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comparison make.lefse.xml @ 0:2f6aaf8b5068 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
author iuc
date Fri, 24 Jun 2016 16:38:20 -0400
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-1:000000000000 0:2f6aaf8b5068
1 <tool profile="16.07" id="mothur_make_lefse" name="Make.lefse" version="@WRAPPER_VERSION@.0">
2 <description>create a lefse formatted input file from mothur's output files</description>
3 <macros>
4 <import>macros.xml</import>
5 </macros>
6 <expand macro="requirements"/>
7 <expand macro="version_command"/>
8 <command detect_errors="aggressive"><![CDATA[
9 ## create symlinks to input datasets
10 ln -s "$otu" otu.dat &&
11 ln -s "$design" design.dat &&
12 ln -s "$constaxonomy" constaxonomy.dat &&
13
14 echo 'make.lefse(
15 #if $otu.is_of_type("mothur.relabund"):
16 relabund=otu.dat,
17 #else
18 shared=otu.dat,
19 #end if
20 #if $design:
21 design=design.dat,
22 #end if
23 #if $constaxonomy:
24 constaxonomy=constaxonomy.dat,
25 #end if
26 #if $label:
27 label=${ str($label).replace(",","-") },
28 #end if
29 scale=$scale
30 )'
31 | sed 's/ //g' ## mothur trips over whitespace
32 | mothur
33 ]]></command>
34 <inputs>
35 <param name="otu" type="data" format="mothur.shared,mothur.relabund" label="shared or relabund - provide a shared or relabund file"/>
36 <param name="label" type="select" optional="true" label="label - OTU Labels" help="If none selected, the first label in your file will be used">
37 <expand macro="labeloptions"/>
38 </param>
39 <param name="constaxonomy" type="data" format="mothur.cons.taxonomy" optional="true" label="constaxonomy - provide a constaxonomy file"/>
40 <param name="design" type="data" format="tabular" optional="true" label="design - provide your design file"/>
41 <param name="scale" type="select" multiple="false" label="scale - select what scale you would like to use to convert your shared file abundances to relative abundances" help="">
42 <option value="totalgroup" selected="true">totalgroup</option>
43 <option value="totalotu">totalotu</option>
44 <option value="averagegroup">averagegroup</option>
45 <option value="averageotu">averageotu</option>
46 </param>
47 </inputs>
48 <outputs>
49 <expand macro="logfile-output"/>
50 <data name="lefse_out" format="tabular" from_work_dir="otu*.lefse" label="${tool.name} on ${on_string}: lefse"/>
51 </outputs>
52 <tests>
53 <test><!-- test with shared file and defaults -->
54 <param name="otu" value="amazon.an.shared" ftype="mothur.shared"/>
55 <output name="lefse_out" md5="295633107cd983be73389e8b92164686" ftype="tabular"/>
56 <expand macro="logfile-test"/>
57 </test>
58 <test><!-- test with relabund file -->
59 <param name="otu" value="amazon.an.relabund" ftype="mothur.relabund"/>
60 <param name="design" value="toymothur.design2" ftype="tabular"/>
61 <param name="label" value="0.18"/>
62 <output name="lefse_out" md5="c1e88702c6db198080c09f3b9c404c63" ftype="tabular"/>
63 <expand macro="logfile-test"/>
64 </test>
65 </tests>
66 <help>
67 <![CDATA[
68
69 @MOTHUR_OVERVIEW@
70
71 **Command Documenation**
72
73 The make.lefse_ allows you to create a lefse formatted input file from mothur's output files.
74
75 .. _make.lefse: http://www.mothur.org/wiki/Make.lefse
76
77 ]]>
78 </help>
79 <citations>
80 <citation type="doi">10.1128/AEM.01541-09</citation>
81 </citations>
82 </tool>