Mercurial > repos > iuc > mothur_heatmap_bin

annotate heatmap.bin.xml @ 3:ac3f8a1a3e43 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 283d5933cd945b7815b3da2ce45baa60d73e9746
author iuc
date Fri, 06 Apr 2018 04:28:46 -0400
parents ac2fa6a167ad
children 35a719cd08da
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b0718c06e329 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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1 <tool profile="16.07" id="mothur_heatmap_bin" name="Heatmap.bin" version="@WRAPPER_VERSION@.0">
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2 <description>Generate a heatmap for OTUs</description>
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
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6 <expand macro="requirements"/>
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7 <expand macro="stdio"/>
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8 <expand macro="version_command"/>
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9 <command><![CDATA[
2
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10 @SHELL_OPTIONS@
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11
2
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12 ## create symlinks to input datasets
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13 ln -s '$input.otu' input_otu.dat &&
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14
2
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15 echo 'heatmap.bin(
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16 #if $input.otu.is_of_type("mothur.rabund"):
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17 rabund=input_otu.dat,
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18 #elif $input.otu.is_of_type("mothur.sabund"):
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19 sabund=input_otu.dat,
ac2fa6a167ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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20 #elif $input.otu.is_of_type("mothur.list"):
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21 list=input_otu.dat,
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22 #elif $input.otu.is_of_type("mothur.relabund"):
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23 relabund=input_otu.dat,
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24 #elif $input.otu.is_of_type("mothur.shared"):
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25 shared=input_otu.dat,
ac2fa6a167ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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26 #end if
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27 #if $input.has_groups == 'yes' and $input.groups:
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28 groups=${ str($input.groups).replace(",","-") },
ac2fa6a167ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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29 #end if
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30 #if $input.label:
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31 label=${ str($input.label).replace(",","-") },
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32 #end if
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33 scale=$scale,
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34 sorted=$sorted,
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35 numotu=$numotu,
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36 fontsize=$fontsize
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37 )'
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38 | sed 's/ //g' ## mothur trips over whitespace
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39 | mothur
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40 | tee mothur.out.log
0
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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="no">list, rabund, sabund</option>
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46 <option value="yes">shared, relabund</option>
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47 </param>
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48 <when value="no">
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49 <param name="otu" type="data" format="mothur.list,mothur.rabund,mothur.sabund" label="list,rabund,sabund - OTU List"/>
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50 <param name="label" type="select" label="label - OTU Labels" multiple="true">
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51 <expand macro="labeloptions"/>
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52 </param>
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53 </when>
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54 <when value="yes">
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55 <param name="otu" type="data" format="mothur.shared,mothur.relabund" label="shared or relabund file - OTU List"/>
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56 <param name="groups" type="select" multiple="true" label="groups - Groups to include">
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57 <options>
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58 <filter type="data_meta" ref="otu" key="groups"/>
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59 </options>
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60 </param>
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61 <param name="label" type="select" multiple="true" label="label - OTU Labels">
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62 <expand macro="labeloptions"/>
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63 </param>
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64 </when>
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65 </conditional>
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66 <param name="scale" type="select" label="scale - Scaling for heatmap">
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67 <option value="log10" selected="true">Log10</option>
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68 <option value="log2">Log2</option>
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69 <option value="linear">Linear</option>
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70 </param>
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71 <param name="sorted" type="select" label="sorted - Sort heatmap">
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72 <option value="shared" selected="true">By shared</option>
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73 <option value="none">Don't sort</option>
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74 <option value="topotu">By Total OTUs</option>
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75 <option value="topgroup">By Total Groups</option>
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76 </param>
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77 <param name="numotu" type="integer" value="0" min="0" label="numotu - Limit the number of OTUs displayed (ignored if 0)"/>
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78 <param name="fontsize" type="integer" value="24" min="0" max="100" label="fontsize - Fontsize (default is 24)"/>
2
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79 <expand macro="param-savelog"/>
0
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80 </inputs>
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81 <outputs>
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82 <expand macro="logfile-output"/>
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83 <collection name="heatmaps" type="list" label="${tool.name} on ${on_string}: Heatmaps">
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84 <discover_datasets pattern=".*?\.(?P&lt;designation&gt;.*)\.bin\.svg"/>
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85 </collection>
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86 </outputs>
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87 <tests>
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88 <test>
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89 <param name="otu" value="amazon.an.list" ftype="mothur.list"/>
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90 <param name="has_groups" value="no"/>
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91 <output_collection name="heatmaps" count="36">
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92 <element name="0.26.heatmap" md5="8f0d5cb95808115e50729e6df60629cc"/>
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93 </output_collection>
2
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94 <param name="savelog" value="true"/>
0
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95 <expand macro="logfile-test"/>
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96 </test>
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97 <test>
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98 <param name="otu" value="amazon.an.relabund" ftype="mothur.relabund"/>
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99 <param name="has_groups" value="yes"/>
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100 <param name="groups" value="forest"/>
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101 <param name="label" value="0.26"/>
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102 <output_collection name="heatmaps" count="1">
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103 <element name="0.26.heatmap" md5="b2b46b7e55f55e2b260cd6dc6ccb4485"/>
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104 </output_collection>
2
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105 <param name="savelog" value="true"/>
0
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106 <expand macro="logfile-test"/>
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107 </test>
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108 <test>
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109 <param name="otu" value="amazon.an.shared" ftype="mothur.shared"/>
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110 <param name="has_groups" value="yes"/>
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111 <param name="label" value="0.03,0.26,0.55"/>
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112 <param name="groups" value="forest,pasture"/>
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113 <param name="fontsize" value="100"/>
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114 <param name="scale" value="linear"/>
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115 <param name="sorted" value="none"/>
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116 <output_collection name="heatmaps" count="3">
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117 <element name="0.26.heatmap" md5="b46ed47e441a30588f60e1554ff703bb"/>
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118 </output_collection>
2
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119 <param name="savelog" value="true"/>
0
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120 <expand macro="logfile-test"/>
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121 </test>
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122 </tests>
2
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123 <help><![CDATA[
0
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124
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125 @MOTHUR_OVERVIEW@
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126
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127
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128 **Command Documentation**
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129
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130 The heatmap.bin_ command generates a heat map from data provided in either a list_ or a shared_ file.
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131
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132 .. _list: https://www.mothur.org/wiki/List_file
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133 .. _shared: https://www.mothur.org/wiki/Shared_file
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134 .. _heatmap.bin: https://www.mothur.org/wiki/Heatmap.bin
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135
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136 v.1.21.0: Updated to Mothur 1.33
2
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137
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138 ]]></help>
0
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139 <expand macro="citations"/>
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140 </tool>