Mercurial > repos > jjohnson > mothur_toolsuite
annotate mothur/tools/mothur/dist.shared.xml @ 0:3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
author | jjohnson |
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date | Tue, 07 Jun 2011 17:32:23 -0400 |
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children | fcc0778f6987 |
rev | line source |
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0
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1 <tool id="mothur_dist_shared" name="Dist.shared" version="1.15.0" force_history_refresh="True"> |
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2 <description>Generate a phylip-formatted dissimilarity distance matrix among multiple groups</description> |
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3 <command interpreter="python"> |
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4 mothur_wrapper.py |
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5 --cmd='dist.shared' |
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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='$__new_file_path__' |
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9 #if len($output.__str__) > 0: |
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10 #if $output.__str__ == 'square': |
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11 --new_datasets='^\S+?\.([a-z]+\.(unique|[0-9.]*)\.(square|lt))\.dist$:square.dist' |
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12 #elif $output.__str__ == 'lt': |
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13 --new_datasets='^\S+?\.([a-z]+\.(unique|[0-9.]*)\.(square|lt))\.dist$:lower.dist' |
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14 #end if |
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15 #else: |
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16 --new_datasets='^\S+?\.([a-z]+\.(unique|[0-9.]*)\.(square|lt))\.dist$:lower.dist' |
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17 #end if |
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18 --READ_cmd='read.otu' |
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19 #if $input.source == 'similarity': |
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20 --READ_list=$input.otu |
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21 #if $otu_group.__str__ != "None" and len($otu_group.__str__) > 0: |
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22 --READ_group='$otu_group' |
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23 #end if |
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24 #if $input.label.__str__ != "None" and len($input.label.__str__) > 0: |
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25 --READ_label='$input.label' |
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26 #end if |
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27 #elif $input.source == 'shared': |
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28 --READ_shared=$input.otu |
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29 #if $input.label.__str__ != "None" and len($input.label.__str__) > 0: |
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30 --READ_label='$input.label' |
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31 #end if |
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32 #end if |
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33 #if $calc.__str__ != "None" and len($calc.__str__) > 0: |
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34 --calc=$calc |
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35 #end if |
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36 #if $output.__str__ != "None" and len($output.__str__) > 0: |
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37 --output=$output |
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38 #end if |
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39 </command> |
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40 <inputs> |
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41 <!-- list,group or shared --> |
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42 <conditional name="input"> |
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43 <param name="source" type="select" label="Generate Collector Curvers for"> |
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44 <option value="similarity">OTU list</option> |
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45 <option value="shared">OTU Shared</option> |
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46 </param> |
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47 <when value="similarity"> |
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48 <param name="otu" type="data" format="list" label="read.otu(list=) - OTU List"/> |
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49 <param name="otu_group" type="data" format="groups" label="read.otu(group=) - Group file for the OTU List"/> |
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50 <param name="label" type="select" label="label - OTU Labels" multiple="true"> |
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51 <options from_dataset="otu"> |
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52 <column name="name" index="0"/> |
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53 <column name="value" index="0"/> |
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54 <filter type="unique_value" name="unq_lbl" column="0" /> |
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55 </options> |
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56 </param> |
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57 <param name="groups" type="select" label="groups - Groups to consider" multiple="true"> |
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58 <options from_dataset="otu_group"> |
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59 <column name="name" index="1"/> |
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60 <column name="value" index="1"/> |
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61 <filter type="unique_value" name="unq_grp" column="1" /> |
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62 </options> |
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63 </param> |
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64 </when> |
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65 <when value="shared"> |
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66 <param name="otu" type="data" format="shared" label="read.otu(shared=) - OTU Shared"/> |
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67 <param name="label" type="select" label="label - OTU Labels" multiple="true"> |
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68 <options from_dataset="otu"> |
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69 <column name="name" index="0"/> |
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70 <column name="value" index="0"/> |
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71 <filter type="unique_value" name="unq_lbl" column="0" /> |
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72 </options> |
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73 </param> |
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74 <param name="groups" type="select" label="groups - Groups to consider" multiple="true"> |
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75 <options from_dataset="otu"> |
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76 <column name="name" index="1"/> |
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77 <column name="value" index="1"/> |
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78 <filter type="unique_value" name="unq_grp" column="1" /> |
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79 </options> |
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80 </param> |
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81 </when> |
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82 </conditional> |
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83 <param name="calc" type="select" label="calc - Calculators (Uses defaults if none selected)" multiple="true"> |
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84 <options from_file="mothur_calulators.loc"> |
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85 <column name="mult2" index="2"/> |
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86 <column name="name" index="0"/> |
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87 <column name="value" index="0"/> |
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88 <filter type="static_value" name="mult2" column="2" value="shar" /> |
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89 </options> |
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90 </param> |
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91 <param name="output" type="select" label="output - Distance Matrix Output Format" help=""> |
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92 <option value="lt">Phylip formatted Lower Triangle Matrix</option> |
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93 <option value="square">Phylip formatted Square Matrix</option> |
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94 </param> |
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95 </inputs> |
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96 <outputs> |
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97 <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" /> |
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98 </outputs> |
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99 <requirements> |
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100 <requirement type="binary">mothur</requirement> |
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101 </requirements> |
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102 <tests> |
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103 </tests> |
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104 <help> |
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105 **Mothur Overview** |
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106 |
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107 Mothur_, initiated by Dr. Patrick Schloss and his software development team |
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108 in the Department of Microbiology and Immunology at The University of Michigan, |
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109 provides bioinformatics for the microbial ecology community. |
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110 |
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111 .. _Mothur: http://www.mothur.org/wiki/Main_Page |
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112 |
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113 **Command Documenation** |
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114 |
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115 The dist.shared_ command will generate a phylip-formatted distance matrix that describes the dissimilarity (1-similarity) among multiple groups. |
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116 |
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117 .. _dist.shared: http://www.mothur.org/wiki/Dist.shared |
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118 |
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119 |
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120 </help> |
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121 </tool> |