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comparison lefse.xml @ 2:8c39f704d21a 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 21:58:54 -0400
parents 1c04b0449893
children 772e6a5b7358
comparison
equal deleted inserted replaced
1:506625098e20 2:8c39f704d21a
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 ln -s '$design' design.dat && 14 ln -s '$design' design.dat &&
15 15
16 echo 'lefse( 16 echo 'lefse(
17 shared=shared.dat, 17 shared=shared.dat,
18 design=design.dat, 18 design=design.dat,
19 #if $class: 19 #if $class:
20 class=$class, 20 class=$class,
21 #end if 21 #end if
22 #if $sclass: 22 #if $sclass:
23 subclass=$sclass, 23 subclass=$sclass,
24 #end if 24 #end if
25 #if $label: 25 #if $label:
26 label=${ str($label).replace(",","-") }, 26 label=${ str($label).replace(",","-") },
27 #end if 27 #end if
28 aalpha=$aalpha, 28 #if $sets:
29 walpha=$walpha, 29 sets=${ str($sets).replace(",","-") },
30 lda=$lda, 30 #end if
31 iters=$iters, 31 aalpha=$aalpha,
32 fboots=$fboots, 32 walpha=$walpha,
33 strict=$strict, 33 lda=$lda,
34 minc=$minc, 34 iters=$iters,
35 wilc=$wilc, 35 fboots=$fboots,
36 curv=$curv, 36 strict=$strict,
37 norm=$norm 37 minc=$minc,
38 )' 38 wilc=$wilc,
39 | sed 's/ //g' ## mothur trips over whitespace 39 curv=$curv,
40 | mothur 40 norm=$norm
41 | tee mothur.out.log 41 )'
42 | sed 's/ //g' ## mothur trips over whitespace
43 | mothur
44 | tee mothur.out.log
42 ]]></command> 45 ]]></command>
43 <inputs> 46 <inputs>
44 <param name="otu" type="data" format="mothur.shared" label="shared - OTU Shared"/> 47 <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"/> 48 <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"> 49 <param name="label" type="select" multiple="true" optional="true" label="label - OTU Label filter">
47 <expand macro="labeloptions"/> 50 <expand macro="labeloptions"/>
48 </param> 51 </param>
52 <param name="sets" type="text" label="sets - Which of the sets in your design file you would like to analyze?" help="separate sets by dashes or commas, e.g. set1,set2 or set1-set2-set3"/>
53 <!-- TODO: update galaxy datatypes to set metadata for design files, then can switch to a select box
54 <param argument="sets" type="select" multiple="true" label="sets - Which of the sets in your design file you would like to analyze."
55 help="The set names are separated by dashes. The defualt is all sets in designfile">
56 <options>
57 <filter type="data_meta" ref="design" key="sets"/>
58 </options>
59 </param>
60 -->
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"/> 61 <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"/> 62 <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=""/> 63 <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=""/> 64 <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=""/> 65 <param name="lda" type="float" value="2.0" label="lda - threshold on the absolute value of the logarithmic LDA score" 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"/> 68 <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=""/> 69 <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=""/> 70 <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=""/> 71 <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"/> 72 <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"/>
73 <expand macro="param-savelog"/>
61 </inputs> 74 </inputs>
62 <outputs> 75 <outputs>
63 <expand macro="logfile-output"/> 76 <expand macro="logfile-output"/>
64 <data name="summary" format="tabular" from_work_dir="shared.*lefse_summary" label="${tool.name} on ${on_string}: summary"/> 77 <data name="summary" format="tabular" from_work_dir="shared.*lefse_summary" label="${tool.name} on ${on_string}: summary"/>
65 </outputs> 78 </outputs>
66 <tests> 79 <tests>
67 <test><!-- test with defaults --> 80 <test><!-- test with defaults -->
68 <param name="otu" value="final.tx.1.subsample.1.pick.shared" ftype="mothur.shared"/> 81 <param name="otu" value="final.tx.1.subsample.1.pick.shared" ftype="mothur.shared"/>
69 <param name="design" value="mouse.design"/> 82 <param name="design" value="mouse.design"/>
70 <output name="summary" md5="d2c3d2e813607aef0844ec2fb53a5955" ftype="tabular"/> 83 <output name="summary" md5="d2c3d2e813607aef0844ec2fb53a5955" ftype="tabular"/>
84 <param name="savelog" value="true"/>
71 <expand macro="logfile-test"/> 85 <expand macro="logfile-test"/>
72 </test> 86 </test>
73 <test><!-- test with label and class select --> 87 <test><!-- test with label and class select -->
74 <param name="otu" value="final.tx.1.subsample.1.pick.shared" ftype="mothur.shared"/> 88 <param name="otu" value="final.tx.1.subsample.1.pick.shared" ftype="mothur.shared"/>
75 <param name="design" value="mouse.design"/> 89 <param name="design" value="mouse.design"/>
76 <param name="label" value="1"/> 90 <param name="label" value="1"/>
77 <param name="class" value="dpw"/> 91 <param name="class" value="dpw"/>
78 <output name="summary" md5="d2c3d2e813607aef0844ec2fb53a5955" ftype="tabular"/> 92 <output name="summary" md5="d2c3d2e813607aef0844ec2fb53a5955" ftype="tabular"/>
93 <param name="savelog" value="true"/>
94 <expand macro="logfile-test"/>
95 </test>
96 <test><!-- test with sets -->
97 <param name="otu" value="final.tx.1.subsample.1.pick.shared" ftype="mothur.shared"/>
98 <param name="design" value="mouse.design"/>
99 <param name="sets" value="8,142"/>
100 <param name="label" value="1"/>
101 <param name="class" value="dpw"/>
102 <output name="summary" md5="64ebfb48d8c3e0bcd993a7ea8aa60e62" ftype="tabular"/>
103 <param name="savelog" value="true"/>
79 <expand macro="logfile-test"/> 104 <expand macro="logfile-test"/>
80 </test> 105 </test>
81 </tests> 106 </tests>
82 <help><![CDATA[ 107 <help><![CDATA[
83 @MOTHUR_OVERVIEW@ 108 @MOTHUR_OVERVIEW@