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comparison indicator.xml @ 4:768bdcfeab90 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 09:48:25 -0500
parents 7064503531b8
children c1250ca75b93
comparison
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3:7064503531b8 4:768bdcfeab90
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 #if $withdesign.tree: 14 #if $withdesign.tree:
15 ln -s "$withdesign.tree" withdesign.tree.dat && 15 ln -s '$withdesign.tree' withdesign.tree.dat &&
16 #end if 16 #end if
17 #if $withdesign.havedesign == "yes": 17 #if $withdesign.havedesign == "yes":
18 ln -s "$withdesign.design" withdesign.design.dat && 18 ln -s '$withdesign.design' withdesign.design.dat &&
19 #end if 19 #end if
20 20
21 echo 'indicator( 21 echo 'indicator(
22 #if $withdesign.tree: 22 #if $withdesign.tree:
23 tree=withdesign.tree.dat, 23 tree=withdesign.tree.dat,
24 #end if 24 #end if
25 #if $otu.is_of_type("mothur.relabund"): 25 #if $otu.is_of_type("mothur.relabund"):
26 relabund=otu.dat, 26 relabund=otu.dat,
27 #elif $otu.is_of_type("mothur.shared"): 27 #elif $otu.is_of_type("mothur.shared"):
28 shared=otu.dat, 28 shared=otu.dat,
29 #end if 29 #end if
30 #if $label: 30 #if $label:
31 label=${ str($label).replace(",","-") }, 31 label=${ str($label).replace(",","-") },
32 #end if 32 #end if
33 #if $withdesign.groups: 33 #if $withdesign.groups:
34 groups=${ str($withdesign.groups).replace(",","-") }, 34 groups=${ str($withdesign.groups).replace(",","-") },
35 #end if 35 #end if
36 #if $withdesign.havedesign == "yes": 36 #if $withdesign.havedesign == "yes":
37 design=withdesign.design.dat, 37 design=withdesign.design.dat,
38 #end if 38 #end if
39 processors='\${GALAXY_SLOTS:-8}' 39 processors='\${GALAXY_SLOTS:-8}'
40 )' 40 )'
41 | sed 's/ //g' ## mothur trips over whitespace 41 | sed 's/ //g' ## mothur trips over whitespace
42 | mothur 42 | mothur
43 | tee mothur.out.log 43 | tee mothur.out.log
44 ]]></command> 44 ]]></command>
45 <inputs> 45 <inputs>
46 <param name="otu" type="data" format="mothur.shared,mothur.relabund" label="shared/relabund - OTU dataset"/> 46 <param name="otu" type="data" format="mothur.shared,mothur.relabund" label="shared/relabund - OTU dataset"/>
47 <param name="label" type="select" optional="true" multiple="false" label="label - OTU Labels"> 47 <param name="label" type="select" optional="true" multiple="false" label="label - OTU Labels">
48 <expand macro="labeloptions"/> 48 <expand macro="labeloptions"/>
135 </output> 135 </output>
136 <output name="tree_out" md5="756bfd16311e141a099cfe96db458d83"/> 136 <output name="tree_out" md5="756bfd16311e141a099cfe96db458d83"/>
137 <expand macro="logfile-test"/> 137 <expand macro="logfile-test"/>
138 </test> 138 </test>
139 </tests> 139 </tests>
140 <help> 140 <help><![CDATA[
141 <![CDATA[
142 141
143 @MOTHUR_OVERVIEW@ 142 @MOTHUR_OVERVIEW@
144 143
145 **Command Documentation** 144 **Command Documentation**
146 145
149 .. _shared: https://www.mothur.org/wiki/Shared_file 148 .. _shared: https://www.mothur.org/wiki/Shared_file
150 .. _relabund: https://www.mothur.org/wiki/Get.relabund 149 .. _relabund: https://www.mothur.org/wiki/Get.relabund
151 .. _indicator: https://www.mothur.org/wiki/Indicator 150 .. _indicator: https://www.mothur.org/wiki/Indicator
152 151
153 v.1.22.0: Updated to Mothur 1.33 152 v.1.22.0: Updated to Mothur 1.33
154 ]]> 153
155 </help> 154 ]]></help>
156 <expand macro="citations"/> 155 <expand macro="citations"/>
157 </tool> 156 </tool>