Mercurial > repos > jjohnson > mothur_toolsuite
annotate mothur/tools/mothur/heatmap.sim.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 |
parents | 3202a38e44d9 |
children | e990ac8a0f58 |
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1 <tool id="mothur_heatmap_sim" name="Heatmap.sim" version="1.16.0" force_history_refresh="True"> |
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2 <description>Generate a heatmap for pariwise similarity</description> |
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3 <command interpreter="python"> |
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4 mothur_wrapper.py |
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5 --cmd='heatmap.sim' |
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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='$__new_file_path__' |
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9 --new_datasets='^\S+?\.((unique|[0-9.]*)(\S+)\.heatmap\.sim\.svg)$:svg' |
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10 #if $input.source == 'similarity': |
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11 --READ_cmd='read.otu' |
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12 --READ_list=$input.otu |
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13 #if $otu_group.__str__ != "None" and len($otu_group.__str__) > 0: |
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14 --READ_group='$otu_group' |
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15 #end if |
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16 #if $input.label.__str__ != "None" and len($input.label.__str__) > 0: |
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17 --label='$input.label' |
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18 #end if |
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19 #if $input.groups.__str__ != "None" and len($input.groups.__str__) > 0: |
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20 --groups=$input.groups |
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21 #end if |
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22 #if $input.calc.__str__ != "None" and len($input.calc.__str__) > 0: |
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23 --calc='$input.calc' |
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24 #end if |
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25 #elif $input.source == 'shared': |
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26 --READ_cmd='read.otu' |
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27 --READ_shared=$input.otu |
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28 #if $input.label.__str__ != "None" and len($input.label.__str__) > 0: |
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29 --label='$input.label' |
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30 #end if |
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31 #if $input.groups.__str__ != "None" and len($input.groups.__str__) > 0: |
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32 --groups=$input.groups |
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33 #end if |
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34 #if $input.calc.__str__ != "None" and len($input.calc.__str__) > 0: |
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35 --calc='$input.calc' |
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36 #end if |
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37 #elif $input.source == 'column': |
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38 --column=$input.dist |
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39 --name=$input.name |
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40 #elif $input.source == 'phylip': |
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41 --phylip=$input.dist |
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42 #if $input.name.__str__ != "None" and len($input.name.__str__) > 0: |
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43 --name=$input.name |
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44 #end if |
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45 #end if |
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46 </command> |
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47 <inputs> |
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48 <!-- get.relabund relabund type should also work --> |
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49 <conditional name="input"> |
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50 <param name="source" type="select" label="Generate Heatmap for"> |
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51 <option value="similarity">OTU list</option> |
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52 <option value="shared">OTU Shared</option> |
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53 <option value="column">Pairwise Column Distance Matrix</option> |
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54 <option value="phylip">Phylip Distance Matrix</option> |
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55 </param> |
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56 <when value="similarity"> |
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57 <param name="otu" type="data" format="list" label="read.otu(list=) - OTU List"/> |
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58 <param name="otu_group" type="data" format="groups" label="read.otu(group=) - Group file for the OTU List"/> |
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59 <param name="label" type="select" label="label - OTU Labels" multiple="true"> |
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60 <options from_dataset="otu"> |
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61 <column name="name" index="0"/> |
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62 <column name="value" index="0"/> |
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63 </options> |
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64 </param> |
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65 <param name="groups" type="select" label="groups - Groups to include" multiple="true"> |
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66 <options from_dataset="otu_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 <param name="calc" type="select" label="calc - Calculators (Uses defaults if none selected)" multiple="true"> |
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73 <options from_file="mothur_calculators.loc"> |
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74 <column name="mult2" index="2"/> |
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75 <column name="name" index="0"/> |
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76 <column name="value" index="0"/> |
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77 <filter type="static_value" name="mult2" column="2" value="shar" /> |
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78 </options> |
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79 </param> |
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80 </when> |
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81 <when value="shared"> |
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82 <param name="otu" type="data" format="shared" label="read.otu(shared=) - OTU Shared"/> |
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83 <param name="label" type="select" label="label - OTU Labels" multiple="true"> |
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84 <options from_dataset="otu"> |
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85 <column name="name" index="0"/> |
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86 <column name="value" index="0"/> |
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87 <filter type="unique_value" name="unq_lbl" column="0" /> |
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88 </options> |
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89 </param> |
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90 <param name="groups" type="select" label="groups - Groups to include" multiple="true"> |
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91 <options from_dataset="otu"> |
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92 <column name="name" index="1"/> |
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93 <column name="value" index="1"/> |
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94 <filter type="unique_value" name="unq_grp" column="1" /> |
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95 </options> |
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96 </param> |
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97 </when> |
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98 <when value="column"> |
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99 <param name="dist" type="data" format="pair.dist" label="column - Distance Matrix"/> |
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100 <param name="name" type="data" format="names" label="name - Names"/> |
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101 </when> |
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102 <when value="phylip"> |
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103 <param name="dist" type="data" format="lower.dist,square.dist" label="phylip - Distance Matrix"/> |
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104 <param name="name" type="data" format="names" optional="true" label="name - Names"/> |
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105 </when> |
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106 </conditional> |
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107 </inputs> |
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108 <outputs> |
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109 <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" /> |
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110 </outputs> |
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111 <requirements> |
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112 <requirement type="binary">mothur</requirement> |
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113 </requirements> |
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114 <tests> |
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115 </tests> |
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116 <help> |
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117 **Mothur Overview** |
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118 |
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119 Mothur_, initiated by Dr. Patrick Schloss and his software development team |
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120 in the Department of Microbiology and Immunology at The University of Michigan, |
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121 provides bioinformatics for the microbial ecology community. |
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122 |
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123 .. _Mothur: http://www.mothur.org/wiki/Main_Page |
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124 |
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125 **Command Documenation** |
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126 |
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127 The heatmap.sim_ command generates a heat map from data provided in either a .list or a .shared file. |
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128 |
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129 .. _heatmap.sim: http://www.mothur.org/wiki/Heatmap.sim |
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130 |
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131 </help> |
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132 </tool> |