Mercurial > repos > iuc > mothur_pca

annotate pca.xml @ 5:7474b222205d draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 7f7605c2c8d8e92f3369dfdc290e5d8d06fa409a
author iuc
date Fri, 03 Aug 2018 14:28:10 -0400
parents 1fdf1610e7dc
children b931ab1fb5da
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56400efc6755 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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1 <tool profile="16.07" id="mothur_pca" name="Pca" version="@WRAPPER_VERSION@.0">
56400efc6755 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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2 <description>Principal Coordinate Analysis for a shared file</description>
56400efc6755 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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3 <macros>
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4 <import>macros.xml</import>
56400efc6755 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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5 </macros>
56400efc6755 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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6 <expand macro="requirements"/>
56400efc6755 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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7 <expand macro="stdio"/>
56400efc6755 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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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
1fdf1610e7dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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13 ln -s '$otu' otu.dat &&
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56400efc6755 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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14
2
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15 echo 'pca(
1fdf1610e7dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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16 #if $otu.is_of_type("mothur.relabund"):
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17 relabund=otu.dat,
1fdf1610e7dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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18 #elif $otu.is_of_type("mothur.shared"):
1fdf1610e7dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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19 shared=otu.dat,
1fdf1610e7dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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20 #end if
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21 #if $label:
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22 label=${ str($label).replace(",","-") },
1fdf1610e7dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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23 #end if
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24 #if $groups:
1fdf1610e7dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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25 groups=${ str($groups).replace(",","-") },
1fdf1610e7dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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26 #end if
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27 metric=$metric
1fdf1610e7dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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28 )'
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29 | sed 's/ //g' ## mothur trips over whitespace
1fdf1610e7dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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30 | mothur
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31 | tee mothur.out.log
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56400efc6755 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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32 ]]></command>
56400efc6755 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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33 <inputs>
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34 <param name="otu" type="data" format="mothur.shared,mothur.relabund" label="shared,relabund - OTU Shared or Relabund file"/>
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35 <param name="label" type="select" label="label - OTU Labels" multiple="true">
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36 <expand macro="labeloptions"/>
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37 </param>
56400efc6755 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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38 <param name="groups" type="select" label="groups - Groups to consider" multiple="true">
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39 <options>
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40 <filter type="data_meta" ref="otu" key="groups"/>
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41 </options>
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42 </param>
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43 <param name="metric" type="boolean" truevalue="true" falsevalue="false" checked="true" label="metric - Calculate pearson correlation coefficient"/>
2
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44 <expand macro="param-savelog"/>
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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 <collection name="pca_axes" type="list" label="${tool.name} on ${on_string}: pca.axes">
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49 <discover_datasets pattern=".*?\.(?P&lt;designation&gt;.*)\.pca\.axes" format="mothur.axes"/>
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50 </collection>
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51 <collection name="pca_loadings" type="list" label="${tool.name} on ${on_string}: pca.loadings">
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52 <discover_datasets pattern=".*?\.(?P&lt;designation&gt;.*)\.pca\.loadings" format="txt"/>
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53 </collection>
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54 </outputs>
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55 <tests>
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56 <test>
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57 <param name="otu" value="amazon.an.shared" ftype="mothur.shared"/>
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58 <param name="groups" value="forest,pasture"/>
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59 <param name="label" value="0.22,0.55"/>
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60 <output_collection name="pca_axes" count="2">
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61 <element name="0.22" md5="4e32155fcfefe7d2f45b896d26b36409" ftype="mothur.axes"/>
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62 </output_collection>
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63 <output_collection name="pca_loadings" count="2">
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64 <element name="0.55" md5="8c76b60484ffcab2ef7230e29071dd51" ftype="txt"/>
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65 </output_collection>
2
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66 <param name="savelog" value="true"/>
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67 <expand macro="logfile-test"/>
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68 </test>
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69 </tests>
2
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70 <help><![CDATA[
0
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71
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72 @MOTHUR_OVERVIEW@
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73
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74 **Command Documentation**
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75
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76 The pca_ command generate principle components plot data for a shared_ or relabund_ file.
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77
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78 .. _shared: https://www.mothur.org/wiki/Shared_file
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79 .. _relabund: https://www.mothur.org/wiki/Get.relabund
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80 .. _pca: https://www.mothur.org/wiki/Pca
2
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81
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82 ]]></help>
5
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83 <expand macro="citations">
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84 <expand macro="citations-ecology"/>
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85 </expand>
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56400efc6755 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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86 </tool>