Mercurial > repos > iuc > mothur_indicator

annotate indicator.xml @ 9:a224c578d941 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4c950508328589b5215b6c96868659a03f9dead8"
author iuc
date Tue, 08 Dec 2020 15:06:51 +0000
parents 0232e2fe594c
children f3e6f88445fb
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e66e20795ddb 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_indicator" name="Indicator" version="@WRAPPER_VERSION@.0">
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2 <description>Identify indicator "species" for nodes on a tree</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[
3
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10 @SHELL_OPTIONS@
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11
3
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12 ## create symlinks to input datasets
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13 ln -s '$otu' otu.dat &&
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14 #if $withdesign.tree:
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15 ln -s '$withdesign.tree' withdesign.tree.dat &&
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16 #end if
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17 #if $withdesign.havedesign == "yes":
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18 ln -s '$withdesign.design' withdesign.design.dat &&
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19 #end if
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20
3
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21 echo 'indicator(
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22 #if $withdesign.tree:
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23 tree=withdesign.tree.dat,
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24 #end if
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25 #if $otu.is_of_type("mothur.relabund"):
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26 relabund=otu.dat,
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27 #elif $otu.is_of_type("mothur.shared"):
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28 shared=otu.dat,
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29 #end if
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30 #if $label:
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31 label=${ str($label).replace(",","-") },
c6524e1efe12 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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32 #end if
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33 #if $withdesign.groups:
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34 groups=${ str($withdesign.groups).replace(",","-") },
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35 #end if
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36 #if $withdesign.havedesign == "yes":
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37 design=withdesign.design.dat,
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38 #end if
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39 processors='\${GALAXY_SLOTS:-8}'
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40 )'
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41 | sed 's/ //g' ## mothur trips over whitespace
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42 | mothur
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43 | tee mothur.out.log
0
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44 ]]></command>
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45 <inputs>
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46 <param name="otu" type="data" format="mothur.shared,mothur.relabund" label="shared/relabund - OTU dataset"/>
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47 <param name="label" type="select" optional="true" multiple="false" label="label - OTU Labels">
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48 <expand macro="labeloptions"/>
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49 </param>
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50 <conditional name="withdesign">
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51 <param name="havedesign" type="select" label="Will you supply a design file?">
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52 <option value="yes">yes</option>
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53 <option value="no">no</option>
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54 </param>
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55 <when value="yes">
2
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56 <param name="tree" type="data" format="mothur.tre" optional="true" label="tree - A newick-formatted tree" help="Optional, if a design file is provided."/>
0
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57 <param name="design" type="data" format="mothur.design" optional="true" label="design - assign groups to new grouping" help="make sure your file is of type mothur.design. Design has 2 columns: group(col 1) and grouping(col 2) (separated by a TAB character)"/>
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58 <param name="groups" type="select" optional="true" multiple="true" label="groups - Pick groups to annalyze">
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59 <options>
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60 <filter type="data_meta" ref="design" key="groups"/>
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61 </options>
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62 </param>
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63 </when>
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64 <when value="no">
2
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65 <param name="tree" type="data" format="mothur.tre" label="tree - A newick-formatted tree" help="Mandatory if no design file is provided"/>
0
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66 <param name="groups" type="select" optional="true" multiple="true" label="groups - Pick groups to annalyze">
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67 <options>
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68 <filter type="data_meta" ref="otu" key="groups"/>
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69 </options>
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70 </param>
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71 </when>
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72 </conditional>
3
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73 <expand macro="param-savelog"/>
0
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74 </inputs>
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75 <outputs>
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76 <expand macro="logfile-output"/>
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77 <data name="tree_out" format="mothur.tre" from_work_dir="withdesign.tree*.tre" label="${tool.name} on ${on_string}: indicator.tre">
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78 <filter>tree</filter>
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79 </data>
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80 <data name="summary" format="tabular" from_work_dir="otu*.summary" label="${tool.name} on ${on_string}: indicator.summary"/>
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81 </outputs>
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82 <tests>
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83 <test><!-- test with design input -->
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84 <param name="otu" value="amazon.an.shared" ftype="mothur.shared"/>
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85 <param name="havedesign" value="yes"/>
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86 <param name="design" value="toymothur.design2" ftype="mothur.design"/>
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87 <param name="label" value="0.03"/>
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88 <param name="groups" value="tardis,dalek"/>
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89 <output name="summary">
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90 <assert_contents>
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91 <has_line_matching expression="^OTU\tIndicator_Groups\tIndicator_Value\tpValue$"/>
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92 <has_text text="forest"/>
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93 <has_text text="pasture"/>
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94 </assert_contents>
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95 </output>
3
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96 <param name="savelog" value="true"/>
0
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97 <expand macro="logfile-test"/>
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98 </test>
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99 <test><!-- test with design input and subset of groups-->
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100 <param name="otu" value="amazon.an.shared" ftype="mothur.shared"/>
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101 <param name="havedesign" value="yes"/>
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102 <param name="design" value="toymothur.design2" ftype="mothur.design"/>
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103 <param name="groups" value="tardis"/>
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104 <output name="summary">
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105 <assert_contents>
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106 <has_line_matching expression="^OTU\tIndicator_Groups\tIndicator_Value\tpValue$"/>
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107 <has_text text="forest"/>
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108 <not_has_text text="pasture"/>
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109 </assert_contents>
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110 </output>
3
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111 <param name="savelog" value="true"/>
0
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112 <expand macro="logfile-test"/>
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113 </test>
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114 <test><!-- test with tree input -->
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115 <param name="otu" value="amazon.an.shared" ftype="mothur.shared"/>
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116 <param name="havedesign" value="no"/>
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117 <param name="tree" value="amazon.an.jclass.unique.tre"/>
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118 <param name="groups" value="forest,pasture"/>
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119 <output name="summary">
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120 <assert_contents>
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121 <has_text text="TreeNode"/>
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122 <has_text text="forest-pasture"/>
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123 </assert_contents>
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124 </output>
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125 <output name="tree_out" md5="a22f90898611e1f4c5d84cfe18dc6ebe"/>
3
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126 <param name="savelog" value="true"/>
0
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127 <expand macro="logfile-test"/>
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128 </test>
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129 <test><!-- test with tree input and subset of groups -->
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130 <param name="otu" value="amazon.an.shared" ftype="mothur.shared"/>
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131 <param name="havedesign" value="no"/>
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132 <param name="tree" value="amazon.an.jclass.unique.tre"/>
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133 <param name="groups" value="forest"/>
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134 <output name="summary">
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135 <assert_contents>
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136 <has_text text="TreeNode"/>
e66e20795ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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137 <not_has_text text="forest-pasture"/>
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138 </assert_contents>
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139 </output>
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140 <output name="tree_out" md5="756bfd16311e141a099cfe96db458d83"/>
3
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141 <param name="savelog" value="true"/>
0
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142 <expand macro="logfile-test"/>
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143 </test>
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144 </tests>
3
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145 <help><![CDATA[
0
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146
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147 @MOTHUR_OVERVIEW@
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148
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149 **Command Documentation**
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150
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151 The indicator_ command reads a shared_ or relabund_ file and a tree file, and outputs a .indicator.summary file and when a tree file is given a .indicator.tre file. The summary file lists the indicator value for each OTU for each node. The new tree contains labels at each internal node. The label is the node number so you can relate the tree to the summary file.
e66e20795ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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152
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153 .. _shared: https://www.mothur.org/wiki/Shared_file
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154 .. _relabund: https://www.mothur.org/wiki/Get.relabund
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155 .. _indicator: https://www.mothur.org/wiki/Indicator
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156
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157 v.1.22.0: Updated to Mothur 1.33
3
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158
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159 ]]></help>
6
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160 <expand macro="citations">
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161 <citation type="doi">10.1890/0012-9615(1997)067[0345:SAAIST]2.0.CO;2</citation>
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162 <expand macro="citations-ecology"/>
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163 </expand>
0
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164 </tool>