Mercurial > repos > iuc > mothur_make_lefse

comparison make.lefse.xml @ 3:e9cd4b205ddd draft

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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 09:32:13 -0500
parents cb917d37d403
children 4dfe3740f6d6
comparison
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2:b1532801d45b 3:e9cd4b205ddd
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 "$otu" otu.dat && 13 ln -s '$otu' otu.dat &&
14 ln -s "$design" design.dat && 14 ln -s '$design' design.dat &&
15 ln -s "$constaxonomy" constaxonomy.dat && 15 ln -s '$constaxonomy' constaxonomy.dat &&
16 16
17 echo 'make.lefse( 17 echo 'make.lefse(
18 #if $otu.is_of_type("mothur.relabund"): 18 #if $otu.is_of_type("mothur.relabund"):
19 relabund=otu.dat, 19 relabund=otu.dat,
20 #else 20 #else
21 shared=otu.dat, 21 shared=otu.dat,
22 #end if 22 #end if
23 #if $design: 23 #if $design:
24 design=design.dat, 24 design=design.dat,
25 #end if 25 #end if
26 #if $constaxonomy: 26 #if $constaxonomy:
27 constaxonomy=constaxonomy.dat, 27 constaxonomy=constaxonomy.dat,
28 #end if 28 #end if
29 #if $label: 29 #if $label:
30 label=${ str($label).replace(",","-") }, 30 label=${ str($label).replace(",","-") },
31 #end if 31 #end if
32 scale=$scale 32 scale=$scale
33 )' 33 )'
34 | sed 's/ //g' ## mothur trips over whitespace 34 | sed 's/ //g' ## mothur trips over whitespace
35 | mothur 35 | mothur
36 | tee mothur.out.log 36 | tee mothur.out.log
37 ]]></command> 37 ]]></command>
38 <inputs> 38 <inputs>
39 <param name="otu" type="data" format="mothur.shared,mothur.relabund" label="shared or relabund - provide a shared or relabund file"/> 39 <param name="otu" type="data" format="mothur.shared,mothur.relabund" label="shared or relabund - provide a shared or relabund file"/>
40 <param name="label" type="select" optional="true" label="label - OTU Labels" help="If none selected, the first label in your file will be used"> 40 <param name="label" type="select" optional="true" label="label - OTU Labels" help="If none selected, the first label in your file will be used">
41 <expand macro="labeloptions"/> 41 <expand macro="labeloptions"/>
65 <param name="label" value="0.18"/> 65 <param name="label" value="0.18"/>
66 <output name="lefse_out" md5="c1e88702c6db198080c09f3b9c404c63" ftype="tabular"/> 66 <output name="lefse_out" md5="c1e88702c6db198080c09f3b9c404c63" ftype="tabular"/>
67 <expand macro="logfile-test"/> 67 <expand macro="logfile-test"/>
68 </test> 68 </test>
69 </tests> 69 </tests>
70 <help> 70 <help><![CDATA[
71 <![CDATA[
72 71
73 @MOTHUR_OVERVIEW@ 72 @MOTHUR_OVERVIEW@
74 73
75 **Command Documentation** 74 **Command Documentation**
76 75
77 The make.lefse_ allows you to create a lefse formatted input file from mothur's output files. 76 The make.lefse_ allows you to create a lefse formatted input file from mothur's output files.
78 77
79 .. _make.lefse: https://www.mothur.org/wiki/Make.lefse 78 .. _make.lefse: https://www.mothur.org/wiki/Make.lefse
80 79
81 ]]> 80 ]]></help>
82 </help>
83 <citations> 81 <citations>
84 <citation type="doi">10.1128/AEM.01541-09</citation> 82 <citation type="doi">10.1128/AEM.01541-09</citation>
85 </citations> 83 </citations>
86 </tool> 84 </tool>