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annotate mothur/tools/mothur/get.oturep.xml @ 6:ce6e81622c6a

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Allow for output file ext to be either .chimera or .chimeras
author Jim Johnson <jj@umn.edu>
date Mon, 27 Jun 2011 09:34:14 -0500
parents 5265aa9067e0
children 7bfe1f843858
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1 <tool id="mothur_get_oturep" name="Get.oturep" version="1.19.0" 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 #if $as_datasets.__str__ == "yes":
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9 --datasetid='$logfile.id' --new_file_path='$__new_file_path__'
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10 --new_datasets='^\S+?\.((unique|[0-9.]*)(\S+)\.rep\.fasta)$:${fasta.ext}','^\S+?\.((unique|[0-9.]*)(\S+)\.rep\.names)$:names'
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11 #end if
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12 --fasta=$fasta
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13 --list=$otu_list
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14 #if $input.source == 'column':
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15 --column=$input.dist
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16 --name=$input.name
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17 #elif $input.source == 'phylip':
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18 --phylip=$input.dist
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19 #if $input.name.__str__ != "None" and len($input.name.__str__) > 0:
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20 --name=$input.name
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21 #end if
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22 #end if
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23 #if $label.__str__ != "None" and len($label.__str__) > 0:
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24 --label='$label'
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25 #end if
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26 #if $pick.type == 'yes':
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27 #if $pick.group.__str__ != "None" and len($pick.group.__str__) > 0:
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28 --group=$pick.group
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29 #end if
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30 #if $pick.groups.__str__ != "None" and len($pick.groups.__str__) > 0:
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31 --groups=$pick.groups
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32 #end if
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33 #end if
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34 #if $sorted.__str__ != "None" and len($sorted.__str__) > 0:
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35 --sorted=$sorted
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36 #end if
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37 $large
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38 </command>
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39 <inputs>
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40 <!-- get.relabund relabund type should also work -->
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41 <param name="fasta" type="data" format="fasta" label="fasta - Fasta"/>
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42 <param name="otu_list" type="data" format="list" label="list - OTU List"/>
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43 <conditional name="input">
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44 <param name="source" type="select" label="Distance Matrix Format">
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45 <option value="column">Pairwise Column Distance Matrix</option>
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46 <option value="phylip">Phylip Distance Matrix</option>
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47 </param>
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48 <when value="column">
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49 <param name="dist" type="data" format="pair.dist" label="column - Distance Matrix"/>
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50 <param name="name" type="data" format="names" label="name - Sequences Name reference"/>
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51 </when>
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52 <when value="phylip">
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53 <param name="dist" type="data" format="lower.dist,square.dist" label="phylip - Distance Matrix"/>
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54 <param name="name" type="data" format="names" optional="true" label="name - Names"/>
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55 </when>
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56 </conditional>
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57 <conditional name="pick">
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58 <param name="type" type="select" label="Parse a group file into abundant and rare groups?" help="">
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59 <option value="no" selected="true">No</option>
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60 <option value="yes">Yes</option>
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61 </param>
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62 <when value="no"/>
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63 <when value="yes">
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64 <param name="group" type="data" format="groups" label="group - Group file for the OTU List"/>
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65 <param name="groups" type="select" label="groups - Group Selection (all used if none are selected)" multiple="true">
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66 <options from_dataset="group">
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67 <column name="name" index="1"/>
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68 <column name="value" index="1"/>
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69 <filter type="unique_value" name="unq_grp" column="1" />
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70 </options>
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71 </param>
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72 </when>
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73 </conditional> <!-- pick -->
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74 <param name="label" type="select" label="label - OTU Labels" multiple="true">
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75 <options from_dataset="otu_list">
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76 <column name="name" index="0"/>
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77 <column name="value" index="0"/>
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78 </options>
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79 </param>
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80 <param name="sorted" type="select" label="sorted - Sort Sequences by">
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81 <option value="">Don't sort</option>
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82 <option value="name">Sequence Name</option>
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83 <option value="number">Bin Number</option>
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84 <option value="size">Bin Size</option>
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85 <option value="group">Group</option>
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86 </param>
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87 <param name="large" type="boolean" checked="false" truevalue="--large=true" falsevalue="" label="large - Distance Matrix is very Large"/>
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88 <param name="as_datasets" type="boolean" truevalue="yes" falsevalue="no" checked="true" label="Create a new history dataset for each label"/>
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89 </inputs>
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90 <outputs>
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91 <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" />
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92 </outputs>
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93 <requirements>
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94 <requirement type="binary">mothur</requirement>
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95 </requirements>
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96 <tests>
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97 </tests>
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98 <help>
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99 **Mothur Overview**
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100
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101 Mothur_, initiated by Dr. Patrick Schloss and his software development team
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102 in the Department of Microbiology and Immunology at The University of Michigan,
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103 provides bioinformatics for the microbial ecology community.
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104
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105 .. _Mothur: http://www.mothur.org/wiki/Main_Page
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106
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107 **Command Documenation**
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108
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109 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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110
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111 .. _get.oturep: http://www.mothur.org/wiki/Get.oturep
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112
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113 </help>
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114 </tool>