Mercurial > repos > iuc > mothur_classify_svm

comparison classify.svm.xml @ 0:ba0b90285bc0 draft default tip

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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 10:29:38 -0500
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1 <tool profile="16.07" id="mothur_classify_svm" name="Classify.svm" version="@WRAPPER_VERSION@.0">
2 <description>description</description>
3 <macros>
4 <import>macros.xml</import>
5 </macros>
6 <expand macro="requirements"/>
7 <expand macro="stdio"/>
8 <expand macro="version_command"/>
9 <command><![CDATA[
10 @SHELL_OPTIONS@
11
12 ## create symlinks to input datasets
13 ln -s '$otu' shared.dat &&
14 ln -s '$design' design.dat &&
15
16 echo 'classify.svm(
17 shared=shared.dat,
18 design=design.dat
19 #if $label:
20 ,label=${ str($label).replace(",","-") }
21 #end if
22 #if $groups:
23 ,groups=${ str($groups).replace(",","-") }
24 #end if
25 )'
26 | sed 's/ //g' ## mothur trips over whitespace
27 | mothur
28 | tee mothur.out.log
29 ]]></command>
30 <inputs>
31 <param argument="shared" name="otu" type="data" format="mothur.shared" label="shared - OTU Shared"/>
32 <param argument="design" type="data" format="mothur.design" label="design - assigns groups to sets" help="design has 2 columns: group(col 1) and grouping(col 2) (separated by a TAB character) use make.design"/>
33 <param argument="label" type="select" multiple="true" optional="true" label="label - OTU Label filter">
34 <expand macro="labeloptions"/>
35 </param>
36 <param argument="groups" type="select" multiple="true" optional="true" label="groups - Groups filter (uses all groups if none are selected)" help="To filter: select select at least 2 groups">
37 <options>
38 <filter type="data_meta" ref="otu" key="groups"/>
39 </options>
40 </param>
41 </inputs>
42 <outputs>
43 <expand macro="logfile-output"/>
44 <data name="summary" format="tabular" from_work_dir="shared.RF*summary" label="${tool.name} on ${on_string}: summary"/>
45 <data name="misclass-summary" format="tabular" from_work_dir="shared.misclassifications*.summary" label="${tool.name} on ${on_string}: misclassifications summary"/>
46 </outputs>
47 <tests>
48 <test><!-- test with defaults -->
49 <param name="otu" value="stool.final.opti_mcc.shared" ftype="mothur.shared"/>
50 <param name="design" value="stool.design"/>
51 <output name="summary" md5="dd5501c82a66b681b6b9961bcf731d7d" ftype="tabular"/>
52 <output name="misclass-summary" ftype="tabular">
53 <assert_contents>
54 <has_line_matching expression="Sample\tRF classification\tActual classification"/>
55 <has_text text="F003D000"/>
56 <has_text text="F003D150"/>
57 </assert_contents>
58 </output>
59 <expand macro="logfile-test"/>
60 </test>
61 <test><!-- test with custom settings -->
62 <param name="otu" value="amazon.an.shared" ftype="mothur.shared"/>
63 <param name="design" value="toymothur.design2"/>
64 <param name="label" value="0.03"/>
65 <param name="groups" value="pasture"/>
66 <output name="summary" md5="dd5501c82a66b681b6b9961bcf731d7d" ftype="tabular"/>
67 <output name="misclass-summary" ftype="tabular">
68 <assert_contents>
69 <has_line_matching expression="Sample\tRF classification\tActual classification"/>
70 <has_text text="F003D000"/>
71 <not_has_text text="F003D150"/>
72 </assert_contents>
73 </output>
74 <expand macro="logfile-test"/>
75 </test>
76 </tests>
77 <help><![CDATA[
78 @MOTHUR_OVERVIEW@
79
80
81 **Command Documentation**
82
83
84 .. _classify.rf: http://www.mothur.org/wiki/Classify.rf
85 ]]></help>
86 <expand macro="citations"/>
87 </tool>