Mercurial > repos > jjohnson > mothur_toolsuite
annotate mothur/tools/mothur/heatmap.bin.xml @ 33:d53b9eb16c2d
mothur_wrapper.py - convert_value needs to return a String
author | Jim Johnson <jj@umn.edu> |
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date | Wed, 11 Sep 2013 16:56:31 -0500 |
parents | 49058b1f8d3f |
children | 95d75b35e4d2 |
rev | line source |
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7 | 1 <tool id="mothur_heatmap_bin" name="Heatmap.bin" version="1.20.0" force_history_refresh="True"> |
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2 <description>Generate a heatmap for OTUs</description> |
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3 <command interpreter="python"> |
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4 mothur_wrapper.py |
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5 --cmd='heatmap.bin' |
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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='$__new_file_path__' |
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10 --new_datasets='^\S+?\.((\S+)\.(unique|[0-9.]*)\.heatmap\.bin\.svg)$:svg' |
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11 #end if |
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12 #if isinstance($input.otu.datatype, $__app__.datatypes_registry.get_datatype_by_extension('shared').__class__): |
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13 --shared=$input.otu |
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14 #elif isinstance($input.otu.datatype, $__app__.datatypes_registry.get_datatype_by_extension('rabund').__class__): |
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15 --rabund=$input.otu |
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16 #elif isinstance($input.otu.datatype, $__app__.datatypes_registry.get_datatype_by_extension('sabund').__class__): |
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17 --sabund=$input.otu |
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18 #elif isinstance($input.otu.datatype, $__app__.datatypes_registry.get_datatype_by_extension('list').__class__): |
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19 --list=$input.otu |
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20 #elif isinstance($input.otu.datatype, $__app__.datatypes_registry.get_datatype_by_extension('relabund').__class__): |
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21 --relabund=$input.otu |
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22 #end if |
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23 #if $input.has_groups != 'no' and $input.groups.__str__ != "None" and len($input.groups.__str__) > 0: |
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24 --groups=$input.groups |
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25 #end if |
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26 #if $input.label.__str__ != "None" and len($input.label.__str__) > 0: |
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27 --label='$input.label' |
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28 #end if |
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29 #if $scale.__str__ != "None" and len($scale.__str__) > 0: |
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30 --scale='$scale' |
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31 #end if |
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32 #if $sorted.__str__ != "None" and len($sorted.__str__) > 0: |
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33 --sorted='$sorted' |
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34 #end if |
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35 #if $numotu > 0: |
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36 --numotu=$numotu |
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37 #end if |
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38 #if 100 > $fontsize > 0: |
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39 --fontsize=$fontsize |
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40 #end if |
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41 </command> |
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42 <inputs> |
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43 <conditional name="input"> |
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44 <param name="has_groups" type="select" label="Generate Heatmap for"> |
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45 <option value="default">shared or relabund</option> |
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46 <option value="no">list, rabund, sabund</option> |
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47 <option value="yes">list, rabund, sabund with groups</option> |
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48 </param> |
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49 <when value="default"> |
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50 <param name="otu" type="data" format="shared,relabund" label="shared,relabund - OTU List"/> |
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51 <param name="groups" type="select" label="groups - Groups to condider" multiple="true"> |
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52 <options> |
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53 <filter type="data_meta" ref="otu" key="groups" /> |
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54 </options> |
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55 </param> |
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56 <param name="label" type="select" label="label - OTU Labels" multiple="true"> |
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57 <options> |
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58 <filter type="data_meta" ref="otu" key="labels" /> |
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59 </options> |
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60 </param> |
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61 </when> |
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62 <when value="no"> |
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63 <param name="otu" type="data" format="list,rabund,sabund" label="list,rabund,sabund - OTU List"/> |
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64 <param name="label" type="select" label="label - OTU Labels" multiple="true"> |
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65 <options> |
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66 <filter type="data_meta" ref="otu" key="labels" /> |
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67 </options> |
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68 </param> |
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69 </when> |
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70 <when value="yes"> |
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71 <param name="otu" type="data" format="list,rabund,sabund" label="list,rabund,sabund - OTU List"/> |
7 | 72 <param name="otu_group" type="data" format="groups" label="group - Group file for the OTU List"/> |
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73 <param name="groups" type="select" label="groups - Groups to include" multiple="true"> |
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74 <options> |
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75 <filter type="data_meta" ref="otu_group" key="groups" /> |
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76 </options> |
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77 </param> |
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78 <param name="label" type="select" label="label - OTU Labels" multiple="true"> |
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79 <options> |
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80 <filter type="data_meta" ref="otu" key="labels" /> |
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81 </options> |
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82 </param> |
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83 </when> |
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84 </conditional> |
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85 <param name="scale" type="select" label="scale - Scaling for heatmap"> |
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86 <option value="">Default</option> |
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87 <option value="log10">Log10</option> |
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88 <option value="log2">Log2</option> |
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89 <option value="linear">Linear</option> |
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90 </param> |
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91 <param name="sorted" type="select" label="sorted - Sort heatmap"> |
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92 <option value="">By shared</option> |
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93 <option value="none">Don't sort</option> |
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94 <option value="topotu">By Total OTUs</option> |
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95 <option value="topgroup">By Total Groups</option> |
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96 </param> |
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97 <param name="numotu" type="integer" value="0" label="numotu - Limit the number of OTUs displayed (ignored if 0)"/> |
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98 <param name="fontsize" type="integer" value="24" label="fontsize - Fontsize (default is 24)"/> |
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99 <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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100 </inputs> |
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101 <outputs> |
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102 <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" /> |
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103 </outputs> |
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104 <requirements> |
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105 <requirement type="package" version="1.27">mothur</requirement> |
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106 </requirements> |
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107 <tests> |
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108 </tests> |
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109 <help> |
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110 **Mothur Overview** |
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111 |
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112 Mothur_, initiated by Dr. Patrick Schloss and his software development team |
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113 in the Department of Microbiology and Immunology at The University of Michigan, |
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114 provides bioinformatics for the microbial ecology community. |
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115 |
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116 .. _Mothur: http://www.mothur.org/wiki/Main_Page |
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117 |
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118 **Command Documenation** |
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119 |
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120 The heatmap.bin_ command generates a heat map from data provided in either a list_ or a shared_ file. |
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121 |
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122 .. _list: http://www.mothur.org/wiki/List_file |
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123 .. _shared: http://www.mothur.org/wiki/Shared_file |
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124 .. _heatmap.bin: http://www.mothur.org/wiki/Heatmap.bin |
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125 |
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126 </help> |
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127 </tool> |