Mercurial > repos > iuc > mothur_indicator

annotate indicator.xml @ 13:543a589ceb67 draft default tip

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit dfdd4c590370ecb3a9806314d43eb5668e36a01a"
author iuc
date Thu, 21 Jan 2021 20:38:33 +0000
parents df705078eb4e
children
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10ae17108e85 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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1 <tool profile="16.07" id="mothur_indicator" name="Indicator" version="@WRAPPER_VERSION@.0">
10ae17108e85 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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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[
4
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10 @SHELL_OPTIONS@
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11
4
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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
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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(",","-") },
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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
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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">
3
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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."/>
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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">
3
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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>
6
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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>
6
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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>
6
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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"/>
10ae17108e85 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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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"/>
6
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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"/>
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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"/>
6
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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>
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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
1
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149 **Command Documentation**
0
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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.
10ae17108e85 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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152
1
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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
0
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156
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157 v.1.22.0: Updated to Mothur 1.33
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158
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159 ]]></help>
9
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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>
df705078eb4e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 7f7605c2c8d8e92f3369dfdc290e5d8d06fa409a
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162 <expand macro="citations-ecology"/>
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163 </expand>
0
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164 </tool>