Mercurial > repos > iuc > mothur_nmds

annotate nmds.xml @ 6:3cc04a065490 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit debdcdbb89f9bf3e2c3eed05cb078eddb27d4684"
author iuc
date Mon, 02 Dec 2019 06:08:07 -0500
parents 98f1cc2bc428
children 35a66c1fae5e
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1 <tool profile="16.07" id="mothur_nmds" name="Nmds" version="@WRAPPER_VERSION@.0">
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2 <description>generate non-metric multidimensional scaling data</description>
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
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6 <expand macro="requirements"/>
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7 <expand macro="stdio"/>
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8 <expand macro="version_command"/>
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9 <command><![CDATA[
2
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10 @SHELL_OPTIONS@
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11
2
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12 ## create symlinks to input datasets
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13 ln -s '$dist' dist.dat &&
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14 ln -s '$axes' axes.dat &&
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15
2
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16 echo 'nmds(
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17 phylip=dist.dat
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18 #if $axes:
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19 ,axes=axes.dat
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20 #end if
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21 ,mindim=$mindim
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22 #if $maxdim >= $mindim:
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23 ,maxdim=$maxdim
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24 #end if
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25 ,iters=$iters
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26 ,maxiters=$maxiters
0
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27
2
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28 ## Mothur can't cope with scientific notation
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29 #set epsilon_decimal = "{:.12f}".format(float($epsilon))
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30 ,epsilon=$epsilon_decimal
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31 )'
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32 | sed 's/ //g' ## mothur trips over whitespace
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33 | mothur
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34 | tee mothur.out.log
0
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35 ]]></command>
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36 <inputs>
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37 <param name="dist" type="data" format="mothur.dist,mothur.lower.dist,mothur.square.dist" label="phylip - Distance Matrix"/>
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38 <param name="axes" type="data" format="mothur.axes" optional="true" label="axes - a starting configuration"/>
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39 <param name="mindim" type="integer" value="2" min="1" label="mindim - minimum dimensions (default 2)"/>
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40 <param name="maxdim" type="integer" value="2" label="maxdim - maximum dimensions (default 2)"/>
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41 <param name="iters" type="integer" value="10" min="1" label="iters - Number of random configuration to try (default 10)"/>
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42 <param name="maxiters" type="integer" value="500" min="1" label="maxiters - Number of iterations to try with each random configuration (default 500)"/>
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43 <param name="epsilon" type="float" optional="true" min="0" value="1e-12" label="epsilon - acceptable stopping precision (default 1e-12)"/>
2
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44 <expand macro="param-savelog"/>
0
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45 </inputs>
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46 <outputs>
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47 <expand macro="logfile-output"/>
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48 <data name="nmds_axes" format="mothur.axes" from_work_dir="dist*.axes" label="${tool.name} on ${on_string}: nmds.axes"/>
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49 <data name="nmds_iters" format="tabular" from_work_dir="dist*.iters" label="${tool.name} on ${on_string}: nmds.iters"/>
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50 <data name="nmds_stress" format="tabular" from_work_dir="dist*.stress" label="${tool.name} on ${on_string}: nmds.stress"/>
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51 </outputs>
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52 <tests>
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53 <test>
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54 <param name="dist" value="amazon.dist"/>
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55 <param name="axes" value="amazon.pcoa.axes"/>
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56 <param name="mindim" value="1"/>
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57 <param name="maxdim" value="2"/>
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58 <param name="iters" value="10"/>
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59 <param name="maxiters" value="500"/>
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60 <param name="epsilon" value="1e-12"/>
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61 <output name="nmds_axes" md5="9a8a5605d9a619ae1c4973a45e963032"/>
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62 <output name="nmds_iters" md5="979702f1c719dac6a7276adf8363a688"/>
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63 <output name="nmds_stress" md5="0b46f64bea0294f2c966d7dc890e9aea"/>
2
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64 <param name="savelog" value="true"/>
0
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65 <expand macro="logfile-test"/>
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66 </test>
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67 </tests>
2
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68 <help><![CDATA[
0
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69
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70 @MOTHUR_OVERVIEW@
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71
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72 .. _Mothur: https://www.mothur.org/wiki/Main_Page
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73
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74 **Command Documentation**
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75
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76 The nmds_ command generates non-metric multidimensional scaling data from a phylip_distance_matrix_.
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77
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78 .. _phylip_distance_matrix: https://www.mothur.org/wiki/Phylip-formatted_distance_matrix
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79 .. _nmds: https://www.mothur.org/wiki/Nmds
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80
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81 v1.20.0: Updated to mothur 1.33
2
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82
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83 ]]></help>
5
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84 <expand macro="citations">
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85 <citation type="bibtex">
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86 @book{cox2000multidimensional,
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87 title={Multidimensional scaling},
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88 author={Cox, Trevor F and Cox, Michael AA},
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89 year={2000},
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90 publisher={Chapman and hall/CRC}
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91 }
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92 </citation>
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93 </expand>
0
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94 </tool>