Mercurial > repos > jjohnson > mothur_toolsuite
annotate mothur/tools/mothur/heatmap.sim.xml @ 13:4f797d3eee3a
Change default processor counts to 8, mothur_wrapper.py can overide processors allocated with ENVIRONMENT variable MOTHUR_MAX_PROCESSORS
author | Jim Johnson <jj@umn.edu> |
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date | Wed, 05 Oct 2011 10:34:44 -0500 |
parents | 7bfe1f843858 |
children | 697156806162 |
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7 | 1 <tool id="mothur_heatmap_sim" name="Heatmap.sim" version="1.20.0" 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 --outputdir='$logfile.extra_files_path' |
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7 #if $as_datasets.__str__ == "yes": |
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8 #if $input.source == 'shared': |
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9 --result='^mothur.\S+\.logfile$:'$logfile |
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10 --datasetid='$logfile.id' --new_file_path='$__new_file_path__' |
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11 --new_datasets='^\S+?\.((unique|[0-9.]*)(\S+)\.heatmap\.sim\.svg)$:svg' |
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12 #else: |
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13 --result='^mothur.\S+\.logfile$:'$logfile,'^\S+\.heatmap\.sim\.svg$:'$heatmap |
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14 #end if |
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15 #else: |
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16 --result='^mothur.\S+\.logfile$:'$logfile |
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17 #end if |
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18 #if $input.source == 'shared': |
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19 --shared=$input.otu |
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20 #if $input.label.__str__ != "None" and len($input.label.__str__) > 0: |
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21 --label='$input.label' |
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22 #end if |
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23 #if $input.groups.__str__ != "None" and len($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 $input.calc.__str__ != "None" and len($input.calc.__str__) > 0: |
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27 --calc='$input.calc' |
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28 #end if |
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29 #elif $input.source == 'column': |
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30 --column=$input.dist |
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31 --name=$input.name |
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32 #elif $input.source == 'phylip': |
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33 --phylip=$input.dist |
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34 #end if |
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35 </command> |
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36 <inputs> |
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37 <conditional name="input"> |
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38 <param name="source" type="select" label="Generate Heatmap for"> |
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39 <option value="shared">shared - Sample Similarity - OTU Shared</option> |
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40 <option value="phylip">phylip - Phylip Distance Matrix</option> |
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41 <option value="column">colomn - Pairwise Column Distance Matrix</option> |
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42 </param> |
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43 <when value="shared"> |
7 | 44 <param name="otu" type="data" format="shared" label="shared - OTU Shared"/> |
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45 <param name="label" type="select" label="label - OTU Labels" multiple="true"> |
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46 <options from_dataset="otu"> |
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47 <column name="name" index="0"/> |
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48 <column name="value" index="0"/> |
7 | 49 <filter type="static_value" name="ignore_header" keep="False" column="0" value = "label"/> |
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50 <filter type="unique_value" name="unq_lbl" column="0" /> |
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51 </options> |
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52 </param> |
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53 <param name="groups" type="select" label="groups - Groups to include" multiple="true"> |
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54 <options from_dataset="otu"> |
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55 <column name="name" index="1"/> |
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56 <column name="value" index="1"/> |
7 | 57 <filter type="static_value" name="ignore_header" keep="False" column="1" value = "Group"/> |
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58 <filter type="unique_value" name="unq_grp" column="1" /> |
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59 </options> |
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60 </param> |
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61 <param name="calc" type="select" label="calc - Calculators (Uses defaults if none selected)" multiple="true"> |
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62 <options from_file="mothur_calculators.loc"> |
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63 <column name="mult2" index="2"/> |
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64 <column name="name" index="0"/> |
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65 <column name="value" index="0"/> |
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66 <filter type="static_value" name="mult2" column="2" value="shar" /> |
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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="column"> |
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71 <param name="dist" type="data" format="pair.dist" label="column - Distance Matrix"/> |
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72 <param name="name" type="data" format="names" label="name - Names"/> |
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73 </when> |
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74 <when value="phylip"> |
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75 <param name="dist" type="data" format="lower.dist,square.dist" label="phylip - Distance Matrix"/> |
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76 </when> |
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77 </conditional> |
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78 <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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79 </inputs> |
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80 <outputs> |
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81 <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" /> |
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82 <data format="svg" name="heatmap" label="${tool.name} on ${on_string}: heatmap.sim.svg"> |
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83 <filter>as_datasets != 'true' and input['source'] != 'shared'</filter> |
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84 </data> |
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85 </outputs> |
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86 <requirements> |
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87 <requirement type="binary">mothur</requirement> |
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88 </requirements> |
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89 <tests> |
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90 </tests> |
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91 <help> |
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92 **Mothur Overview** |
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93 |
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94 Mothur_, initiated by Dr. Patrick Schloss and his software development team |
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95 in the Department of Microbiology and Immunology at The University of Michigan, |
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96 provides bioinformatics for the microbial ecology community. |
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97 |
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98 .. _Mothur: http://www.mothur.org/wiki/Main_Page |
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99 |
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100 **Command Documenation** |
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101 |
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102 The heatmap.sim_ command generates a heat map from data provided in either a shared_ file, a phylip_ distance matrix, or a column_ distance matrix and a name_ file. For calc parameter choices see: http://www.mothur.org/wiki/Calculators |
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103 |
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104 .. _shared: http://www.mothur.org/wiki/Shared_file |
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105 .. _phylip: http://www.mothur.org/wiki/Phylip-formatted_distance_matrix |
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106 .. _column: http://www.mothur.org/wiki/Column-formatted_distance_matrix |
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107 .. _name: http://www.mothur.org/wiki/Name_file |
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108 .. _heatmap.sim: http://www.mothur.org/wiki/Heatmap.sim |
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109 |
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110 </help> |
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111 </tool> |