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comparison get.groups.xml @ 0:33c6376bd824 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
author iuc
date Fri, 24 Jun 2016 16:31:53 -0400
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children 1e6a7d59a872
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-1:000000000000 0:33c6376bd824
1 <tool profile="16.07" id="mothur_get_groups" name="Get.groups" version="@WRAPPER_VERSION@.0">
2 <description>Select groups</description>
3 <macros>
4 <import>macros.xml</import>
5 </macros>
6 <expand macro="requirements"/>
7 <expand macro="version_command"/>
8 <command detect_errors="aggressive"><![CDATA[
9 ## create symlinks to input datasets
10 ln -s "$group_in" group_in.dat &&
11 ln -s "$fasta_in" fasta_in.dat &&
12 ln -s "$name_in" name_in.dat &&
13 ln -s "$list_in" list_in.dat &&
14 ln -s "$shared_in" shared_in.dat &&
15 ln -s "$taxonomy_in" taxonomy_in.dat &&
16 ln -s "$design_in" design_in.dat &&
17 #if $groupnames.source == 'accnos':
18 ln -s "$groupnames.accnos" groupnames.accnos.dat &&
19 #end if
20
21 echo 'get.groups(
22 #if $group_in.is_of_type("mothur.groups"):
23 group=group_in.dat
24 #else
25 count=group_in.dat
26 #end if
27 #if $groupnames.source == 'groups':
28 #if $groupnames.groups:
29 ,groups=${ str($groupnames.groups).replace(",","-") }
30 #end if
31 #else
32 ,accnos=groupnames.accnos.dat
33 #end if
34 #if $fasta_in:
35 ,fasta=fasta_in.dat
36 #end if
37 #if $name_in:
38 ,name=name_in.dat
39 #end if
40 #if $list_in:
41 ,list=list_in.dat
42 #end if
43 #if $shared_in:
44 ,shared=shared_in.dat
45 #end if
46 #if $taxonomy_in:
47 ,taxonomy=taxonomy_in.dat
48 #end if
49 #if $design_in:
50 ,design=design_in.dat
51 #end if
52 )'
53 | sed 's/ //g' ## mothur trips over whitespace
54 | mothur
55 ]]></command>
56 <inputs>
57 <param name="group_in" type="data" format="mothur.groups,mothur.count_table" label="group or count_table file"/>
58 <conditional name="groupnames">
59 <param name="source" type="select" label="Select Group Names from">
60 <option value="groups">A List of Group Names</option>
61 <option value="accnos">A History Group Name Accnos Dataset</option>
62 </param>
63 <when value="groups">
64 <param name="groups" type="select" multiple="true" label="groups - Pick groups to include">
65 <options>
66 <filter type="data_meta" ref="group_in" key="groups"/>
67 </options>
68 </param>
69 </when>
70 <when value="accnos">
71 <param name="accnos" type="data" format="mothur.accnos" label="accnos - Group Names from your history"/>
72 </when>
73 </conditional>
74 <param name="fasta_in" type="data" format="fasta,mothur.align" optional="true" label="fasta - Fasta Sequences"/>
75 <param name="name_in" type="data" format="mothur.names" optional="true" label="name - Sequences Name reference"/>
76 <param name="list_in" type="data" format="mothur.list" optional="true" label="list - OTU List"/>
77 <param name="shared_in" type="data" format="mothur.shared" optional="true" label="shared - OTU Shared"/>
78 <param name="taxonomy_in" type="data" format="mothur.seq.taxonomy" optional="true" label="taxonomy - Taxonomy"/>
79 <param name="design_in" type="data" format="tabular" optional="true" label="design - assign groups to new grouping" help="design has 2 columns: group(col 1) and grouping(col 2) (separated by a TAB character) use make.design"/>
80 </inputs>
81 <outputs>
82 <expand macro="logfile-output"/>
83 <data name="group_out" format="mothur.groups" from_work_dir="group_in*.pick.*" label="${tool.name} on ${on_string}: pick.groups"/>
84 <data name="fasta_out" format_source="fasta_in" from_work_dir="fasta_in*.pick.*" label="${tool.name} on ${on_string}: pick.fasta">
85 <filter>fasta_in</filter>
86 </data>
87 <data name="name_out" format="mothur.names" from_work_dir="name_in*.pick.*" label="${tool.name} on ${on_string}: pick.name">
88 <filter>name_in</filter>
89 </data>
90 <collection name="listfiles" type="list" label="${tool.name} on ${on_string}: pick.list">
91 <filter>list_in</filter>
92 <discover_datasets pattern="list_in.*?\.(?P&lt;designation&gt;.*)\.pick\.dat" format="mothur.list"/>
93 </collection>
94 <collection name="sharedfiles" type="list" label="${tool.name} on ${on_string}: pick.shared">
95 <filter>shared_in</filter>
96 <discover_datasets pattern="shared_in.*?\.(?P&lt;designation&gt;.*)\.pick\.dat" format="mothur.shared"/>
97 </collection>
98 <data name="taxonomy_out" format="mothur.seq.taxonomy" from_work_dir="taxonomy_in*.pick.*" label="${tool.name} on ${on_string}: pick.taxonomy">
99 <filter>taxonomy_in</filter>
100 </data>
101 <data name="design_out" format="mothur.design" from_work_dir="design_in*.pick.*" label="${tool.name} on ${on_string}: pick.design">
102 <filter>design_in</filter>
103 </data>
104 </outputs>
105 <tests>
106 <test><!-- test with group file -->
107 <param name="group_in" value="amazon.groups" ftype="mothur.groups"/>
108 <param name="source" value="groups"/>
109 <param name="groups" value="forest,pasture"/>
110 <output name="group_out" md5="fb60628ae445e7b06f9833f632b2cd0c" ftype="mothur.groups"/>
111 <expand macro="logfile-test"/>
112 </test>
113 <test><!-- test with accnos file -->
114 <param name="group_in" value="amazon.groups" ftype="mothur.groups"/>
115 <param name="source" value="accnos"/>
116 <param name="accnos" value="amazon.groupaccnos" ftype="mothur.accnos"/>
117 <output name="group_out" md5="fb60628ae445e7b06f9833f632b2cd0c" ftype="mothur.groups"/>
118 <expand macro="logfile-test"/>
119 </test>
120 <test><!-- test with accnos file and most extra files-->
121 <param name="group_in" value="amazon.groups" ftype="mothur.groups"/>
122 <param name="source" value="accnos"/>
123 <param name="accnos" value="amazon.groupaccnos" ftype="mothur.accnos"/>
124 <param name="fasta_in" value="amazon.fasta" ftype="fasta"/>
125 <param name="name_in" value="amazon1.names" ftype="mothur.names"/>
126 <param name="list_in" value="amazon.an.list" ftype="mothur.list"/>
127 <param name="shared_in" value="amazon.an.shared" ftype="mothur.shared"/>
128 <output name="group_out" md5="fb60628ae445e7b06f9833f632b2cd0c" ftype="mothur.groups"/>
129 <output name="fasta_out" md5="0bc9320647234e8367c3b1b654f9302d" ftype="fasta"/>
130 <output name="name_out" md5="1f0324a017e1b71e6ed0af257b0013f3" ftype="mothur.names"/>
131 <output_collection name="listfiles" count="36">
132 <element name="0.38" md5="49878dfbe53d5144f3bd885c629de822" ftype="mothur.list"/>
133 </output_collection>
134 <output_collection name="sharedfiles" count="36">
135 <element name="0.38" md5="3c78742e0a480ca3353f9b591fc9bf36" ftype="mothur.shared"/>
136 </output_collection>
137 <expand macro="logfile-test"/>
138 </test>
139 </tests>
140 <help>
141 <![CDATA[
142
143 @MOTHUR_OVERVIEW@
144
145
146 **Command Documenation**
147
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_.
149
150 .. _name: http://www.mothur.org/wiki/Name_file
151 .. _group: http://www.mothur.org/wiki/Group_file
152 .. _list: http://www.mothur.org/wiki/List_file
153 .. _taxonomy: http://www.mothur.org/wiki/Taxonomy_outline
154 .. _get.groups: http://www.mothur.org/wiki/Get.groups
155
156 ]]>
157 </help>
158 <expand macro="citations"/>
159 </tool>