Mercurial > repos > iuc > mothur_sens_spec

annotate sens.spec.xml @ 0:78776d48bbad 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 05:38:07 -0400
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children edde8e7c2946
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0
78776d48bbad 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_sens_spec" name="Sens.spec" version="@WRAPPER_VERSION@.0">
78776d48bbad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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2 <description>Determine the quality of OTU assignment</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[
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10 @SHELL_OPTIONS@
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11
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12 ## create symlinks to input datasets
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13 ln -s "$otu" otu.dat &&
78776d48bbad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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14 ln -s "$dist" dist.dat &&
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15
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16 echo 'sens.spec(
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17 list=otu.dat,
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18 #if $dist.is_of_type("mothur.dist"):
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19 column=dist.dat,
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20 #else
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21 phylip=dist.dat,
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22 #end if
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23 #if $label:
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24 label=${ str($label).replace(",","-") },
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25 #end if
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26 precision=$precision,
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27 cutoff=$cutoff,
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28 hard=$hard
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29 )'
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30 | sed 's/ //g' ## mothur trips over whitespace
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31 | mothur
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32 | tee mothur.out.log
78776d48bbad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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33 ]]></command>
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34 <inputs>
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35 <param name="otu" type="data" format="mothur.list" label="list - OTU List"/>
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36 <param name="dist" type="data" format="mothur.dist,phylip,tabular" label="phylip,column - Distance Matrix"/>
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37 <param name="label" type="select" optional="true" label="label - Select OTU Labels to include" multiple="true" help="By default all are included if no selection is made.">
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38 <options>
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39 <filter type="data_meta" ref="otu" key="labels"/>
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40 </options>
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41 </param>
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42 <param name="precision" type="integer" value="100" min="0" optional="true" label="precision - Precision for rounding distance values"/>
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43 <param name="cutoff" type="float" value="-1" label="cutoff - Distance Cutoff threshold - ignored if not > 0" help="Ignore pairwise distances larger than this, a common value would be 0.10"/>
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44 <param name="hard" type="boolean" checked="false" truevalue="true" falsevalue="false" label="hard - Use hard cutoff instead of rounding"/>
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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="sensspec" format="tabular" from_work_dir="otu*.sensspec" label="${tool.name} on ${on_string}: sensspec"/>
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49 </outputs>
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50 <tests>
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51 <test>
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52 <param name="otu" value="amazon.an.list" ftype="mothur.list"/>
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53 <param name="dist" value="amazon.dist" ftype="mothur.dist"/>
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54 <output name="sensspec" md5="5eb92a89c4e1fd78c10e5bbe55ee2a7a" ftype="tabular"/>
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55 <expand macro="logfile-test"/>
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56 </test>
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57 <test>
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58 <param name="otu" value="amazon.an.list" ftype="mothur.list"/>
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59 <param name="dist" value="amazon.dist" ftype="mothur.dist"/>
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60 <param name="cutoff" value="0.10"/>
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61 <param name="label" value="0.03,0.05,0.22"/>
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62 <output name="sensspec" md5="8e2f46ef59b1ac097a9de2e0ab669bb2" ftype="tabular"/>
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63 <expand macro="logfile-test"/>
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64 </test>
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65 </tests>
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66 <help>
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67 <![CDATA[
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68
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69 @MOTHUR_OVERVIEW@
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70
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71 **Command Documentation**
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72
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73 The sens.spec_ command takes a list_ and either a column_ or phylip_ distance matrix to determine the quality of OTU assignment.
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74
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75
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76 .. _list: https://www.mothur.org/wiki/List_file
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77 .. _column: https://www.mothur.org/wiki/Column-formatted_distance_matrix
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78 .. _phylip: https://www.mothur.org/wiki/Phylip-formatted_distance_matrix
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79 .. _sens.spec: https://www.mothur.org/wiki/Sens.spec
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80 ]]>
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81 </help>
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82 <expand macro="citations"/>
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83 </tool>