Mercurial > repos > iuc > mothur_get_groups

comparison get.groups.xml @ 1:1e6a7d59a872 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 18:13:49 -0400
parents 33c6376bd824
children 378f8103cf1b
comparison
equal deleted inserted replaced
0:33c6376bd824 1:1e6a7d59a872
2 <description>Select groups</description> 2 <description>Select groups</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 "$group_in" group_in.dat && 13 ln -s "$group_in" group_in.dat &&
11 ln -s "$fasta_in" fasta_in.dat && 14 ln -s "$fasta_in" fasta_in.dat &&
12 ln -s "$name_in" name_in.dat && 15 ln -s "$name_in" name_in.dat &&
13 ln -s "$list_in" list_in.dat && 16 ln -s "$list_in" list_in.dat &&
50 ,design=design_in.dat 53 ,design=design_in.dat
51 #end if 54 #end if
52 )' 55 )'
53 | sed 's/ //g' ## mothur trips over whitespace 56 | sed 's/ //g' ## mothur trips over whitespace
54 | mothur 57 | mothur
58 | tee mothur.out.log
55 ]]></command> 59 ]]></command>
56 <inputs> 60 <inputs>
57 <param name="group_in" type="data" format="mothur.groups,mothur.count_table" label="group or count_table file"/> 61 <param name="group_in" type="data" format="mothur.groups,mothur.count_table" label="group or count_table file"/>
58 <conditional name="groupnames"> 62 <conditional name="groupnames">
59 <param name="source" type="select" label="Select Group Names from"> 63 <param name="source" type="select" label="Select Group Names from">
78 <param name="taxonomy_in" type="data" format="mothur.seq.taxonomy" optional="true" label="taxonomy - Taxonomy"/> 82 <param name="taxonomy_in" type="data" format="mothur.seq.taxonomy" optional="true" label="taxonomy - Taxonomy"/>
79 <param name="design_in" type="data" format="tabular" optional="true" label="design - assign groups to new grouping" help="design has 2 columns: group(col 1) and grouping(col 2) (separated by a TAB character) use make.design"/> 83 <param name="design_in" type="data" format="tabular" optional="true" label="design - assign groups to new grouping" help="design has 2 columns: group(col 1) and grouping(col 2) (separated by a TAB character) use make.design"/>
80 </inputs> 84 </inputs>
81 <outputs> 85 <outputs>
82 <expand macro="logfile-output"/> 86 <expand macro="logfile-output"/>
83 <data name="group_out" format="mothur.groups" from_work_dir="group_in*.pick.*" label="${tool.name} on ${on_string}: pick.groups"/> 87 <data name="group_out" format="mothur.groups" from_work_dir="group_in*.pick.*" label="${tool.name} on ${on_string}: pick.groups">
88 <filter>group_in.ext == "mothur.groups"</filter>
89 </data>
90 <data name="count_out" format="mothur.count_table" from_work_dir="group_in*.pick.*" label="${tool.name} on ${on_string}: pick.count_table">
91 <filter>group_in.ext == "mothur.count_table"</filter>
92 </data>
84 <data name="fasta_out" format_source="fasta_in" from_work_dir="fasta_in*.pick.*" label="${tool.name} on ${on_string}: pick.fasta"> 93 <data name="fasta_out" format_source="fasta_in" from_work_dir="fasta_in*.pick.*" label="${tool.name} on ${on_string}: pick.fasta">
85 <filter>fasta_in</filter> 94 <filter>fasta_in</filter>
86 </data> 95 </data>
87 <data name="name_out" format="mothur.names" from_work_dir="name_in*.pick.*" label="${tool.name} on ${on_string}: pick.name"> 96 <data name="name_out" format="mothur.names" from_work_dir="name_in*.pick.*" label="${tool.name} on ${on_string}: pick.name">
88 <filter>name_in</filter> 97 <filter>name_in</filter>
141 <![CDATA[ 150 <![CDATA[
142 151
143 @MOTHUR_OVERVIEW@ 152 @MOTHUR_OVERVIEW@
144 153
145 154
146 **Command Documenation** 155 **Command Documentation**
147 156
148 The get.groups_ command selects sequences from a specific group or set of groups from the following file types: fasta, fasta, name_, group_, list_, taxonomy_. 157 The get.groups_ command selects sequences from a specific group or set of groups from the following file types: fasta, fasta, name_, group_, list_, taxonomy_.
149 158
150 .. _name: http://www.mothur.org/wiki/Name_file 159 .. _name: https://www.mothur.org/wiki/Name_file
151 .. _group: http://www.mothur.org/wiki/Group_file 160 .. _group: https://www.mothur.org/wiki/Group_file
152 .. _list: http://www.mothur.org/wiki/List_file 161 .. _list: https://www.mothur.org/wiki/List_file
153 .. _taxonomy: http://www.mothur.org/wiki/Taxonomy_outline 162 .. _taxonomy: https://www.mothur.org/wiki/Taxonomy_outline
154 .. _get.groups: http://www.mothur.org/wiki/Get.groups 163 .. _get.groups: https://www.mothur.org/wiki/Get.groups
155 164
156 ]]> 165 ]]>
157 </help> 166 </help>
158 <expand macro="citations"/> 167 <expand macro="citations"/>
159 </tool> 168 </tool>