Mercurial > repos > iuc > mothur_remove_otulabels

annotate remove.otulabels.xml @ 0:a88be48a8ddd 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 16:47:29 -0400
parents
children 50874b7ffc15
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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a88be48a8ddd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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1 <tool profile="16.07" id="mothur_remove_otulabels" name="Remove.otulabels" version="@WRAPPER_VERSION@.0">
a88be48a8ddd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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2 <description>Removes OTU labels</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="version_command"/>
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8 <command detect_errors="aggressive"><![CDATA[
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9 ## create symlinks to input datasets
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10 ln -s "$infile.otu" infile.otu.dat &&
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11 ln -s "$accnos" accnos.dat &&
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12
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13 echo 'remove.otulabels(
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14 #if $infile.otu.is_of_type("mothur.cons.taxonomy"):
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15 constaxonomy=infile.otu.data,
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16 #end if
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17 #if $infile.otu.is_of_type("mothur.otu.corr"):
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18 otucorr=infile.otu.dat,
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19 #end if
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20 #if $infile.otu.is_of_type("mothur.axes"):
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21 corraxes=infile.otu.dat,
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22 #end if
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23 #if $infile.otu.is_of_type("mothur.list"):
a88be48a8ddd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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24 list=infile.otu.dat,
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25 #end if
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26 #if $infile.otu.is_of_type("mothur.shared"):
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27 shared=infile.otu.dat,
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28 #end if
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29 #if $infile.intype == "in_shared" and $infile.label:
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30 label=infile.label.dat,
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31 #end if
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32 accnos=accnos.dat
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33 )'
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34 | sed 's/ //g' ## mothur trips over whitespace
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35 | mothur
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36 ]]></command>
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37 <inputs>
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38 <param name="accnos" type="data" format="mothur.otulabels" label="accnos - otulabels" help="Required"/>
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39 <conditional name="infile">
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40 <param name="intype" type="select" label="Which type of files will you be supplying?" help="">
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41 <option value="in_shared">Shared or List file</option>
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42 <option value="in_other">Constaxonomy / OtuCorr / CorrAxes file</option>
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43 </param>
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44 <when value="in_shared">
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45 <param name="otu" type="data" format="mothur.list,mothur.shared" label="shared/list - allows you to input a list file you wish to select OTUs from. "/>
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46 <param name="label" type="select" label="label - pick (one) OTU Label" optional="true" help="By default first label in your file is used">
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47 <expand macro="labeloptions"/>
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48 </param>
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49 </when>
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50 <when value="in_other">
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51 <param name="otu" type="data" format="mothur.cons.taxonomy,mothur.otu.corr,mothur.axes" label="cons.taxonomy/otu.corr/axes file" help="constaxonomy file can be obtained by the running classify.otu tool, otucorr from otu.association tool, and corraxes from corr.axes command"/>
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52 </when>
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53 </conditional>
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54 </inputs>
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55 <outputs>
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56 <expand macro="logfile-output"/>
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57 <data name="pick_out" format_source="otu" from_work_dir="infile.otu*.pick.dat" label="${tool.name} on ${on_string}: pick"/>
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58 </outputs>
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59 <tests>
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60 <test><!-- test with shared/list input and label selection -->
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61 <param name="accnos" value="amazon.accnos.otulabels"/>
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62 <param name="intype" value="in_shared"/>
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63 <param name="otu" value="amazon.an.list" ftype="mothur.list"/>
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64 <param name="label" value="0.22"/>
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65 <ouptut name="pick_out" md5="8ab2a6afd9a2547e3c4ffe2e83375c33" ftype="mothur.list"/>
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66 <expand macro="logfile-test"/>
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67 </test>
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68 <test><!-- test with constaxonomy/otucorr/corraxes file -->
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69 <param name="accnos" value="amazon.accnos.otulabels"/>
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70 <param name="intype" value="in_other"/>
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71 <param name="otu" value="amazon.pcoa.axes" ftype="mothur.axes"/>
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72 <output name="pick_out" md5="9bffef40bf6e879737835cf7323c5ce4" ftype="mothur.axes"/>
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73 <expand macro="logfile-test"/>
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74 </test>
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75 </tests>
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76 <help>
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77 <![CDATA[
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78
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79 @MOTHUR_OVERVIEW@
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80
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81 **Command Documenation**
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82
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83 The remove.otulabels_ command removes otu labels from the output from classify.otu_, corr.axes_ and otu.association_. This can be useful especially with subsampled datasets or when groups have been selected.
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84
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85 .. _classify.otu: http://www.mothur.org/wiki/Classify.otu
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86 .. _corr.axes: http://www.mothur.org/wiki/Corr.axes
a88be48a8ddd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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87 .. _otu.association: http://www.mothur.org/wiki/Otu.association
a88be48a8ddd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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88 .. _remove.otulabels: http://www.mothur.org/wiki/Remove.otulabels
a88be48a8ddd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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89 ]]>
a88be48a8ddd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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90 </help>
a88be48a8ddd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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91 <expand macro="citations"/>
a88be48a8ddd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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92 </tool>