Mercurial > repos > iuc > mothur_remove_otus

annotate remove.otus.xml @ 8:6bdb704814f4 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4c950508328589b5215b6c96868659a03f9dead8"
author iuc
date Tue, 08 Dec 2020 13:56:06 +0000
parents 45d51905b3b5
children 2a833eb1005c
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1 <tool profile="16.07" id="mothur_remove_otus" name="Remove.otus" version="@WRAPPER_VERSION@.0">
2
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2 <description>Removes OTUs from various file formats</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 '$infile.otu' infile.otu.dat &&
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14 ln -s '$accnos' accnos.dat &&
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15
2
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16 echo 'remove.otus(
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17 #if $infile.otu.is_of_type("mothur.cons.taxonomy"):
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18 constaxonomy=infile.otu.data,
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19 #end if
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20 #if $infile.otu.is_of_type("mothur.otu.corr"):
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21 otucorr=infile.otu.dat,
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22 #end if
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23 #if $infile.otu.is_of_type("mothur.axes"):
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24 corraxes=infile.otu.dat,
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25 #end if
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26 #if $infile.otu.is_of_type("mothur.list"):
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27 list=infile.otu.dat,
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28 #end if
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29 #if $infile.otu.is_of_type("mothur.shared"):
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30 shared=infile.otu.dat,
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31 #end if
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32 #if $infile.intype == "in_shared" and $infile.label:
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33 label=${ str($infile.label).replace(",","-") },
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34 #end if
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35 accnos=accnos.dat
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36 )'
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37 | sed 's/ //g' ## mothur trips over whitespace
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38 | mothur
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39 | tee mothur.out.log
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40 ]]></command>
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41 <inputs>
2
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42 <param name="accnos" type="data" format="mothur.otulabels" label="accnos - otulabels" help="Required"/>
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43 <conditional name="infile">
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44 <param name="intype" type="select" label="Which type of files will you be supplying?" help="">
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45 <option value="in_shared">Shared or List file</option>
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46 <option value="in_other">Constaxonomy / OtuCorr / CorrAxes file</option>
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47 </param>
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48 <when value="in_shared">
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49 <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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50 <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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51 <expand macro="labeloptions"/>
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52 </param>
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53 </when>
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54 <when value="in_other">
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55 <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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56 </when>
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57 </conditional>
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58 <expand macro="param-savelog"/>
0
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59 </inputs>
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60 <outputs>
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61 <expand macro="logfile-output"/>
2
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62 <data name="pick_out" format_source="otu" from_work_dir="infile.otu*.pick.dat" label="${tool.name} on ${on_string}: pick"/>
0
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63 </outputs>
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64 <tests>
2
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65 <test><!-- test with shared/list input and label selection -->
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66 <param name="accnos" value="amazon.accnos.otulabels"/>
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67 <param name="intype" value="in_shared"/>
0
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68 <param name="otu" value="amazon.an.list" ftype="mothur.list"/>
2
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69 <param name="label" value="0.22"/>
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70 <output name="pick_out" ftype="mothur.list">
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71 <assert_contents>
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72 <expand macro="test-list-format"/>
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73 <has_text text="U68686"/>
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74 <has_text text="0.22"/>
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75 <not_has_text text="0.03"/>
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76 </assert_contents>
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77 </output>
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78 <param name="savelog" value="true"/>
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79 <expand macro="logfile-test"/>
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80 </test>
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81 <test><!-- test with constaxonomy/otucorr/corraxes file -->
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82 <param name="accnos" value="amazon.accnos.otulabels"/>
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83 <param name="intype" value="in_other"/>
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84 <param name="otu" value="amazon.pcoa.axes" ftype="mothur.axes"/>
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85 <output name="pick_out" ftype="mothur.axes">
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86 <assert_contents>
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87 <expand macro="test-axes-format"/>
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88 <has_text text="U68686"/>
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89 </assert_contents>
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90 </output>
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91 <param name="savelog" value="true"/>
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92 <expand macro="logfile-test"/>
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93 </test>
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94 </tests>
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95 <help><![CDATA[
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96
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97 @MOTHUR_OVERVIEW@
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98
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99 **Command Documentation**
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100
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101 The remove.otus command removes otu labels from cons.taxonomy, corr.axes, otu.corr, shared and list files. This can be useful especially with subsampled datasets or when groups have been selected.
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102
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103 .. _remove.otus: https://www.mothur.org/wiki/Remove.otus
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104
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105 ]]></help>
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106 <expand macro="citations"/>
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107 </tool>