Mercurial > repos > iuc > mothur_sub_sample

annotate sub.sample.xml @ 0:8ccebd04ca3d 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 16:51:17 -0400
parents
children f18e9f139d14
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8ccebd04ca3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
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1 <tool profile="16.07" id="mothur_sub_sample" name="Sub.sample" version="@WRAPPER_VERSION@.0">
8ccebd04ca3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
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2 <description>Create a sub sample</description>
8ccebd04ca3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
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3 <macros>
8ccebd04ca3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
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4 <import>macros.xml</import>
8ccebd04ca3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
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5 </macros>
8ccebd04ca3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
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6 <expand macro="requirements"/>
8ccebd04ca3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
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7 <expand macro="version_command"/>
8ccebd04ca3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
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8 <command detect_errors="aggressive"><![CDATA[
8ccebd04ca3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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9 ## create symlinks to input datasets
8ccebd04ca3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
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10 ln -s "$input.otu" input_otu.dat &&
8ccebd04ca3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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11 ln -s "$count" count.dat &&
8ccebd04ca3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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12 ln -s "$taxonomy" taxonomy.dat &&
8ccebd04ca3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
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13 #if $input.format == "fasta":
8ccebd04ca3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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14 ln -s "$input.name_in" input_name_in.dat &&
8ccebd04ca3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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15 #end if
8ccebd04ca3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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16 #if ($input.format == "fasta" or $input.format == "list") and $input.use_group.to_filter == "yes":
8ccebd04ca3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
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17 ln -s "$input.use_group.group_in" input_use_group_group_in.dat &&
8ccebd04ca3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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18 #end if
8ccebd04ca3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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19
8ccebd04ca3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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20 echo 'sub.sample(
8ccebd04ca3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
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21 #if $input.format == "fasta":
8ccebd04ca3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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22 fasta=input_otu.dat
8ccebd04ca3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
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23 #if $input.name_in:
8ccebd04ca3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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24 ,name=input_name_in.dat
8ccebd04ca3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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25 #end if
8ccebd04ca3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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26 #else
8ccebd04ca3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
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27 #if $input.format == "list":
8ccebd04ca3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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28 list=input_otu.dat
8ccebd04ca3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
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29 #elif $input.format == "sabund":
8ccebd04ca3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
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30 sabund=input_otu.dat
8ccebd04ca3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
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31 #elif $input.format == "rabund":
8ccebd04ca3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
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32 rabund=input_otu.dat
8ccebd04ca3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
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33 #elif $input.format == "shared":
8ccebd04ca3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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34 shared=input_otu.dat
8ccebd04ca3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
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35 #if $input.groups:
8ccebd04ca3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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36 ,groups=${ str($input.groups).replace(",","-") }
8ccebd04ca3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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37 #end if
8ccebd04ca3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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38 #end if
8ccebd04ca3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
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39 #if $input.label:
8ccebd04ca3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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40 ,label=${ str($input.label).replace(",","-") }
8ccebd04ca3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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41 #end if
8ccebd04ca3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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42 #end if
8ccebd04ca3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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43 #if $input.format == "fasta" or $input.format == "list":
8ccebd04ca3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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44 #if $input.use_group.to_filter == "yes":
8ccebd04ca3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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45 ,group=input_use_group_group_in.dat
8ccebd04ca3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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46 #if $input.use_group.groups:
8ccebd04ca3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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47 ,groups=${ str($input.use_group.groups).replace(",","-") }
8ccebd04ca3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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48 #end if
8ccebd04ca3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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49 ,persample=$input.use_group.persample
8ccebd04ca3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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50 #end if
8ccebd04ca3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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51 #end if
8ccebd04ca3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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52 #if $count:
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53 ,count=count.dat
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54 #end if
8ccebd04ca3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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55 #if $taxonomy:
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56 ,taxonomy=taxonomy.dat
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57 #end if
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58 #if $size:
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59 ,size=$size
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60 #end if
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61 )'
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62 | sed 's/ //g' ## mothur trips over whitespace
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63 | mothur
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64 ]]></command>
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65 <inputs>
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66 <conditional name="input">
8ccebd04ca3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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67 <param name="format" type="select" label="Select type of data to sub sample">
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68 <option value="fasta">FASTA</option>
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69 <option value="list">OTU List</option>
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70 <option value="shared">OTU Shared</option>
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71 <option value="sabund">OTU Shared Abundance (sabund)</option>
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72 <option value="rabund">OTU Relative Abundance (rabund)</option>
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73 </param>
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74 <when value="fasta">
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75 <param name="otu" type="data" format="fasta" label="fasta - "/>
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76 <param name="name_in" type="data" format="mothur.names" optional="true" label="name - Group Names from your history"/>
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77 <conditional name="use_group">
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78 <param name="to_filter" type="select" label="Use groups?">
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79 <option value="no">No</option>
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80 <option value="yes">Yes</option>
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81 </param>
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82 <when value="no"/>
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83 <when value="yes">
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84 <param name="group_in" type="data" format="mothur.groups" label="group - Groups"/>
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85 <param name="groups" type="select" optional="true" label="groups - Pick groups to include" multiple="true">
8ccebd04ca3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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86 <options>
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87 <filter type="data_meta" ref="group_in" key="groups"/>
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88 </options>
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89 </param>
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90 <param name="persample" type="boolean" truevalue="true" falsevalue="false" checked="false" label="persample - select subsample of the same size from each of the groups"/>
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91 </when>
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92 </conditional>
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93 </when>
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94 <when value="list">
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95 <param name="otu" type="data" format="mothur.list" label="list - OTU List"/>
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96 <conditional name="use_group">
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97 <param name="to_filter" type="select" label="Use groups">
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98 <option value="no">No</option>
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99 <option value="yes">Yes</option>
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100 </param>
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101 <when value="no"/>
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102 <when value="yes">
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103 <param name="group_in" type="data" format="mothur.groups" label="group - Groups"/>
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104 <param name="groups" type="select" optional="true" label="groups - Pick groups to include" multiple="true">
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105 <options>
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106 <filter type="data_meta" ref="group_in" key="groups"/>
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107 </options>
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108 </param>
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109 <param name="persample" type="boolean" truevalue="true" falsevalue="false" checked="false" label="persample - select subsample of the same size from each of the groups"/>
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110 </when>
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111 </conditional>
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112 <param name="label" type="select" label="label - OTU Labels" optional="true" multiple="true">
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113 <expand macro="labeloptions"/>
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114 </param>
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115 </when>
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116 <when value="shared">
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117 <param name="otu" type="data" format="mothur.shared" label="shared - OTU Shared"/>
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118 <param name="groups" type="select" optional="true" label="groups - Pick groups to include" multiple="true">
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119 <options>
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120 <filter type="data_meta" ref="otu" key="groups"/>
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121 </options>
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122 </param>
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123 <param name="label" type="select" label="label - OTU Labels" optional="true" multiple="true">
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124 <expand macro="labeloptions"/>
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125 </param>
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126 </when>
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127 <when value="sabund">
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128 <param name="otu" type="data" format="mothur.sabund" label="sabund - OTU Species Abundance"/>
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129 <param name="label" type="select" label="label - OTU Labels" optional="true" multiple="true">
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130 <expand macro="labeloptions"/>
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131 </param>
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132 </when>
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133 <when value="rabund">
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134 <param name="otu" type="data" format="mothur.rabund" label="rabund - OTU Relative Abundance"/>
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135 <param name="label" type="select" label="label - OTU Labels" optional="true" multiple="true">
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136 <expand macro="labeloptions"/>
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137 </param>
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138 </when>
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139 </conditional>
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140 <param name="size" type="integer" value="" min="1" optional="true" label="size - If set, the number of samples to pick"/>
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141 <param name="count" type="data" format="mothur.count_table" optional="true" label="count - a count_table" help="generated by count.seqs"/>
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142 <param name="taxonomy" type="data" format="taxonomy" optional="true" label="taxonomy - allows a taxonomy file"/>
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143 </inputs>
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144 <outputs>
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145 <expand macro="logfile-output"/>
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146 <data name="fasta_out" format_source="otu" from_work_dir="input_otu*.subsample.*" label="${tool.name} on ${on_string}: subsample.fasta">
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147 <filter>input['format'] == 'fasta'</filter>
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148 </data>
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149 <collection name="list_out" type="list" label="${tool.name} on ${on_string}: subsample.list">
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150 <filter>input['format'] == 'list'</filter>
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151 <discover_datasets pattern=".*?\.(?P&lt;designation&gt;.*)\.subsample\.dat" format="mothur.list"/>
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152 </collection>
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153 <collection name="shared_out" type="list" label="${tool.name} on ${on_string}: subsample.shared">
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154 <filter>input['format'] == 'shared'</filter>
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155 <discover_datasets pattern=".*?\.(?P&lt;designation&gt;.*)\.subsample\.dat" format="mothur.shared"/>
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156 </collection>
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157 <data name="sabund_out" format="mothur.sabund" from_work_dir="input_otu*.subsample.*" label="${tool.name} on ${on_string}: subsample.sabund">
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158 <filter>input['format'] == 'sabund'</filter>
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159 </data>
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160 <data name="rabund_out" format="mothur.rabund" from_work_dir="input_otu*.subsample.*" label="${tool.name} on ${on_string}: subsample.rabund">
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161 <filter>input['format'] == 'rabund'</filter>
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162 </data>
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163 <data name="names_out" format="mothur.names" from_work_dir="input_name_in*.subsample.*" label="${tool.name} on ${on_string}: subsample.names">
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164 <filter>input['format'] == 'fasta' and input['name_in']</filter>
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165 </data>
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166 <data name="group_out" format="mothur.groups" from_work_dir="input_use_group_group_in*.subsample.*" label="${tool.name} on ${on_string}: subsample.groups">
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167 <filter>(input['format'] == 'fasta' or input['format'] == 'list') and input['use_group']['to_filter'] == 'yes'</filter>
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168 </data>
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169 </outputs>
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170 <tests>
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171 <test><!-- test with list -->
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172 <param name="format" value="list"/>
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173 <param name="otu" value="amazon.an.list" ftype="mothur.list"/>
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174 <output_collection name="list_out" count="36">
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175 <element name="0.20" ftype="mothur.list">
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176 <assert_contents>
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177 <has_text text="label"/>
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178 <has_text text="numOtus"/>
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179 </assert_contents>
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180 </element>
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181 </output_collection>
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182 <expand macro="logfile-test"/>
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183 </test>
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184 <test><!-- test with list and group file and label select-->
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185 <param name="format" value="list"/>
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186 <param name="otu" value="amazon.an.list" ftype="mothur.list"/>
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187 <param name="to_filter" value="yes"/>
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188 <param name="group_in" value="amazon.groups" ftype="mothur.groups"/>
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189 <param name="groups" value="forest,pasture"/>
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190 <param name="label" value="0.20,0.45,0.55"/>
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191 <output_collection name="list_out" count="3">
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192 <element name="0.20" ftype="mothur.list">
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193 <assert_contents>
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194 <has_text text="label"/>
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195 <has_text text="numOtus"/>
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196 </assert_contents>
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197 </element>
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198 </output_collection>
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199 <expand macro="logfile-test"/>
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200 </test>
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201 <test><!-- test with fasta -->
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202 <param name="format" value="fasta"/>
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203 <param name="otu" value="amazon.fasta" ftype="fasta"/>
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204 <output name="fasta_out" ftype="fasta">
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205 <assert_contents>
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206 <has_text text=">U"/>
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207 </assert_contents>
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208 </output>
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209 <expand macro="logfile-test"/>
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210 </test>
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211 <test><!-- test with fasta and group file and name file -->
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212 <param name="format" value="fasta"/>
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213 <param name="otu" value="amazon.fasta" ftype="fasta"/>
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214 <param name="to_filter" value="yes"/>
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215 <param name="group_in" value="amazon.groups" ftype="mothur.groups"/>
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216 <param name="groups" value="forest,pasture"/>
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217 <param name="name_in" value="amazon1.names" ftype="mothur.names"/>
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218 <output name="fasta_out" ftype="fasta">
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219 <assert_contents>
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220 <has_text_matching expression=">U[0-9]+"/>
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221 </assert_contents>
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222 </output>
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223 <output name="group_out" ftype="mothur.groups">
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224 <assert_contents>
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225 <has_line_matching expression="^U[0-9]+\t(forest|pasture)$"/>
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226 </assert_contents>
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227 </output>
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228 <output name="names_out" ftype="mothur.names">
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229 <assert_contents>
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230 <has_line_matching expression="^U[0-9]+\tU[0-9]+$"/>
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231 </assert_contents>
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232 </output>
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233 <expand macro="logfile-test"/>
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234 </test>
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235 <test><!-- test with shared -->
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236 <param name="format" value="shared"/>
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237 <param name="otu" value="amazon.an.shared" ftype="mothur.shared"/>
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238 <param name="label" value="unique,0.20"/>
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239 <param name="groups" value="forest"/>
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240 <output_collection name="shared_out" count="2">
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241 <element name="0.20" ftype="mothur.shared">
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242 <assert_contents>
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243 <has_text text="label"/>
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244 <has_text text="numOtus"/>
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245 <has_text text="forest"/>
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246 <not_has_text text="pasture"/>
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247 </assert_contents>
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248 </element>
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249 </output_collection>
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250 <expand macro="logfile-test"/>
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251 </test>
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252 <test><!-- test with rabund -->
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253 <param name="format" value="rabund"/>
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254 <param name="otu" value="amazon.an.rabund" ftype="mothur.rabund"/>
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255 <output name="rabund_out" ftype="mothur.rabund">
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256 <assert_contents>
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257 <has_text text="unique"/>
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258 <has_text text="0.55"/>
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259 </assert_contents>
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260 </output>
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261 <expand macro="logfile-test"/>
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262 </test>
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263 <test><!-- test with sabund -->
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264 <param name="format" value="sabund"/>
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265 <param name="otu" value="amazon.an.sabund" ftype="mothur.sabund"/>
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266 <output name="sabund_out" ftype="mothur.sabund">
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267 <assert_contents>
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268 <has_text text="unique"/>
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269 <has_text text="0.55"/>
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270 </assert_contents>
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271 </output>
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272 <expand macro="logfile-test"/>
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273 </test>
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274 </tests>
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275 <help>
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276 <![CDATA[
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277
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278 @MOTHUR_OVERVIEW@
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279
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280 **Command Documenation**
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281
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282 The sub.sample_ command can be used as a way to normalize your data, or to create a smaller set from your original set. It takes as an input the following file types: fasta, list_, shared_, rabund_ and sabund_ to generate a new file that contains a sampling of your original file.
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283
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284 .. _list: http://www.mothur.org/wiki/List_file
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285 .. _shared: http://www.mothur.org/wiki/Shared_file
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286 .. _rabund: http://www.mothur.org/wiki/Rabund_file
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287 .. _sabund: http://www.mothur.org/wiki/Sabund_file
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288 .. _sub.sample: http://www.mothur.org/wiki/Sub.sample
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289
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290 ]]>
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291 </help>
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292 <expand macro="citations"/>
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293 </tool>