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comparison get.otus.xml @ 0:a1aea42f0f8e 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 05:54:16 -0400
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-1:000000000000 0:a1aea42f0f8e
1 <tool profile="16.07" id="mothur_get_otus" name="Get.otus" version="@WRAPPER_VERSION@.0">
2 <description>Get otus containing sequences from specified 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 "$otu" otu.dat &&
14 ln -s "$group_in" group_in.dat &&
15 #if $groupnames.source == 'accnos':
16 ln -s "$groupnames.accnos_in" groupnames.accnos_in.dat &&
17 #end if
18
19 echo 'get.otus(
20 list=otu.dat,
21 group=group_in.dat
22 #if $label:
23 ,label=${ str($label).replace(",","-") }
24 #end if
25 #if $groupnames.source == 'groups':
26 ,groups=${ str($groupnames.groups).replace(",","-") }
27 #else
28 ,accnos=groupnames.accnos_in.dat
29 #end if
30 )'
31 | sed 's/ //g' ## mothur trips over whitespace
32 | mothur
33 | tee mothur.out.log
34 ]]></command>
35 <inputs>
36 <param name="otu" type="data" format="mothur.list" label="list - OTU List"/>
37 <param name="label" type="select" optional="true" multiple="false" label="label - OTU Label" help="select exactly one label. If none selected, the first label in your file will be used">
38 <expand macro="labeloptions"/>
39 </param>
40 <param name="group_in" type="data" format="mothur.groups" label="group - Groups"/>
41 <conditional name="groupnames">
42 <param name="source" type="select" label="Select Group Names from">
43 <option value="groups">A List of Group Names</option>
44 <option value="accnos">A History Group Name Accnos Dataset</option>
45 </param>
46 <when value="groups">
47 <param name="groups" type="select" multiple="true" force_select="true" label="groups - Pick groups to include">
48 <help>At least one group must be selected</help>
49 <options>
50 <filter type="data_meta" ref="group_in" key="groups"/>
51 </options>
52 </param>
53 </when>
54 <when value="accnos">
55 <param name="accnos_in" type="data" format="mothur.accnos" optional="true" label="accnos - Group Names from your history"/>
56 </when>
57 </conditional>
58 </inputs>
59 <outputs>
60 <expand macro="logfile-output"/>
61 <data name="group_out" format="mothur.groups" from_work_dir="group_in*.pick.*" label="${tool.name} on ${on_string}: pick.groups"/>
62 <data name="list_out" format="mothur.list" from_work_dir="otu*.pick.*" label="${tool.name} on ${on_string}: pick.list"/>
63 </outputs>
64 <tests>
65 <test><!-- test with group file -->
66 <param name="otu" value="amazon.an.list" ftype="mothur.list"/>
67 <param name="group_in" value="amazon.groups" ftype="mothur.groups"/>
68 <param name="source" value="groups"/>
69 <param name="groups" value="forest,pasture"/>
70 <output name="list_out" md5="a771e0879bbb84e2764db70f66ae1277" ftype="mothur.list"/>
71 <output name="group_out" md5="954ef97da9dcd152b912bcda19a6f96c" ftype="mothur.groups"/>
72 <expand macro="logfile-test"/>
73 </test>
74 <test><!-- test with accnos file and label select -->
75 <param name="otu" value="amazon.an.list" ftype="mothur.list"/>
76 <param name="label" value="0.03"/>
77 <param name="group_in" value="amazon.groups" ftype="mothur.groups"/>
78 <param name="source" value="accnos"/>
79 <param name="accnos_in" value="amazon.groupaccnos" ftype="mothur.accnos"/>
80 <output name="list_out" md5="2069739b1f7bbbe47cc237833450e57c" ftype="mothur.list"/>
81 <output name="group_out" md5="09ffabe975dc49f1bf251ea60c569526" ftype="mothur.groups"/>
82 <expand macro="logfile-test"/>
83 </test>
84 </tests>
85 <help>
86 <![CDATA[
87
88 @MOTHUR_OVERVIEW@
89
90 **Command Documentation**
91
92 The get.otus_ command selects otus from a list_ containing sequences from a specific group or set of groups.
93
94 .. _list: https://www.mothur.org/wiki/List_file
95 .. _get.otus: https://www.mothur.org/wiki/Get.otus
96
97 v.1.20.0: Updated to Mothur 1.33
98 ]]>
99 </help>
100 <expand macro="citations"/>
101 </tool>