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comparison remove.groups.xml @ 0:e320a3719431 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 16:46:44 -0400
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children c32dad34e5ec
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-1:000000000000 0:e320a3719431
1 <tool profile="16.07" id="mothur_remove_groups" name="Remove.groups" version="@WRAPPER_VERSION@.0">
2 <description>Remove groups from groups,fasta,names,list,taxonomy</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 #if $groupnames.source == "other":
11 ln -s "$groupnames.group_in" groupnames_group_in.dat &&
12 ln -s "$groupnames.fasta_in" groupnames_fasta_in.dat &&
13 ln -s "$groupnames.name_in" groupnames_name_in.dat &&
14 ln -s "$groupnames.list_in" groupnames_list_in.dat &&
15 ln -s "$groupnames.taxonomy_in" groupnames_taxonomy_in.dat &&
16 #else
17 ln -s "$groupnames.shared_in" groupnames_shared_in.dat &&
18 #end if
19
20 echo 'remove.groups(
21 #if $groupnames.source == "other":
22 #if $group_in.is_of_type("mothur.groups"):
23 group=groupnames_group_in.dat
24 #else
25 count=groupnames_group_in.dat
26 #end if
27 #if $groupnames.fasta_in:
28 ,fasta=groupnames_fasta_in.dat
29 #end if
30 #if $groupnames.name_in:
31 ,name=groupnames_name_in.dat
32 #end if
33 #if $groupnames.list_in:
34 ,list=groupnames_list_in.dat
35 #end if
36 #if $groupnames.taxonomy_in:
37 ,taxonomy=groupnames_taxonomy_in.dat
38 #end if
39 #else
40 shared=groupnames_shared_in.dat
41 #end if
42 ,groups=${ str($groupnames.groups).replace(",","-") }
43 )'
44 | sed 's/ //g' ## mothur trips over whitespace
45 | mothur
46 ]]></command>
47 <inputs>
48 <conditional name="groupnames">
49 <param name="source" type="select" label="Select Input Type">
50 <option value="shared">shared file</option>
51 <option value="other">fasta, name, taxonomy, or list with a group file or count table</option>
52 </param>
53 <when value="other">
54 <param name="group_in" type="data" format="mothur.groups,mothur.count_table" label="group or count table - Groups"/>
55 <param name="groups" type="select" label="groups - Pick groups to remove" multiple="true" optional="false">
56 <options>
57 <filter type="data_meta" ref="group_in" key="groups"/>
58 </options>
59 </param>
60 <param name="fasta_in" type="data" format="fasta" optional="true" label="fasta - Fasta Sequences"/>
61 <param name="name_in" type="data" format="mothur.names" optional="true" label="name - Sequences Name reference"/>
62 <param name="list_in" type="data" format="mothur.list" optional="true" label="list - OTU List"/>
63 <param name="taxonomy_in" type="data" format="mothur.seq.taxonomy" optional="true" label="taxonomy - Taxonomy"/>
64 </when>
65 <when value="shared">
66 <param name="shared_in" type="data" format="mothur.shared" optional="true" label="shared - OTU Shared"/>
67 <param name="groups" type="select" label="groups - Pick groups to remove" multiple="true" optional="false">
68 <options>
69 <filter type="data_meta" ref="shared_in" key="groups"/>
70 </options>
71 </param>
72 </when>
73 </conditional>
74 </inputs>
75 <outputs>
76 <expand macro="logfile-output"/>
77 <data name="fasta_out" format_source="fasta_in" from_work_dir="groupnames_fasta_in*.pick.*" label="${tool.name} on ${on_string}: pick.fasta">
78 <filter>groupname['source'] == 'other' and fasta_in</filter>
79 </data>
80 <data name="group_out" format="mothur.groups" from_work_dir="groupnames_group_in*.pick.*" label="${tool.name} on ${on_string}: pick.groups">
81 <filter>groupname['source'] == 'other' and group_in</filter>
82 </data>
83 <data name="name_out" format="mothur.names" from_work_dir="groupnames_name_in*.pick.*" label="${tool.name} on ${on_string}: pick.names">
84 <filter>groupname['source'] == 'other' and name_in</filter>
85 </data>
86 <data name="taxonomy_out" format="mothur.seq.taxonomy" from_work_dir="groupnames_taxonomy_in*.pick.*" label="${tool.name} on ${on_string}: pick.taxonomy">
87 <filter>groupname['source'] == 'other' and taxonomy_in</filter>
88 </data>
89 <collection name="list_out" type="list" label="${tool.name} on ${on_string}: pick.list">
90 <filter>groupname['source'] == 'other' and list_in</filter>
91 <discover_datasets pattern=".*?\.(?P&lt;designation&gt;.*)\.pick\.dat" format="mothur.list"/>
92 </collection>
93 <collection name="shared_out" type="list" label="${tool.name} on ${on_string}: pick.shared">
94 <filter>groupname['source'] == 'shared'</filter>
95 <discover_datasets pattern=".*?\.(?P&lt;designation&gt;.*)\.pick\.dat" format="mothur.shared"/>
96 </collection>
97 </outputs>
98 <tests>
99 <test><!-- test with shared file -->
100 <param name="source" value="shared"/>
101 <param name="shared_in" value="amazon.an.shared"/>
102 <param name="groups" value="pasture"/>
103 <output_collection name="shared_out" count="36">
104 <element name="0.26" md5="c5043237225f0292ce1bfbd2766b96ea" ftype="mothur.shared"/>
105 </output_collection>
106 <expand macro="logfile-test"/>
107 </test>
108 <test><!-- test with group file and fasta/names/list/taxonomy files -->
109 <param name="source" value="other"/>
110 <param name="group_in" value="amazon.groups" ftype="mothur.groups"/>
111 <param name="fasta_in" value="amazon.fasta" ftype="fasta"/>
112 <param name="name_in" value="amazon.names" ftype="mothur.names"/>
113 <param name="list_in" value="amazon.an.list" ftype="mothur.list"/>
114 <param name="taxonomy_in" value="amazon.wang.wang.taxonomy" ftype="mothur.seq.taxonomy"/>
115 <param name="groups" value="pasture"/>
116 <output name="fasta_out" md5="f0e662d1d82e96b4977864925493dbf5" ftype="fasta"/>
117 <output name="taxonomy_out" md5="8fcaadcb5ad40873e270ad7e2cebe7fa" ftype="mothur.seq.taxonomy"/>
118 <output name="group_out" md5="6d689ead98f3eb1af41f1a78386d0b50" ftype="mothur.groups"/>
119 <output name="name_out" md5="55dbcadbb414d95bae8a282a93c10e63" ftype="mothur.names"/>
120 <output_collection name="list_out" count="36">
121 <element name="0.26" md5="71282909924de5f43452f1a5dbf623e8" ftype="mothur.list"/>
122 </output_collection>
123 <expand macro="logfile-test"/>
124 </test>
125 </tests>
126 <help><![CDATA[
127
128 @MOTHUR_OVERVIEW@
129
130 **Command Documenation**
131
132 The remove.groups_ command removes sequences from a specific group or set of groups from the following file types: fasta, name_, group_, list_, taxonomy_.
133
134 .. _name: http://www.mothur.org/wiki/Name_file
135 .. _group: http://www.mothur.org/wiki/Group_file
136 .. _list: http://www.mothur.org/wiki/List_file
137 .. _taxonomy: http://www.mothur.org/wiki/Taxonomy_outline
138 .. _remove.groups: http://www.mothur.org/wiki/Remove.groups
139
140 ]]>
141 </help>
142 <expand macro="citations"/>
143 </tool>