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comparison lefse.xml @ 0:844a4a7c3782 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit ea40e3d84e7850eb4226d6c85f709dcad18d4ba9
author iuc
date Thu, 18 May 2017 18:17:42 -0400
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children 4c5e2530dfc9
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-1:000000000000 0:844a4a7c3782
1 <tool profile="16.07" id="mothur_lefse" name="Lefse" 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 'lefse(
17 shared=shared.dat,
18 design=design.dat,
19 #if $class:
20 class=$class,
21 #end if
22 #if $sclass:
23 subclass=$sclass,
24 #end if
25 #if $label:
26 label=${ str($label).replace(",","-") },
27 #end if
28 aalpha=$aalpha,
29 walpha=$walpha,
30 lda=$lda,
31 iters=$iters,
32 fboots=$fboots,
33 strict=$strict,
34 minc=$minc,
35 wilc=$wilc,
36 curv=$curv,
37 norm=$norm
38 )'
39 | sed 's/ //g' ## mothur trips over whitespace
40 | mothur
41 | tee mothur.out.log
42 ]]></command>
43 <inputs>
44 <param name="otu" type="data" format="mothur.shared" label="shared - OTU Shared"/>
45 <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"/>
46 <param name="label" type="select" multiple="true" optional="true" label="label - OTU Label filter">
47 <expand macro="labeloptions"/>
48 </param>
49 <param name="class" type="text" optional="true" value="" label="class -indicate the which category you would like used for the Kruskal Wallis analysis" help="If none is provided first category is used"/>
50 <param name="sclass" type="text" optional="true" value="" label="subclass - indicate the which category you would like used for the Kruskal Wallis analysis" help="If none is provided second category is used"/>
51 <param name="aalpha" type="float" value="0.05" label="aalpha - alpha value for the Krukal Wallis Anova test" help=""/>
52 <param name="walpha" type="float" value="0.05" label="walpha - alpha value for the Wilcoxon test" help=""/>
53 <param name="lda" type="float" value="2.0" label="lda - threshold on the absolute value of the logarithmic LDA score" help=""/>
54 <param name="iters" type="integer" value="30" min="0" label="iters - number of bootstrap iteration for LDA" help=""/>
55 <param name="fboots" type="float" value="0.67" label="fboots - set the subsampling fraction value for each bootstrap iteration" help=""/>
56 <param name="strict" type="integer" value="0" min="0" max="2" label="strict - set the multiple testing correction options" help=" 0 no correction (more strict, default), 1 correction for independent comparisons, 2 correction for independent comparison"/>
57 <param name="minc" type="integer" value="10" min="0" label="minc - minimum number of samples per subclass for performing wilcoxon test" help=""/>
58 <param name="wilc" type="boolean" truevalue="T" falsevalue="F" checked="true" label="wilc - indicate whether to perform the Wilcoxon test" help=""/>
59 <param name="curv" type="boolean" truevalue="T" falsevalue="F" checked="false" label="curv - whether perform the wilcoxon testing the Curtis's approach (beta)" help=""/>
60 <param name="norm" type="boolean" truevalue="T" falsevalue="F" checked="true" label="norm - multiply relative abundances by 1000000" help="Recommended when very low values are present"/>
61 </inputs>
62 <outputs>
63 <expand macro="logfile-output"/>
64 <data name="summary" format="tabular" from_work_dir="shared.*lefse_summary" label="${tool.name} on ${on_string}: summary"/>
65 </outputs>
66 <tests>
67 <test><!-- test with defaults -->
68 <param name="otu" value="final.tx.1.subsample.1.pick.shared" ftype="mothur.shared"/>
69 <param name="design" value="mouse.design"/>
70 <output name="summary" md5="d2c3d2e813607aef0844ec2fb53a5955" ftype="tabular"/>
71 <expand macro="logfile-test"/>
72 </test>
73 <test><!-- test with label and class select -->
74 <param name="otu" value="final.tx.1.subsample.1.pick.shared" ftype="mothur.shared"/>
75 <param name="design" value="mouse.design"/>
76 <param name="label" value="1"/>
77 <param name="class" value="dpw"/>
78 <output name="summary" md5="d2c3d2e813607aef0844ec2fb53a5955" ftype="tabular"/>
79 <expand macro="logfile-test"/>
80 </test>
81 </tests>
82 <help><![CDATA[
83 @MOTHUR_OVERVIEW@
84
85
86 **Command Documentation**
87
88
89 .. _lefse: https://www.mothur.org/wiki/Lefse
90 ]]></help>
91 <expand macro="citations"/>
92 </tool>