Mercurial > repos > iuc > mothur_sub_sample

annotate sub.sample.xml @ 1:f18e9f139d14 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit ea40e3d84e7850eb4226d6c85f709dcad18d4ba9
author iuc
date Thu, 18 May 2017 18:44:02 -0400
parents 8ccebd04ca3d
children 1f5904c5ee42
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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"/>
1
f18e9f139d14 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit ea40e3d84e7850eb4226d6c85f709dcad18d4ba9
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7 <expand macro="stdio"/>
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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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8 <expand macro="version_command"/>
1
f18e9f139d14 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit ea40e3d84e7850eb4226d6c85f709dcad18d4ba9
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9 <command><![CDATA[
f18e9f139d14 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit ea40e3d84e7850eb4226d6c85f709dcad18d4ba9
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10 @SHELL_OPTIONS@
f18e9f139d14 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit ea40e3d84e7850eb4226d6c85f709dcad18d4ba9
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11
0
8ccebd04ca3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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12 ## create symlinks to input datasets
8ccebd04ca3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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13 ln -s "$input.otu" input_otu.dat &&
8ccebd04ca3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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14 ln -s "$count" count.dat &&
8ccebd04ca3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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15 ln -s "$taxonomy" taxonomy.dat &&
8ccebd04ca3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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16 #if $input.format == "fasta":
8ccebd04ca3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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17 ln -s "$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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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 #if ($input.format == "fasta" or $input.format == "list") and $input.use_group.to_filter == "yes":
8ccebd04ca3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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20 ln -s "$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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21 #end if
8ccebd04ca3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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22
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23 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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24 #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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25 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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26 #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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27 ,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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28 #end if
8ccebd04ca3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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29 #else
8ccebd04ca3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
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30 #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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31 list=input_otu.dat
8ccebd04ca3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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32 #elif $input.format == "sabund":
8ccebd04ca3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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33 sabund=input_otu.dat
8ccebd04ca3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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34 #elif $input.format == "rabund":
8ccebd04ca3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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35 rabund=input_otu.dat
8ccebd04ca3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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36 #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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37 shared=input_otu.dat
8ccebd04ca3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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38 #if $input.groups:
8ccebd04ca3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
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39 ,groups=${ 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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40 #end if
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 #if $input.label:
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43 ,label=${ 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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44 #end if
8ccebd04ca3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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45 #end if
8ccebd04ca3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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46 #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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47 #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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48 ,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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49 #if $input.use_group.groups:
8ccebd04ca3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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50 ,groups=${ str($input.use_group.groups).replace(",","-") }
8ccebd04ca3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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51 #end if
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52 ,persample=$input.use_group.persample
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53 #end if
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54 #end if
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55 #if $count:
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56 ,count=count.dat
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57 #end if
8ccebd04ca3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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58 #if $taxonomy:
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59 ,taxonomy=taxonomy.dat
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60 #end if
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61 #if $size:
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62 ,size=$size
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63 #end if
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64 )'
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65 | sed 's/ //g' ## mothur trips over whitespace
8ccebd04ca3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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66 | mothur
1
f18e9f139d14 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit ea40e3d84e7850eb4226d6c85f709dcad18d4ba9
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67 | tee mothur.out.log
0
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68 ]]></command>
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69 <inputs>
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70 <conditional name="input">
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71 <param name="format" type="select" label="Select type of data to sub sample">
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72 <option value="fasta">FASTA</option>
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73 <option value="list">OTU List</option>
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74 <option value="shared">OTU Shared</option>
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75 <option value="sabund">OTU Shared Abundance (sabund)</option>
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76 <option value="rabund">OTU Relative Abundance (rabund)</option>
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77 </param>
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78 <when value="fasta">
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79 <param name="otu" type="data" format="fasta" label="fasta - "/>
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80 <param name="name_in" type="data" format="mothur.names" optional="true" label="name - Group Names from your history"/>
8ccebd04ca3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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81 <conditional name="use_group">
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82 <param name="to_filter" type="select" label="Use groups?">
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83 <option value="no">No</option>
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84 <option value="yes">Yes</option>
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85 </param>
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86 <when value="no"/>
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87 <when value="yes">
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88 <param name="group_in" type="data" format="mothur.groups" label="group - Groups"/>
8ccebd04ca3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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89 <param name="groups" type="select" optional="true" label="groups - Pick groups to include" multiple="true">
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90 <options>
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91 <filter type="data_meta" ref="group_in" key="groups"/>
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92 </options>
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93 </param>
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94 <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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95 </when>
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96 </conditional>
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97 </when>
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98 <when value="list">
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99 <param name="otu" type="data" format="mothur.list" label="list - OTU List"/>
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100 <conditional name="use_group">
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101 <param name="to_filter" type="select" label="Use groups">
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102 <option value="no">No</option>
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103 <option value="yes">Yes</option>
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104 </param>
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105 <when value="no"/>
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106 <when value="yes">
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107 <param name="group_in" type="data" format="mothur.groups" label="group - Groups"/>
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108 <param name="groups" type="select" optional="true" label="groups - Pick groups to include" multiple="true">
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109 <options>
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110 <filter type="data_meta" ref="group_in" key="groups"/>
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111 </options>
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112 </param>
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113 <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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114 </when>
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115 </conditional>
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116 <param name="label" type="select" label="label - OTU Labels" optional="true" multiple="true">
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117 <expand macro="labeloptions"/>
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118 </param>
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119 </when>
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120 <when value="shared">
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121 <param name="otu" type="data" format="mothur.shared" label="shared - OTU Shared"/>
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122 <param name="groups" type="select" optional="true" label="groups - Pick groups to include" multiple="true">
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123 <options>
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124 <filter type="data_meta" ref="otu" key="groups"/>
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125 </options>
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126 </param>
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127 <param name="label" type="select" label="label - OTU Labels" optional="true" multiple="true">
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128 <expand macro="labeloptions"/>
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129 </param>
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130 </when>
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131 <when value="sabund">
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132 <param name="otu" type="data" format="mothur.sabund" label="sabund - OTU Species Abundance"/>
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133 <param name="label" type="select" label="label - OTU Labels" optional="true" multiple="true">
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134 <expand macro="labeloptions"/>
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135 </param>
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136 </when>
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137 <when value="rabund">
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138 <param name="otu" type="data" format="mothur.rabund" label="rabund - OTU Relative Abundance"/>
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139 <param name="label" type="select" label="label - OTU Labels" optional="true" multiple="true">
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140 <expand macro="labeloptions"/>
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141 </param>
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142 </when>
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143 </conditional>
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144 <param name="size" type="integer" value="" min="1" optional="true" label="size - If set, the number of samples to pick"/>
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145 <param name="count" type="data" format="mothur.count_table" optional="true" label="count - a count_table" help="generated by count.seqs"/>
1
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146 <param name="taxonomy" type="data" format="mothur.seq.taxonomy,mothur.ref.taxonomy" optional="true" label="taxonomy - allows a taxonomy file"/>
0
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147 </inputs>
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148 <outputs>
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149 <expand macro="logfile-output"/>
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150 <data name="fasta_out" format_source="otu" from_work_dir="input_otu*.subsample.*" label="${tool.name} on ${on_string}: subsample.fasta">
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151 <filter>input['format'] == 'fasta'</filter>
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152 </data>
1
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153 <data name="taxonomy_out" format_source="taxonomy" from_work_dir="taxonomy.subsample.dat" label="${tool.name} on ${on_string}: subsample.taxonomy">
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154 <filter>taxonomy</filter>
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155 </data>
0
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156 <collection name="list_out" type="list" label="${tool.name} on ${on_string}: subsample.list">
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157 <filter>input['format'] == 'list'</filter>
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158 <discover_datasets pattern=".*?\.(?P&lt;designation&gt;.*)\.subsample\.dat" format="mothur.list"/>
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159 </collection>
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160 <collection name="shared_out" type="list" label="${tool.name} on ${on_string}: subsample.shared">
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161 <filter>input['format'] == 'shared'</filter>
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162 <discover_datasets pattern=".*?\.(?P&lt;designation&gt;.*)\.subsample\.dat" format="mothur.shared"/>
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163 </collection>
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164 <data name="sabund_out" format="mothur.sabund" from_work_dir="input_otu*.subsample.*" label="${tool.name} on ${on_string}: subsample.sabund">
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165 <filter>input['format'] == 'sabund'</filter>
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166 </data>
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167 <data name="rabund_out" format="mothur.rabund" from_work_dir="input_otu*.subsample.*" label="${tool.name} on ${on_string}: subsample.rabund">
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168 <filter>input['format'] == 'rabund'</filter>
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169 </data>
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170 <data name="names_out" format="mothur.names" from_work_dir="input_name_in*.subsample.*" label="${tool.name} on ${on_string}: subsample.names">
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171 <filter>input['format'] == 'fasta' and input['name_in']</filter>
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172 </data>
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173 <data name="group_out" format="mothur.groups" from_work_dir="input_use_group_group_in*.subsample.*" label="${tool.name} on ${on_string}: subsample.groups">
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174 <filter>(input['format'] == 'fasta' or input['format'] == 'list') and input['use_group']['to_filter'] == 'yes'</filter>
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175 </data>
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176 </outputs>
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177 <tests>
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178 <test><!-- test with list -->
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179 <param name="format" value="list"/>
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180 <param name="otu" value="amazon.an.list" ftype="mothur.list"/>
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181 <output_collection name="list_out" count="36">
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182 <element name="0.20" ftype="mothur.list">
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183 <assert_contents>
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184 <has_text text="label"/>
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185 <has_text text="numOtus"/>
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186 </assert_contents>
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187 </element>
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188 </output_collection>
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189 <expand macro="logfile-test"/>
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190 </test>
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191 <test><!-- test with list and group file and label select-->
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192 <param name="format" value="list"/>
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193 <param name="otu" value="amazon.an.list" ftype="mothur.list"/>
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194 <param name="to_filter" value="yes"/>
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195 <param name="group_in" value="amazon.groups" ftype="mothur.groups"/>
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196 <param name="groups" value="forest,pasture"/>
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197 <param name="label" value="0.20,0.45,0.55"/>
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198 <output_collection name="list_out" count="3">
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199 <element name="0.20" ftype="mothur.list">
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200 <assert_contents>
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201 <has_text text="label"/>
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202 <has_text text="numOtus"/>
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203 </assert_contents>
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204 </element>
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205 </output_collection>
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206 <expand macro="logfile-test"/>
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207 </test>
1
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208 <test><!-- test with fasta and taxonomy -->
0
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209 <param name="format" value="fasta"/>
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210 <param name="otu" value="amazon.fasta" ftype="fasta"/>
1
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211 <param name="taxonomy" value="amazon.wang.wang.taxonomy" ftype="mothur.seq.taxonomy"/>
0
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212 <output name="fasta_out" ftype="fasta">
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213 <assert_contents>
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214 <has_text text=">U"/>
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215 </assert_contents>
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216 </output>
1
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217 <output name="taxonomy_out" ftype="mothur.seq.taxonomy">
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218 <assert_contents>
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219 <has_line_matching expression="^U[0-9]+\tBacteria.*$"/>
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220 </assert_contents>
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221 </output>
0
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222 <expand macro="logfile-test"/>
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223 </test>
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224 <test><!-- test with fasta and group file and name file -->
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225 <param name="format" value="fasta"/>
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226 <param name="otu" value="amazon.fasta" ftype="fasta"/>
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227 <param name="to_filter" value="yes"/>
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228 <param name="group_in" value="amazon.groups" ftype="mothur.groups"/>
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229 <param name="groups" value="forest,pasture"/>
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230 <param name="name_in" value="amazon1.names" ftype="mothur.names"/>
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231 <output name="fasta_out" ftype="fasta">
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232 <assert_contents>
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233 <has_text_matching expression=">U[0-9]+"/>
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234 </assert_contents>
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235 </output>
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236 <output name="group_out" ftype="mothur.groups">
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237 <assert_contents>
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238 <has_line_matching expression="^U[0-9]+\t(forest|pasture)$"/>
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239 </assert_contents>
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240 </output>
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241 <output name="names_out" ftype="mothur.names">
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242 <assert_contents>
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243 <has_line_matching expression="^U[0-9]+\tU[0-9]+$"/>
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244 </assert_contents>
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245 </output>
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246 <expand macro="logfile-test"/>
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247 </test>
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248 <test><!-- test with shared -->
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249 <param name="format" value="shared"/>
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250 <param name="otu" value="amazon.an.shared" ftype="mothur.shared"/>
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251 <param name="label" value="unique,0.20"/>
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252 <param name="groups" value="forest"/>
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253 <output_collection name="shared_out" count="2">
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254 <element name="0.20" ftype="mothur.shared">
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255 <assert_contents>
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256 <has_text text="label"/>
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257 <has_text text="numOtus"/>
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258 <has_text text="forest"/>
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259 <not_has_text text="pasture"/>
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260 </assert_contents>
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261 </element>
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262 </output_collection>
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263 <expand macro="logfile-test"/>
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264 </test>
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265 <test><!-- test with rabund -->
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266 <param name="format" value="rabund"/>
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267 <param name="otu" value="amazon.an.rabund" ftype="mothur.rabund"/>
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268 <output name="rabund_out" ftype="mothur.rabund">
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269 <assert_contents>
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270 <has_text text="unique"/>
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271 <has_text text="0.55"/>
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272 </assert_contents>
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273 </output>
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274 <expand macro="logfile-test"/>
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275 </test>
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276 <test><!-- test with sabund -->
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277 <param name="format" value="sabund"/>
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278 <param name="otu" value="amazon.an.sabund" ftype="mothur.sabund"/>
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279 <output name="sabund_out" ftype="mothur.sabund">
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280 <assert_contents>
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281 <has_text text="unique"/>
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282 <has_text text="0.55"/>
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283 </assert_contents>
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284 </output>
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285 <expand macro="logfile-test"/>
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286 </test>
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287 </tests>
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288 <help>
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289 <![CDATA[
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290
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291 @MOTHUR_OVERVIEW@
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292
1
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293 **Command Documentation**
0
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294
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295 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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296
1
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297 .. _list: https://www.mothur.org/wiki/List_file
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298 .. _shared: https://www.mothur.org/wiki/Shared_file
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299 .. _rabund: https://www.mothur.org/wiki/Rabund_file
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300 .. _sabund: https://www.mothur.org/wiki/Sabund_file
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301 .. _sub.sample: https://www.mothur.org/wiki/Sub.sample
0
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302
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303 ]]>
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304 </help>
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305 <expand macro="citations"/>
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306 </tool>