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comparison get.groups.xml @ 0:e2b43f377f7d draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
author iuc
date Fri, 19 May 2017 05:31:10 -0400
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children 1715be05e718
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-1:000000000000 0:e2b43f377f7d
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="stdio"/>
8 <expand macro="version_command"/>
9 <command><![CDATA[
10 @SHELL_OPTIONS@
11
12 ## create symlinks to input datasets
13 ln -s "$group_in" group_in.dat &&
14 ln -s "$fasta_in" fasta_in.dat &&
15 ln -s "$name_in" name_in.dat &&
16 ln -s "$list_in" list_in.dat &&
17 ln -s "$shared_in" shared_in.dat &&
18 ln -s "$taxonomy_in" taxonomy_in.dat &&
19 ln -s "$design_in" design_in.dat &&
20 #if $groupnames.source == 'accnos':
21 ln -s "$groupnames.accnos" groupnames.accnos.dat &&
22 #end if
23
24 echo 'get.groups(
25 #if $group_in.is_of_type("mothur.groups"):
26 group=group_in.dat
27 #else
28 count=group_in.dat
29 #end if
30 #if $groupnames.source == 'groups':
31 #if $groupnames.groups:
32 ,groups=${ str($groupnames.groups).replace(",","-") }
33 #end if
34 #else
35 ,accnos=groupnames.accnos.dat
36 #end if
37 #if $fasta_in:
38 ,fasta=fasta_in.dat
39 #end if
40 #if $name_in:
41 ,name=name_in.dat
42 #end if
43 #if $list_in:
44 ,list=list_in.dat
45 #end if
46 #if $shared_in:
47 ,shared=shared_in.dat
48 #end if
49 #if $taxonomy_in:
50 ,taxonomy=taxonomy_in.dat
51 #end if
52 #if $design_in:
53 ,design=design_in.dat
54 #end if
55 )'
56 | sed 's/ //g' ## mothur trips over whitespace
57 | mothur
58 | tee mothur.out.log
59 ]]></command>
60 <inputs>
61 <param name="group_in" type="data" format="mothur.groups,mothur.count_table" label="group or count_table file"/>
62 <conditional name="groupnames">
63 <param name="source" type="select" label="Select Group Names from">
64 <option value="groups">A List of Group Names</option>
65 <option value="accnos">A History Group Name Accnos Dataset</option>
66 </param>
67 <when value="groups">
68 <param name="groups" type="select" multiple="true" label="groups - Pick groups to include">
69 <options>
70 <filter type="data_meta" ref="group_in" key="groups"/>
71 </options>
72 </param>
73 </when>
74 <when value="accnos">
75 <param name="accnos" type="data" format="mothur.accnos" label="accnos - Group Names from your history"/>
76 </when>
77 </conditional>
78 <param name="fasta_in" type="data" format="fasta,mothur.align" optional="true" label="fasta - Fasta Sequences"/>
79 <param name="name_in" type="data" format="mothur.names" optional="true" label="name - Sequences Name reference"/>
80 <param name="list_in" type="data" format="mothur.list" optional="true" label="list - OTU List"/>
81 <param name="shared_in" type="data" format="mothur.shared" optional="true" label="shared - OTU Shared"/>
82 <param name="taxonomy_in" type="data" format="mothur.seq.taxonomy" optional="true" label="taxonomy - Taxonomy"/>
83 <param name="design_in" type="data" format="tabular" optional="true" label="design - assign groups to new grouping" help="design has 2 columns: group(col 1) and grouping(col 2) (separated by a TAB character) use make.design"/>
84 </inputs>
85 <outputs>
86 <expand macro="logfile-output"/>
87 <data name="group_out" format="mothur.groups" from_work_dir="group_in*.pick.*" label="${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 ${on_string}: pick.count_table">
91 <filter>group_in.ext == "mothur.count_table"</filter>
92 </data>
93 <data name="fasta_out" format_source="fasta_in" from_work_dir="fasta_in*.pick.*" label="${tool.name} on ${on_string}: pick.fasta">
94 <filter>fasta_in</filter>
95 </data>
96 <data name="name_out" format="mothur.names" from_work_dir="name_in*.pick.*" label="${tool.name} on ${on_string}: pick.name">
97 <filter>name_in</filter>
98 </data>
99 <collection name="listfiles" type="list" label="${tool.name} on ${on_string}: pick.list">
100 <filter>list_in</filter>
101 <discover_datasets pattern="list_in.*?\.(?P&lt;designation&gt;.*)\.pick\.dat" format="mothur.list"/>
102 </collection>
103 <collection name="sharedfiles" type="list" label="${tool.name} on ${on_string}: pick.shared">
104 <filter>shared_in</filter>
105 <discover_datasets pattern="shared_in.*?\.(?P&lt;designation&gt;.*)\.pick\.dat" format="mothur.shared"/>
106 </collection>
107 <data name="taxonomy_out" format="mothur.seq.taxonomy" from_work_dir="taxonomy_in*.pick.*" label="${tool.name} on ${on_string}: pick.taxonomy">
108 <filter>taxonomy_in</filter>
109 </data>
110 <data name="design_out" format="mothur.design" from_work_dir="design_in*.pick.*" label="${tool.name} on ${on_string}: pick.design">
111 <filter>design_in</filter>
112 </data>
113 </outputs>
114 <tests>
115 <test><!-- test with group file -->
116 <param name="group_in" value="amazon.groups" ftype="mothur.groups"/>
117 <param name="source" value="groups"/>
118 <param name="groups" value="forest,pasture"/>
119 <output name="group_out" md5="fb60628ae445e7b06f9833f632b2cd0c" ftype="mothur.groups"/>
120 <expand macro="logfile-test"/>
121 </test>
122 <test><!-- test with accnos file -->
123 <param name="group_in" value="amazon.groups" ftype="mothur.groups"/>
124 <param name="source" value="accnos"/>
125 <param name="accnos" value="amazon.groupaccnos" ftype="mothur.accnos"/>
126 <output name="group_out" md5="fb60628ae445e7b06f9833f632b2cd0c" ftype="mothur.groups"/>
127 <expand macro="logfile-test"/>
128 </test>
129 <test><!-- test with accnos file and most extra files-->
130 <param name="group_in" value="amazon.groups" ftype="mothur.groups"/>
131 <param name="source" value="accnos"/>
132 <param name="accnos" value="amazon.groupaccnos" ftype="mothur.accnos"/>
133 <param name="fasta_in" value="amazon.fasta" ftype="fasta"/>
134 <param name="name_in" value="amazon1.names" ftype="mothur.names"/>
135 <param name="list_in" value="amazon.an.list" ftype="mothur.list"/>
136 <param name="shared_in" value="amazon.an.shared" ftype="mothur.shared"/>
137 <output name="group_out" md5="fb60628ae445e7b06f9833f632b2cd0c" ftype="mothur.groups"/>
138 <output name="fasta_out" md5="0bc9320647234e8367c3b1b654f9302d" ftype="fasta"/>
139 <output name="name_out" md5="1f0324a017e1b71e6ed0af257b0013f3" ftype="mothur.names"/>
140 <output_collection name="listfiles" count="36">
141 <element name="0.38" md5="49878dfbe53d5144f3bd885c629de822" ftype="mothur.list"/>
142 </output_collection>
143 <output_collection name="sharedfiles" count="36">
144 <element name="0.38" md5="3c78742e0a480ca3353f9b591fc9bf36" ftype="mothur.shared"/>
145 </output_collection>
146 <expand macro="logfile-test"/>
147 </test>
148 </tests>
149 <help>
150 <![CDATA[
151
152 @MOTHUR_OVERVIEW@
153
154
155 **Command Documentation**
156
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_.
158
159 .. _name: https://www.mothur.org/wiki/Name_file
160 .. _group: https://www.mothur.org/wiki/Group_file
161 .. _list: https://www.mothur.org/wiki/List_file
162 .. _taxonomy: https://www.mothur.org/wiki/Taxonomy_outline
163 .. _get.groups: https://www.mothur.org/wiki/Get.groups
164
165 ]]>
166 </help>
167 <expand macro="citations"/>
168 </tool>