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comparison classify.rf.xml @ 0:4f4e85809481 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
author iuc
date Fri, 19 May 2017 05:45:34 -0400
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-1:000000000000 0:4f4e85809481
1 <tool profile="16.07" id="mothur_classify_rf" name="Classify.rf" 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.rf(
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 #if $otupersplit:
26 ,otupersplit=$otupersplit
27 #end if
28 #if $seed:
29 ,seed=$seed
30 #end if
31 )'
32 | sed 's/ //g' ## mothur trips over whitespace
33 | mothur
34 | tee mothur.out.log
35 ]]></command>
36 <inputs>
37 <param name="otu" type="data" format="mothur.shared" label="shared - OTU Shared"/>
38 <param name="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"/>
39 <param name="label" type="select" multiple="true" optional="true" label="label - OTU Label filter">
40 <expand macro="labeloptions"/>
41 </param>
42 <param name="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">
43 <options>
44 <filter type="data_meta" ref="otu" key="groups"/>
45 </options>
46 </param>
47 <param name="otupersplit" type="select" optional="true" label="otupersplit">
48 <option value="log2">log2</option>
49 <option value="squareroot">square root</option>
50 </param>
51 <param name="seed" type="integer" value="" min="0" optional="true" label="seed" help="Will be randomly chosen if left blank"/>
52 </inputs>
53 <outputs>
54 <expand macro="logfile-output"/>
55 <data name="summary" format="tabular" from_work_dir="shared.RF*summary" label="${tool.name} on ${on_string}: summary"/>
56 <data name="misclass-summary" format="tabular" from_work_dir="shared.misclassifications*.summary" label="${tool.name} on ${on_string}: misclassifications summary"/>
57 </outputs>
58 <tests>
59 <test><!-- test with defaults -->
60 <param name="otu" value="final.tx.1.subsample.1.pick.shared" ftype="mothur.shared"/>
61 <param name="design" value="mouse.design"/>
62 <output name="summary" md5="dd5501c82a66b681b6b9961bcf731d7d" ftype="tabular"/>
63 <output name="misclass-summary" ftype="tabular">
64 <assert_contents>
65 <has_line_matching expression="Sample\tRF classification\tActual classification"/>
66 <has_text text="F003D000"/>
67 <has_text text="F003D150"/>
68 </assert_contents>
69 </output>
70 <expand macro="logfile-test"/>
71 </test>
72 <test><!-- test with custom settings -->
73 <param name="otu" value="final.tx.1.subsample.1.pick.shared" ftype="mothur.shared"/>
74 <param name="design" value="mouse.design"/>
75 <param name="label" value="1"/>
76 <param name="otupersplit" value="log2"/>
77 <param name="groups" value="F003D000,F003D002,F003D006,F003D008,F003D142,F003D144,F003D146,F003D148"/>
78 <param name="seed" value="42"/> <!-- tool will unpredictable segfault without this -->
79 <output name="summary" md5="dd5501c82a66b681b6b9961bcf731d7d" ftype="tabular"/>
80 <output name="misclass-summary" ftype="tabular">
81 <assert_contents>
82 <has_line_matching expression="Sample\tRF classification\tActual classification"/>
83 <has_text text="F003D000"/>
84 <not_has_text text="F003D150"/>
85 </assert_contents>
86 </output>
87 <expand macro="logfile-test"/>
88 </test>
89 </tests>
90 <help><![CDATA[
91 @MOTHUR_OVERVIEW@
92
93
94 **Command Documentation**
95
96
97 .. _classify.rf: https://www.mothur.org/wiki/Classify.rf
98 ]]></help>
99 <expand macro="citations"/>
100 </tool>