Mercurial > repos > iuc > mothur_nmds

comparison nmds.xml @ 3:ad7485b03fa1 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 09:37:02 -0500
parents 2af26863e7ca
children 8df78ef3976f
comparison
equal deleted inserted replaced
2:97e7aea68d7d 3:ad7485b03fa1
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 "$dist" dist.dat && 13 ln -s '$dist' dist.dat &&
14 ln -s "$axes" axes.dat && 14 ln -s '$axes' axes.dat &&
15 15
16 echo 'nmds( 16 echo 'nmds(
17 phylip=dist.dat 17 phylip=dist.dat
18 #if $axes: 18 #if $axes:
19 ,axes=axes.dat 19 ,axes=axes.dat
20 #end if 20 #end if
21 ,mindim=$mindim 21 ,mindim=$mindim
22 #if $maxdim >= $mindim: 22 #if $maxdim >= $mindim:
23 ,maxdim=$maxdim 23 ,maxdim=$maxdim
24 #end if 24 #end if
25 ,iters=$iters 25 ,iters=$iters
26 ,maxiters=$maxiters 26 ,maxiters=$maxiters
27 27
28 ## Mothur can't cope with scientific notation 28 ## Mothur can't cope with scientific notation
29 #set epsilon_decimal = "{:.12f}".format(float($epsilon)) 29 #set epsilon_decimal = "{:.12f}".format(float($epsilon))
30 ,epsilon=$epsilon_decimal 30 ,epsilon=$epsilon_decimal
31 )' 31 )'
32 | sed 's/ //g' ## mothur trips over whitespace 32 | sed 's/ //g' ## mothur trips over whitespace
33 | mothur 33 | mothur
34 | tee mothur.out.log 34 | tee mothur.out.log
35 ]]></command> 35 ]]></command>
36 <inputs> 36 <inputs>
37 <param name="dist" type="data" format="mothur.dist,mothur.lower.dist,mothur.square.dist" label="phylip - Distance Matrix"/> 37 <param name="dist" type="data" format="mothur.dist,mothur.lower.dist,mothur.square.dist" label="phylip - Distance Matrix"/>
38 <param name="axes" type="data" format="mothur.axes" optional="true" label="axes - a starting configuration"/> 38 <param name="axes" type="data" format="mothur.axes" optional="true" label="axes - a starting configuration"/>
39 <param name="mindim" type="integer" value="2" min="1" label="mindim - minimum dimensions (default 2)"/> 39 <param name="mindim" type="integer" value="2" min="1" label="mindim - minimum dimensions (default 2)"/>
61 <output name="nmds_iters" md5="979702f1c719dac6a7276adf8363a688"/> 61 <output name="nmds_iters" md5="979702f1c719dac6a7276adf8363a688"/>
62 <output name="nmds_stress" md5="0b46f64bea0294f2c966d7dc890e9aea"/> 62 <output name="nmds_stress" md5="0b46f64bea0294f2c966d7dc890e9aea"/>
63 <expand macro="logfile-test"/> 63 <expand macro="logfile-test"/>
64 </test> 64 </test>
65 </tests> 65 </tests>
66 <help> 66 <help><![CDATA[
67 <![CDATA[
68 67
69 @MOTHUR_OVERVIEW@ 68 @MOTHUR_OVERVIEW@
70 69
71 .. _Mothur: https://www.mothur.org/wiki/Main_Page 70 .. _Mothur: https://www.mothur.org/wiki/Main_Page
72 71
76 75
77 .. _phylip_distance_matrix: https://www.mothur.org/wiki/Phylip-formatted_distance_matrix 76 .. _phylip_distance_matrix: https://www.mothur.org/wiki/Phylip-formatted_distance_matrix
78 .. _nmds: https://www.mothur.org/wiki/Nmds 77 .. _nmds: https://www.mothur.org/wiki/Nmds
79 78
80 v1.20.0: Updated to mothur 1.33 79 v1.20.0: Updated to mothur 1.33
81 ]]> 80
82 </help> 81 ]]></help>
83 <expand macro="citations"/> 82 <expand macro="citations"/>
84 </tool> 83 </tool>