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comparison merge.groups.xml @ 1:8e771931d548 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit ea40e3d84e7850eb4226d6c85f709dcad18d4ba9
author iuc
date Thu, 18 May 2017 18:32:00 -0400
parents ed5f1b592d84
children 8ae8f906cfe9
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0:ed5f1b592d84 1:8e771931d548
2 <description>Merge groups in a shared file</description> 2 <description>Merge groups in a shared file</description>
3 <macros> 3 <macros>
4 <import>macros.xml</import> 4 <import>macros.xml</import>
5 </macros> 5 </macros>
6 <expand macro="requirements"/> 6 <expand macro="requirements"/>
7 <expand macro="stdio"/>
7 <expand macro="version_command"/> 8 <expand macro="version_command"/>
8 <command detect_errors="aggressive"><![CDATA[ 9 <command><![CDATA[
10 @SHELL_OPTIONS@
11
9 ## create symlinks to input datasets 12 ## create symlinks to input datasets
10 ln -s "$otu" otu.dat && 13 ln -s "$otu" otu.dat &&
11 ln -s "$group" group.dat && 14 ln -s "$group" group.dat &&
12 #if $design.source == "hist": 15 #if $design.source == "hist":
13 ln -s "$design.design_dataset" design_dataset.dat && 16 ln -s "$design.design_dataset" design_dataset.dat &&
34 ,label=${ str($label).replace(",","-") } 37 ,label=${ str($label).replace(",","-") }
35 #end if 38 #end if
36 )' 39 )'
37 | sed 's/ //g' ## mothur trips over whitespace 40 | sed 's/ //g' ## mothur trips over whitespace
38 | mothur 41 | mothur
42 | tee mothur.out.log
39 ]]></command> 43 ]]></command>
40 <configfiles> 44 <configfiles>
41 <configfile name="generated_design"><![CDATA[ 45 <configfile name="generated_design"><![CDATA[
42 #if $design.source == 'build': 46 #if $design.source == 'build':
43 #for $grouping in $design.groupings: 47 #for $grouping in $design.groupings:
133 <help> 137 <help>
134 <![CDATA[ 138 <![CDATA[
135 139
136 @MOTHUR_OVERVIEW@ 140 @MOTHUR_OVERVIEW@
137 141
138 **Command Documenation** 142 **Command Documentation**
139 143
140 The merge.groups_ command reads a shared_ file and a design file and merges the groups in the shared file that are in the same grouping in the design file. 144 The merge.groups_ command reads a shared_ file and a design file and merges the groups in the shared file that are in the same grouping in the design file.
141 145
142 A design file partitions a list of names into groups. It is a tab-delimited file with 2 columns: name and group, e.g. : 146 A design file partitions a list of names into groups. It is a tab-delimited file with 2 columns: name and group, e.g. :
143 ======= ======= 147 ======= =======
148 cobra reptile 152 cobra reptile
149 ======= ======= 153 ======= =======
150 154
151 The Make_Design tool can construct a design file from a Mothur dataset that contains group names. 155 The Make_Design tool can construct a design file from a Mothur dataset that contains group names.
152 156
153 .. _shared: http://www.mothur.org/wiki/Shared_file 157 .. _shared: https://www.mothur.org/wiki/Shared_file
154 .. _merge.groups: http://www.mothur.org/wiki/Merge.groups 158 .. _merge.groups: https://www.mothur.org/wiki/Merge.groups
155 ]]> 159 ]]>
156 </help> 160 </help>
157 <expand macro="citations"/> 161 <expand macro="citations"/>
158 </tool> 162 </tool>