Mercurial > repos > iuc > mothur_cooccurrence

comparison cooccurrence.xml @ 2:c2cf32e92e83 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 22:13:29 -0400
parents 6cb0335df5db
children 57fe046c8fbe
comparison
equal deleted inserted replaced
1:f83d1ed69978 2:c2cf32e92e83
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($groups).replace(",","-") }
25 #end if 25 #end if
26 )' 26 )'
27 | sed 's/ //g' ## mothur trips over whitespace 27 | sed 's/ //g' ## mothur trips over whitespace
28 | mothur 28 | mothur
29 | tee mothur.out.log 29 | tee mothur.out.log
30 ]]></command> 30 ]]></command>
31 <inputs> 31 <inputs>
32 <param name="otu" type="data" format="mothur.shared" label="shared - OTU Shared file"/> 32 <param name="otu" type="data" format="mothur.shared" label="shared - OTU Shared file"/>
33 <param name="iters" type="integer" value="1000" min="1" optional="true" label="iters - Number of iterations to try (default 1000)"/> 33 <param name="iters" type="integer" value="1000" min="1" optional="true" label="iters - Number of iterations to try (default 1000)"/>
34 <param name="metric" type="select" label="metric - test metric for scoring"> 34 <param name="metric" type="select" label="metric - test metric for scoring">
54 </options> 54 </options>
55 </param> 55 </param>
56 <param name="label" type="select" optional="true" label="label - Select OTU Labels to include" multiple="true" help="By default all are included if no selection is made."> 56 <param name="label" type="select" optional="true" label="label - Select OTU Labels to include" multiple="true" help="By default all are included if no selection is made.">
57 <expand macro="labeloptions"/> 57 <expand macro="labeloptions"/>
58 </param> 58 </param>
59 <expand macro="param-savelog"/>
59 </inputs> 60 </inputs>
60 <outputs> 61 <outputs>
61 <expand macro="logfile-output"/> 62 <expand macro="logfile-output"/>
62 <data name="out_summary" format="tabular" from_work_dir="otu*.summary" label="${tool.name} on ${on_string}: cooccurence.summary"/> 63 <data name="out_summary" format="tabular" from_work_dir="otu*.summary" label="${tool.name} on ${on_string}: cooccurence.summary"/>
63 </outputs> 64 </outputs>
70 <has_text text="cscore"/> 71 <has_text text="cscore"/>
71 <has_text text="unique"/> 72 <has_text text="unique"/>
72 <has_text text="0.05"/> 73 <has_text text="0.05"/>
73 </assert_contents> 74 </assert_contents>
74 </output> 75 </output>
76 <param name="savelog" value="true"/>
75 <expand macro="logfile-test"/> 77 <expand macro="logfile-test"/>
76 </test> 78 </test>
77 <test><!-- test with label and group select --> 79 <test><!-- test with label and group select -->
78 <param name="otu" value="amazon.an.shared" ftype="mothur.shared"/> 80 <param name="otu" value="amazon.an.shared" ftype="mothur.shared"/>
79 <param name="metric" value="vratio"/> 81 <param name="metric" value="vratio"/>
85 <has_text text="vratio"/> 87 <has_text text="vratio"/>
86 <not_has_text text="unique"/> 88 <not_has_text text="unique"/>
87 <has_text text="0.05"/> 89 <has_text text="0.05"/>
88 </assert_contents> 90 </assert_contents>
89 </output> 91 </output>
92 <param name="savelog" value="true"/>
90 <expand macro="logfile-test"/> 93 <expand macro="logfile-test"/>
91 </test> 94 </test>
92 </tests> 95 </tests>
93 <help> 96 <help><![CDATA[
94 <![CDATA[
95 97
96 @MOTHUR_OVERVIEW@ 98 @MOTHUR_OVERVIEW@
97 99
98 **Command Documentation** 100 **Command Documentation**
99 101
160 162
161 .. _shared: https://www.mothur.org/wiki/Shared_file 163 .. _shared: https://www.mothur.org/wiki/Shared_file
162 .. _cooccurrence: https://www.mothur.org/wiki/Cooccurrence 164 .. _cooccurrence: https://www.mothur.org/wiki/Cooccurrence
163 165
164 v1.26.0: Updated to Mothur 1.33 166 v1.26.0: Updated to Mothur 1.33
165 ]]> 167
166 </help> 168 ]]></help>
167 <expand macro="citations"/> 169 <expand macro="citations"/>
168 </tool> 170 </tool>