Mercurial > repos > jjohnson > mothur_toolsuite
annotate mothur/tools/mothur/get.oturep.xml @ 1:fcc0778f6987
Migrated tool version 1.16.0 from old tool shed archive to new tool shed repository
author | jjohnson |
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date | Tue, 07 Jun 2011 17:35:35 -0400 |
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Migrated tool version 1.16.0 from old tool shed archive to new tool shed repository
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1 <tool id="mothur_get_oturep" name="Get.oturep" version="1.16.0" force_history_refresh="True"> |
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2 <description>Generate a fasta with a representative sequence for each OTU</description> |
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3 <command interpreter="python"> |
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4 mothur_wrapper.py |
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5 --cmd='get.oturep' |
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6 --result='^mothur.\S+\.logfile$:'$logfile |
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7 --outputdir='$logfile.extra_files_path' |
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8 --datasetid='$logfile.id' --new_file_path='$__new_file_path__' |
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9 --new_datasets='^\S+?\.((unique|[0-9.]*)(\S+)\.rep\.fasta)$:fasta','^\S+?\.((unique|[0-9.]*)(\S+)\.rep\.names)$:names' |
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10 --fasta=$fasta |
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11 --list=$otu_list |
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12 #if $input.source == 'column': |
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13 --column=$input.dist |
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14 --name=$input.name |
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15 #elif $input.source == 'phylip': |
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16 --phylip=$input.dist |
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17 #if $input.name.__str__ != "None" and len($input.name.__str__) > 0: |
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18 --name=$input.name |
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19 #end if |
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20 #end if |
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21 #if $label.__str__ != "None" and len($label.__str__) > 0: |
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22 --label='$label' |
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23 #end if |
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24 #if $groups.__str__ != "None" and len($groups.__str__) > 0: |
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25 --groups=$groups |
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26 #end if |
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27 #if $sorted.__str__ != "None" and len($sorted.__str__) > 0: |
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28 --sorted=$sorted |
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29 #end if |
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30 $large |
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31 </command> |
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32 <inputs> |
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33 <!-- get.relabund relabund type should also work --> |
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34 <param name="fasta" type="data" format="fasta" label="fasta - Fasta"/> |
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35 <param name="otu_list" type="data" format="list" label="list - OTU List"/> |
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36 <conditional name="input"> |
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37 <param name="source" type="select" label="Distance Matrix"> |
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38 <option value="column">Pairwise Column Distance Matrix</option> |
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39 <option value="phylip">Phylip Distance Matrix</option> |
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40 </param> |
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41 <when value="column"> |
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42 <param name="dist" type="data" format="pair.dist" label="column - Distance Matrix"/> |
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43 <param name="name" type="data" format="names" label="name - Sequences Name reference"/> |
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44 </when> |
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45 <when value="phylip"> |
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46 <param name="dist" type="data" format="lower.dist,square.dist" label="phylip - Distance Matrix"/> |
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47 <param name="name" type="data" format="names" optional="true" label="name - Names"/> |
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48 </when> |
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49 </conditional> |
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50 <param name="group" type="data" format="groups" optional="true" label="group - Group file for the OTU List"/> |
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51 <param name="groups" type="select" label="groups - Groups to consider" multiple="true"> |
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52 <options from_dataset="group"> |
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53 <column name="name" index="1"/> |
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54 <column name="value" index="1"/> |
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55 </options> |
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56 </param> |
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57 <param name="label" type="select" label="label - OTU Labels" multiple="true"> |
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58 <options from_dataset="otu_list"> |
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59 <column name="name" index="0"/> |
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60 <column name="value" index="0"/> |
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61 </options> |
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62 </param> |
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63 <param name="sorted" type="select" label="sorted - Sort Sequences by"> |
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64 <option value="">Don't sort</option> |
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65 <option value="name">Sequence Name</option> |
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66 <option value="number">Bin Number</option> |
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67 <option value="size">Bin Size</option> |
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68 <option value="group">Group</option> |
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69 </param> |
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70 |
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71 <param name="large" type="boolean" checked="false" truevalue="--large=true" falsevalue="" label="large - Distance Matrix is very Large"/> |
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72 </inputs> |
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73 <outputs> |
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74 <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" /> |
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75 </outputs> |
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76 <requirements> |
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77 <requirement type="binary">mothur</requirement> |
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78 </requirements> |
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79 <tests> |
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80 </tests> |
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81 <help> |
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82 **Mothur Overview** |
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83 |
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84 Mothur_, initiated by Dr. Patrick Schloss and his software development team |
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85 in the Department of Microbiology and Immunology at The University of Michigan, |
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86 provides bioinformatics for the microbial ecology community. |
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87 |
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88 .. _Mothur: http://www.mothur.org/wiki/Main_Page |
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89 |
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90 **Command Documenation** |
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91 |
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92 The get.oturep_ command generates a fasta-formatted sequence file containing only a representative sequence for each OTU. The opposite of the bin.seqs command. |
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93 |
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94 .. _get.oturep: http://www.mothur.org/wiki/Get.oturep |
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95 |
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96 </help> |
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97 </tool> |