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comparison count.groups.xml @ 0:2d98db6098be 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 16:28:23 -0400
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children 13a947a26f7a
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-1:000000000000 0:2d98db6098be
1 <tool profile="16.07" id="mothur_count_groups" name="Count.groups" version="@WRAPPER_VERSION@.0">
2 <description>counts the number of sequences represented by a specific group or set of 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" group.dat &&
11 #if $groupnames.source == "accnos":
12 ln -s "$groupnames.accnos" groupnames.accnos.dat &&
13 #end if
14
15 echo 'count.groups(
16 #if $group.is_of_type("mothur.shared"):
17 shared=group.dat
18 #elif $group.is_of_type("mothur.count_table"):
19 count=group.dat
20 #else:
21 group=group.dat
22 #end if
23 #if $groupnames.source == "groups":
24 #if $groupnames.groups:
25 ,groups=$groupnames.groups
26 #end if
27 #elif $groupnames.source == "accnos":
28 #if $groupnames.accnos:
29 ,accnos=groupnames.accnos.dat
30 #end if
31 #end if
32 )'
33 | sed 's/ //g' ## mothur trips over whitespace
34 | mothur &&
35
36 ## parse relevant tool output from logfile to file
37 cat mothur.*.logfile
38 | head -n-7
39 | sed '1,29d'
40 > "$grp_count"
41 ]]></command>
42 <inputs>
43 <param name="group" type="data" format="mothur.groups,mothur.shared,mothur.count_table" label="group, shared, or count_table - Group file for sequence count"/>
44 <conditional name="groupnames">
45 <param name="source" type="select" label="Filter group names">
46 <option value="none">Report on All Groups</option>
47 <option value="groups">A List of Group Names</option>
48 <option value="accnos">A History Group Name Accnos Dataset</option>
49 </param>
50 <when value="none"/>
51 <when value="groups">
52 <param name="groups" type="select" label="groups - Pick groups to include" multiple="true">
53 <help>All groups displayed if none are selected.</help>
54 <options>
55 <filter type="data_meta" ref="group" key="groups"/>
56 </options>
57 </param>
58 </when>
59 <when value="accnos">
60 <param name="accnos" type="data" format="mothur.accnos" optional="true" label="accnos - Group Names from your history"/>
61 </when>
62 </conditional>
63 </inputs>
64 <outputs>
65 <expand macro="logfile-output"/>
66 <data name="grp_count" format="tabular" label="${tool.name} on ${on_string}: group.count"/>
67 <data name="summary" format="tabular" from_work_dir="group*.summary" label="${tool.name} on ${on_string}: summary"/>
68 </outputs>
69 <tests>
70 <test>
71 <param name="group" value="amazon.an.shared" ftype="mothur.shared"/>
72 <param name="groups" value="forest,pasture"/>
73 <output name="summary" md5="58508af98ed02e00a707f0f7812c2359"/>
74 <output name="grp_count" md5="34ea2b8be163cf6c9c68d624d92fc73d"/>
75 <expand macro="logfile-test"/>
76 </test>
77 </tests>
78 <help>
79 <![CDATA[
80
81 @MOTHUR_OVERVIEW@
82
83 **Command Documenation**
84
85 The count.groups_ command counts sequences from a specific group or set of groups from a group_ or shared_ file.
86
87 .. _shared: http://www.mothur.org/wiki/Shared_file
88 .. _group: http://www.mothur.org/wiki/Group_file
89 .. _count.groups: http://www.mothur.org/wiki/Count.groups
90 ]]>
91 </help>
92 <expand macro="citations"/>
93 </tool>