Mercurial > repos > iuc > mothur_cooccurrence

comparison cooccurrence.xml @ 3:1bebb226e793 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 09:16:00 -0500
parents 72f9b9aca28d
children 7947bd3c6e8a
comparison
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2:2962e2eeb642 3:1bebb226e793
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 'cooccurrence( 15 echo 'cooccurrence(
16 shared=otu.dat, 16 shared=otu.dat,
17 metric=$metric, 17 metric=$metric,
18 matrixmodel=$matrixmodel, 18 matrixmodel=$matrixmodel,
19 iters=$iters 19 iters=$iters
20 #if $label: 20 #if $label:
21 ,label=${ str($label).replace(",","-") } 21 ,label=${ str($label).replace(",","-") }
22 #end if 22 #end if
23 #if $groups: 23 #if $groups:
24 ,groups=${ str($groups).replace(",","-") } 24 ,groups=${ str($groups).replace(",","-") }
25 #end if 25 #end if
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="otu" type="data" format="mothur.shared" label="shared - OTU Shared file"/> 32 <param name="otu" type="data" format="mothur.shared" label="shared - OTU Shared file"/>
33 <param name="iters" type="integer" value="1000" min="1" optional="true" label="iters - Number of iterations to try (default 1000)"/> 33 <param name="iters" type="integer" value="1000" min="1" optional="true" label="iters - Number of iterations to try (default 1000)"/>
34 <param name="metric" type="select" label="metric - test metric for scoring"> 34 <param name="metric" type="select" label="metric - test metric for scoring">
88 </assert_contents> 88 </assert_contents>
89 </output> 89 </output>
90 <expand macro="logfile-test"/> 90 <expand macro="logfile-test"/>
91 </test> 91 </test>
92 </tests> 92 </tests>
93 <help> 93 <help><![CDATA[
94 <![CDATA[
95 94
96 @MOTHUR_OVERVIEW@ 95 @MOTHUR_OVERVIEW@
97 96
98 **Command Documentation** 97 **Command Documentation**
99 98
160 159
161 .. _shared: https://www.mothur.org/wiki/Shared_file 160 .. _shared: https://www.mothur.org/wiki/Shared_file
162 .. _cooccurrence: https://www.mothur.org/wiki/Cooccurrence 161 .. _cooccurrence: https://www.mothur.org/wiki/Cooccurrence
163 162
164 v1.26.0: Updated to Mothur 1.33 163 v1.26.0: Updated to Mothur 1.33
165 ]]> 164
166 </help> 165 ]]></help>
167 <expand macro="citations"/> 166 <expand macro="citations"/>
168 </tool> 167 </tool>