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comparison nmds.xml @ 0:82eea76f38ef 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 16:42:28 -0400
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-1:000000000000 0:82eea76f38ef
1 <tool profile="16.07" id="mothur_nmds" name="Nmds" version="@WRAPPER_VERSION@.0">
2 <description>generate non-metric multidimensional scaling data</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 "$dist" dist.dat &&
11 ln -s "$axes" axes.dat &&
12
13 echo 'nmds(
14 phylip=dist.dat
15 #if $axes:
16 ,axes=axes.dat
17 #end if
18 ,mindim=$mindim
19 #if $maxdim >= $mindim:
20 ,maxdim=$maxdim
21 #end if
22 ,iters=$iters
23 ,maxiters=$maxiters
24
25 ## Mothur can't cope with scientific notation
26 #set epsilon_decimal = "{:.12f}".format(float($epsilon))
27 ,epsilon=$epsilon_decimal
28 )'
29 | sed 's/ //g' ## mothur trips over whitespace
30 | mothur
31 ]]></command>
32 <inputs>
33 <param name="dist" type="data" format="mothur.lower.dist,mothur.square.dist" label="phylip - Distance Matrix"/>
34 <param name="axes" type="data" format="mothur.axes" optional="true" label="axes - a starting configuration"/>
35 <param name="mindim" type="integer" value="2" min="1" label="mindim - minimum dimensions (default 2)"/>
36 <param name="maxdim" type="integer" value="2" label="maxdim - maximum dimensions (default 2)"/>
37 <param name="iters" type="integer" value="10" min="1" label="iters - Number of random configuration to try (default 10)"/>
38 <param name="maxiters" type="integer" value="500" min="1" label="maxiters - Number of iterations to try with each random configuration (default 500)"/>
39 <param name="epsilon" type="float" optional="true" min="0" value="1e-12" label="epsilon - acceptable stopping precision (default 1e-12)"/>
40 </inputs>
41 <outputs>
42 <expand macro="logfile-output"/>
43 <data name="nmds_axes" format="mothur.axes" from_work_dir="dist*.axes" label="${tool.name} on ${on_string}: nmds.axes"/>
44 <data name="nmds_iters" format="tabular" from_work_dir="dist*.iters" label="${tool.name} on ${on_string}: nmds.iters"/>
45 <data name="nmds_stress" format="tabular" from_work_dir="dist*.stress" label="${tool.name} on ${on_string}: nmds.stress"/>
46 </outputs>
47 <tests>
48 <test>
49 <param name="dist" value="amazon.dist"/>
50 <param name="axes" value="amazon.pcoa.axes"/>
51 <param name="mindim" value="1"/>
52 <param name="maxdim" value="2"/>
53 <param name="iters" value="10"/>
54 <param name="maxiters" value="500"/>
55 <param name="epsilon" value="1e-12"/>
56 <output name="nmds_axes" md5="9a8a5605d9a619ae1c4973a45e963032"/>
57 <output name="nmds_iters" md5="979702f1c719dac6a7276adf8363a688"/>
58 <output name="nmds_stress" md5="0b46f64bea0294f2c966d7dc890e9aea"/>
59 <expand macro="logfile-test"/>
60 </test>
61 </tests>
62 <help>
63 <![CDATA[
64
65 @MOTHUR_OVERVIEW@
66
67 .. _Mothur: http://www.mothur.org/wiki/Main_Page
68
69 **Command Documenation**
70
71 The nmds_ command generates non-metric multidimensional scaling data from a phylip_distance_matrix_.
72
73 .. _phylip_distance_matrix: http://www.mothur.org/wiki/Phylip-formatted_distance_matrix
74 .. _nmds: http://www.mothur.org/wiki/Nmds
75
76 v1.20.0: Updated to mothur 1.33
77 ]]>
78 </help>
79 <expand macro="citations"/>
80 </tool>