Mercurial > repos > jjohnson > mothur_toolsuite
annotate mothur/tools/mothur/venn.xml @ 7:7bfe1f843858
Support Mothur v1.20
trim.seqs - added name parameter and optional trim.names output
phylo.diversity - group optional, put group and groups in conditional - breaks
get.lineage remove.lineage - allow multiple taxons
dist.shared - added processors
consensus.seqs - add cutoff parameter
trim.seqs,phylo.diversity,get.lineage,remove.lineage,dist.shared,consensus.seqs
new tools - chimera.uchime deunique.tree count.seqs
shared/relabund files - Column headings
refactor lib/galaxy/datatypes/metagenomics.py
add filters to label and group selects in tool configs
mothur_wrapper.py updated with new tools params
author | Jim Johnson <jj@umn.edu> |
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date | Mon, 27 Jun 2011 10:12:25 -0500 |
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children | 697156806162 |
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7 | 1 <tool id="mothur_venn" name="Venn" version="1.20.0" force_history_refresh="True"> |
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2 <description>Generate Venn diagrams for groups </description> |
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3 <command interpreter="python"> |
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4 mothur_wrapper.py |
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5 --cmd='venn' |
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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='$__new_file_path__' |
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10 --new_datasets='^\S+?\.(\S+\.svg)$:svg' |
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11 #end if |
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12 #if $input.source == 'shared': |
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13 --shared=$input.otu |
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14 #if $input.label.__str__ != "None" and len($input.label.__str__) > 0: |
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15 --label='$input.label' |
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16 #end if |
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17 #if $input.calc.__str__ != "None" and len($input.calc.__str__) > 0: |
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18 --calc='$input.calc' |
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19 #end if |
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20 $nseqs |
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21 $permute |
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22 #if $input.groups.__str__ != "None" and len($input.groups.__str__) > 0: |
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23 --groups=$input.groups |
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24 #end if |
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25 #elif $input.source == 'similarity': |
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26 --list=$input.otu |
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27 #if $input.label.__str__ != "None" and len($input.label.__str__) > 0: |
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28 --label='$input.label' |
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29 #end if |
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30 #if $input.calc.__str__ != "None" and len($input.calc.__str__) > 0: |
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31 --calc='$input.calc' |
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32 #end if |
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33 #if $input.abund >= 5: |
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34 --abund='$input.abund' |
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35 #end if |
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36 |
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37 #end if |
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38 </command> |
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39 <inputs> |
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40 <conditional name="input"> |
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41 <param name="source" type="select" label="Generate Heatmap for"> |
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42 <option value="shared">OTU Shared</option> |
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43 <option value="similarity">OTU list</option> |
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44 </param> |
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45 <when value="shared"> |
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46 <param name="otu" type="data" format="shared" label="shared - OTU Shared"/> |
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47 <param name="calc" type="select" multiple="true" label="calc - Calculators (Uses defaults if none selected)"> |
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48 <option value="sharedsobs">Shared Sobs</option> |
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49 <option value="sharedchao">Shared Chao</option> |
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50 <option value="sharedace">Shared Ace</option> |
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51 </param> |
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52 <param name="label" type="select" label="label - OTU Labels" multiple="true"> |
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53 <options from_dataset="otu"> |
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54 <column name="name" index="0"/> |
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55 <column name="value" index="0"/> |
7 | 56 <filter type="static_value" name="ignore_header" keep="False" column="0" value = "label"/> |
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57 <filter type="unique_value" name="unq_lbl" column="0" /> |
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58 </options> |
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59 </param> |
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60 <param name="groups" type="select" label="groups - Groups to consider" multiple="true"> |
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61 <options from_dataset="otu"> |
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62 <column name="name" index="1"/> |
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63 <column name="value" index="1"/> |
7 | 64 <filter type="static_value" name="ignore_header" keep="False" column="1" value = "Group"/> |
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65 <filter type="unique_value" name="unq_grp" column="1" /> |
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66 </options> |
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67 </param> |
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68 </when> |
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69 <when value="similarity"> |
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70 <param name="otu" type="data" format="list" label="list - OTU List"/> |
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71 <param name="calc" type="select" multiple="true" label="calc - Calculators (Uses defaults if none selected)"> |
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72 <option value="sobs">Sobs</option> |
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73 <option value="chao">Chao</option> |
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74 <option value="ace">Ace</option> |
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75 </param> |
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76 <param name="abund" type="integer" value="10" label="abund - Abundance when using the ace calculator ( >= 5 )"> |
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77 <validator type="in_range" min="5" /> |
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78 </param> |
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79 <param name="label" type="select" label="label - OTU Labels" multiple="true"> |
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80 <options from_dataset="otu"> |
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81 <column name="name" index="0"/> |
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82 <column name="value" index="0"/> |
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83 </options> |
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84 </param> |
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85 </when> |
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86 </conditional> |
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87 <param name="nseqs" type="boolean" truevalue="--nseqs=true" falsevalue="" checked="false" label="nseqs - Output the number of sequences represented by the otus in the picture"/> |
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88 <param name="permute" type="boolean" truevalue="--permute=true" falsevalue="" checked="false" label="permute - Create pictures with all possible 4-way permutations of groups"/> |
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89 <param name="as_datasets" type="boolean" truevalue="yes" falsevalue="no" checked="false" label="Create a new history dataset for each image"/> |
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90 </inputs> |
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91 <outputs> |
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92 <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" /> |
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93 </outputs> |
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94 <requirements> |
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95 <requirement type="binary">mothur</requirement> |
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96 </requirements> |
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97 <tests> |
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98 </tests> |
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99 <help> |
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100 **Mothur Overview** |
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101 |
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102 Mothur_, initiated by Dr. Patrick Schloss and his software development team |
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103 in the Department of Microbiology and Immunology at The University of Michigan, |
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104 provides bioinformatics for the microbial ecology community. |
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105 |
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106 .. _Mothur: http://www.mothur.org/wiki/Main_Page |
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107 |
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108 **Command Documenation** |
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109 |
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110 The venn_ command generates Venn diagrams to compare the richness shared among 2, 3, or 4 groups. For calc parameter choices see: http://www.mothur.org/wiki/Calculators |
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111 |
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112 .. _venn: http://www.mothur.org/wiki/Venn |
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113 |
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114 </help> |
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115 </tool> |