Mercurial > repos > iuc > mothur_get_communitytype

comparison get.communitytype.xml @ 2:92b64ed4e08b draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
author iuc
date Tue, 20 Mar 2018 22:01:40 -0400
parents e86199dc2a7c
children beb4e0832f3b
comparison
equal deleted inserted replaced
1:d7f03792fa5f 2:92b64ed4e08b
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 '$otu' shared.dat && 13 ln -s '$otu' shared.dat &&
14 14
15 echo 'get.communitytype( 15 echo 'get.communitytype(
16 shared=shared.dat, 16 shared=shared.dat,
17 #if $label: 17 #if $label:
18 label=${ str($label).replace(",","-") }, 18 label=${ str($label).replace(",","-") },
19 #end if 19 #end if
20 #if $groups: 20 #if $groups:
21 groups=${ str($groups).replace(",","-") }, 21 groups=${ str($groups).replace(",","-") },
22 #end if 22 #end if
23 method=$m.method, 23 method=$m.method,
24 #if $m.method == 'kmeans' or $m.method == 'pams': 24 #if $m.method == 'kmeans' or $m.method == 'pams':
25 calc=$m.calc, 25 calc=$m.calc,
26 iters=$m.iters, 26 iters=$m.iters,
27 #end if 27 #end if
28 #if int($subsample) == 0: 28 #if int($subsample) == 0:
29 subsample=T, 29 subsample=T,
30 #elif int($subsample) > 0: 30 #elif int($subsample) > 0:
31 subsample=$subsample, 31 subsample=$subsample,
32 #end if 32 #end if
33 minpartitions=$minpartitions, 33 minpartitions=$minpartitions,
34 maxpartitions=$maxpartitions, 34 maxpartitions=$maxpartitions,
35 optimizegap=$optimizegap, 35 optimizegap=$optimizegap,
36 processors='\${GALAXY_SLOTS:-8}' 36 processors='\${GALAXY_SLOTS:-8}'
37 )' 37 )'
38 | sed 's/ //g' ## mothur trips over whitespace 38 | sed 's/ //g' ## mothur trips over whitespace
39 | mothur 39 | mothur
40 | tee mothur.out.log 40 | tee mothur.out.log
41 ]]></command> 41 ]]></command>
42 <inputs> 42 <inputs>
43 <param name="otu" type="data" format="mothur.shared" label="shared - Shared file"/> 43 <param name="otu" type="data" format="mothur.shared" label="shared - Shared file"/>
44 <param name="label" type="select" label="label - OTU Labels" multiple="true" optional="true"> 44 <param name="label" type="select" label="label - OTU Labels" multiple="true" optional="true">
45 <expand macro="labeloptions"/> 45 <expand macro="labeloptions"/>
75 </conditional> 75 </conditional>
76 <param name="minpartitions" type="integer" value="5" min="0" label="minpartitions" help=""/> 76 <param name="minpartitions" type="integer" value="5" min="0" label="minpartitions" help=""/>
77 <param name="maxpartitions" type="integer" value="10" min="0" label="minpartitions" help=""/> 77 <param name="maxpartitions" type="integer" value="10" min="0" label="minpartitions" help=""/>
78 <param name="optimizegap" type="integer" value="3" min="0" label="minpartitions" help=""/> 78 <param name="optimizegap" type="integer" value="3" min="0" label="minpartitions" help=""/>
79 <param name="subsample" type="integer" value="-1" min="-1" label="subsample" help="Ignored if negative, when set to 0 it uses the size of your smallest group (subsample=T)"/> 79 <param name="subsample" type="integer" value="-1" min="-1" label="subsample" help="Ignored if negative, when set to 0 it uses the size of your smallest group (subsample=T)"/>
80 <expand macro="param-savelog"/>
80 </inputs> 81 </inputs>
81 <outputs> 82 <outputs>
82 <expand macro="logfile-output"/> 83 <expand macro="logfile-output"/>
83 <data name="summary" format="tabular" from_work_dir="shared*.summary" label="${tool.name} on ${on_string}: summary"> 84 <data name="summary" format="tabular" from_work_dir="shared*.summary" label="${tool.name} on ${on_string}: summary">
84 <filter> m['method'] == 'dmm' </filter> 85 <filter> m['method'] == 'dmm' </filter>
110 <element name="1.dmm.1.mix" md5="9c338b1fb5aea4baae2dbf242331d27c" ftype="mothur.relabund"/> 111 <element name="1.dmm.1.mix" md5="9c338b1fb5aea4baae2dbf242331d27c" ftype="mothur.relabund"/>
111 </output_collection> 112 </output_collection>
112 <output_collection name="posterior" count="5"> 113 <output_collection name="posterior" count="5">
113 <element name="1.dmm.1.mix" md5="fae04096d53d6980d8eb712e6ec8b0d2" ftype="tabular"/> 114 <element name="1.dmm.1.mix" md5="fae04096d53d6980d8eb712e6ec8b0d2" ftype="tabular"/>
114 </output_collection> 115 </output_collection>
116 <param name="savelog" value="true"/>
115 <expand macro="logfile-test"/> 117 <expand macro="logfile-test"/>
116 </test> 118 </test>
117 <test><!-- test with all settings --> 119 <test><!-- test with all settings -->
118 <param name="otu" value="final.tx.1.subsample.1.pick.shared" ftype="mothur.shared"/> 120 <param name="otu" value="final.tx.1.subsample.1.pick.shared" ftype="mothur.shared"/>
119 <param name="label" value="1"/> 121 <param name="label" value="1"/>
139 <element name="1.kmeans.1.mix" md5="514780678b8d9413566df3355d427e27" ftype="mothur.relabund"/> 141 <element name="1.kmeans.1.mix" md5="514780678b8d9413566df3355d427e27" ftype="mothur.relabund"/>
140 </output_collection> 142 </output_collection>
141 <output_collection name="posterior" count="4"> 143 <output_collection name="posterior" count="4">
142 <element name="1.kmeans.1.mix" md5="43f4dfc2bcd1cf20db4f89ee90b6041c" ftype="tabular"/> 144 <element name="1.kmeans.1.mix" md5="43f4dfc2bcd1cf20db4f89ee90b6041c" ftype="tabular"/>
143 </output_collection> 145 </output_collection>
146 <param name="savelog" value="true"/>
144 <expand macro="logfile-test"/> 147 <expand macro="logfile-test"/>
145 </test> 148 </test>
146 </tests> 149 </tests>
147 <help><![CDATA[ 150 <help><![CDATA[
148 @MOTHUR_OVERVIEW@ 151 @MOTHUR_OVERVIEW@