.shared"): 18 #elif $otu.is_of_type("mothur.shared"):
19 shared=otu.dat, 19 shared=otu.dat,
20 makerelabund=$makerelabund 20 makerelabund=$makerelabund
21 #end if 21 #end if
22 #if $label: 22 #if $label:
23 ,label=${ str($label).replace(",","-") } 23 ,label=${ str($label).replace(",","-") }
24 #end if 24 #end if
25 #if $groups: 25 #if $groups:
26 ,groups=${ str($groups).replace(",","-") } 26 ,groups=${ str($groups).replace(",","-") }
27 #end if 27 #end if
28 #if $method: 28 #if $method:
29 ,method=${ str($method).replace(",","-") } 29 ,method=${ str($method).replace(",","-") }
30 #end if 30 #end if
31 )' 31 )'
32 | sed 's/ //g' ## mothur trips over whitespace 32 | sed 's/ //g' ## mothur trips over whitespace
33 | mothur 33 | mothur
34 | tee mothur.out.log 34 | tee mothur.out.log
35 ]]></command> 35 ]]></command>
36 <inputs> 36 <inputs>
37 <param name="otu" type="data" format="mothur.shared,mothur.relabund" label="shared,relabund - OTU Shared or Relabund file"/> 37 <param name="otu" type="data" format="mothur.shared,mothur.relabund" label="shared,relabund - OTU Shared or Relabund file"/>
38 <param name="label" type="select" multiple="true" label="label - OTU Labels"> 38 <param name="label" type="select" multiple="true" label="label - OTU Labels">
39 <expand macro="labeloptions"/> 39 <expand macro="labeloptions"/>
72 <element name="0.26.norm" md5="1204d65c732fd880585180e956610026" ftype="mothur.shared"/> 72 <element name="0.26.norm" md5="1204d65c732fd880585180e956610026" ftype="mothur.shared"/>
73 </output_collection> 73 </output_collection>
74 <expand macro="logfile-test"/> 74 <expand macro="logfile-test"/>
75 </test> 75 </test>
76 </tests> 76 </tests>
77 <help> 77 <help><![CDATA[
78 <![CDATA[
79 78
80 @MOTHUR_OVERVIEW@ 79 @MOTHUR_OVERVIEW@
81 80
82 **Command Documentation** 81 **Command Documentation**
83 82
84 The normalize.shared_ command normalizes the number of sequences per group to a specified level. The input is a shared_ or relabund_ file. 83 The normalize.shared_ command normalizes the number of sequences per group to a specified level. The input is a shared_ or relabund_ file.
85 84
86 .. _shared: https://www.mothur.org/wiki/Shared_file 85 .. _shared: https://www.mothur.org/wiki/Shared_file
87 .. _relabund: https://www.mothur.org/wiki/Get.relabund 86 .. _relabund: https://www.mothur.org/wiki/Get.relabund
88 .. _normalize.shared: https://www.mothur.org/wiki/Normalize.shared 87 .. _normalize.shared: https://www.mothur.org/wiki/Normalize.shared
89 ]]> 88
90 </help> 89 ]]></help>
91 <expand macro="citations"/> 90 <expand macro="citations"/>
92 </tool> 91 </tool>