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comparison nmds.xml @ 0:a522f1b60172 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
author iuc
date Fri, 19 May 2017 05:33:06 -0400
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children f14fdaf6a00d
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-1:000000000000 0:a522f1b60172
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="stdio"/>
8 <expand macro="version_command"/>
9 <command><![CDATA[
10 @SHELL_OPTIONS@
11
12 ## create symlinks to input datasets
13 ln -s "$dist" dist.dat &&
14 ln -s "$axes" axes.dat &&
15
16 echo 'nmds(
17 phylip=dist.dat
18 #if $axes:
19 ,axes=axes.dat
20 #end if
21 ,mindim=$mindim
22 #if $maxdim >= $mindim:
23 ,maxdim=$maxdim
24 #end if
25 ,iters=$iters
26 ,maxiters=$maxiters
27
28 ## Mothur can't cope with scientific notation
29 #set epsilon_decimal = "{:.12f}".format(float($epsilon))
30 ,epsilon=$epsilon_decimal
31 )'
32 | sed 's/ //g' ## mothur trips over whitespace
33 | mothur
34 | tee mothur.out.log
35 ]]></command>
36 <inputs>
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"/>
39 <param name="mindim" type="integer" value="2" min="1" label="mindim - minimum dimensions (default 2)"/>
40 <param name="maxdim" type="integer" value="2" label="maxdim - maximum dimensions (default 2)"/>
41 <param name="iters" type="integer" value="10" min="1" label="iters - Number of random configuration to try (default 10)"/>
42 <param name="maxiters" type="integer" value="500" min="1" label="maxiters - Number of iterations to try with each random configuration (default 500)"/>
43 <param name="epsilon" type="float" optional="true" min="0" value="1e-12" label="epsilon - acceptable stopping precision (default 1e-12)"/>
44 </inputs>
45 <outputs>
46 <expand macro="logfile-output"/>
47 <data name="nmds_axes" format="mothur.axes" from_work_dir="dist*.axes" label="${tool.name} on ${on_string}: nmds.axes"/>
48 <data name="nmds_iters" format="tabular" from_work_dir="dist*.iters" label="${tool.name} on ${on_string}: nmds.iters"/>
49 <data name="nmds_stress" format="tabular" from_work_dir="dist*.stress" label="${tool.name} on ${on_string}: nmds.stress"/>
50 </outputs>
51 <tests>
52 <test>
53 <param name="dist" value="amazon.dist"/>
54 <param name="axes" value="amazon.pcoa.axes"/>
55 <param name="mindim" value="1"/>
56 <param name="maxdim" value="2"/>
57 <param name="iters" value="10"/>
58 <param name="maxiters" value="500"/>
59 <param name="epsilon" value="1e-12"/>
60 <output name="nmds_axes" md5="9a8a5605d9a619ae1c4973a45e963032"/>
61 <output name="nmds_iters" md5="979702f1c719dac6a7276adf8363a688"/>
62 <output name="nmds_stress" md5="0b46f64bea0294f2c966d7dc890e9aea"/>
63 <expand macro="logfile-test"/>
64 </test>
65 </tests>
66 <help>
67 <![CDATA[
68
69 @MOTHUR_OVERVIEW@
70
71 .. _Mothur: https://www.mothur.org/wiki/Main_Page
72
73 **Command Documentation**
74
75 The nmds_ command generates non-metric multidimensional scaling data from a phylip_distance_matrix_.
76
77 .. _phylip_distance_matrix: https://www.mothur.org/wiki/Phylip-formatted_distance_matrix
78 .. _nmds: https://www.mothur.org/wiki/Nmds
79
80 v1.20.0: Updated to mothur 1.33
81 ]]>
82 </help>
83 <expand macro="citations"/>
84 </tool>