Mercurial > repos > iuc > mothur_remove_groups

comparison remove.groups.xml @ 0:e7a69b6134c5 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 05:14:41 -0400
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children 75433aae83fb
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-1:000000000000 0:e7a69b6134c5
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="stdio"/>
8 <expand macro="version_command"/>
9 <command><![CDATA[
10 @SHELL_OPTIONS@
11
12 ## create symlinks to input datasets
13 #if $groupnames.source == "other":
14 ln -s "$groupnames.group_in" groupnames_group_in.dat &&
15 ln -s "$groupnames.fasta_in" groupnames_fasta_in.dat &&
16 ln -s "$groupnames.name_in" groupnames_name_in.dat &&
17 ln -s "$groupnames.list_in" groupnames_list_in.dat &&
18 ln -s "$groupnames.taxonomy_in" groupnames_taxonomy_in.dat &&
19 #else
20 ln -s "$groupnames.shared_in" groupnames_shared_in.dat &&
21 #end if
22
23 echo 'remove.groups(
24 #if $groupnames.source == "other":
25 #if $group_in.is_of_type("mothur.groups"):
26 group=groupnames_group_in.dat
27 #else
28 count=groupnames_group_in.dat
29 #end if
30 #if $groupnames.fasta_in:
31 ,fasta=groupnames_fasta_in.dat
32 #end if
33 #if $groupnames.name_in:
34 ,name=groupnames_name_in.dat
35 #end if
36 #if $groupnames.list_in:
37 ,list=groupnames_list_in.dat
38 #end if
39 #if $groupnames.taxonomy_in:
40 ,taxonomy=groupnames_taxonomy_in.dat
41 #end if
42 #else
43 shared=groupnames_shared_in.dat
44 #end if
45 ,groups=${ str($groupnames.groups).replace(",","-") }
46 )'
47 | sed 's/ //g' ## mothur trips over whitespace
48 | mothur
49 | tee mothur.out.log
50 ]]></command>
51 <inputs>
52 <conditional name="groupnames">
53 <param name="source" type="select" label="Select Input Type">
54 <option value="shared">shared file</option>
55 <option value="other">fasta, name, taxonomy, or list with a group file or count table</option>
56 </param>
57 <when value="other">
58 <param name="group_in" type="data" format="mothur.groups,mothur.count_table" label="group or count table - Groups"/>
59 <param name="groups" type="select" label="groups - Pick groups to remove" multiple="true" optional="false">
60 <options>
61 <filter type="data_meta" ref="group_in" key="groups"/>
62 </options>
63 </param>
64 <param name="fasta_in" type="data" format="mothur.align,fasta" optional="true" label="fasta - Fasta Sequences"/>
65 <param name="name_in" type="data" format="mothur.names" optional="true" label="name - Sequences Name reference"/>
66 <param name="list_in" type="data" format="mothur.list" optional="true" label="list - OTU List"/>
67 <param name="taxonomy_in" type="data" format="mothur.seq.taxonomy" optional="true" label="taxonomy - Taxonomy"/>
68 </when>
69 <when value="shared">
70 <param name="shared_in" type="data" format="mothur.shared" optional="true" label="shared - OTU Shared"/>
71 <param name="groups" type="select" label="groups - Pick groups to remove" multiple="true" optional="false">
72 <options>
73 <filter type="data_meta" ref="shared_in" key="groups"/>
74 </options>
75 </param>
76 </when>
77 </conditional>
78 </inputs>
79 <outputs>
80 <expand macro="logfile-output"/>
81 <data name="fasta_out" format_source="fasta_in" from_work_dir="groupnames_fasta_in*.pick.*" label="${tool.name} on ${on_string}: pick.fasta">
82 <filter>groupnames['source'] == 'other' and groupnames['fasta_in']</filter>
83 </data>
84 <data name="group_out" format="mothur.groups" from_work_dir="groupnames_group_in*.pick.*" label="${tool.name} on ${on_string}: pick.groups">
85 <filter>groupnames['source'] == 'other' and groupnames['group_in'].ext == 'mothur.groups'</filter>
86 </data>
87 <data name="count_out" format="mothur.count_table" from_work_dir="groupnames_group_in*.pick.*" label="${tool.name} on ${on_string}: pick.count_table">
88 <filter>groupnames['source'] == 'other' and groupnames['group_in'].ext == 'mothur.count_table'</filter>
89 </data>
90 <data name="name_out" format="mothur.names" from_work_dir="groupnames_name_in*.pick.*" label="${tool.name} on ${on_string}: pick.names">
91 <filter>groupnames['source'] == 'other' and groupnames['name_in']</filter>
92 </data>
93 <data name="taxonomy_out" format="mothur.seq.taxonomy" from_work_dir="groupnames_taxonomy_in*.pick.*" label="${tool.name} on ${on_string}: pick.taxonomy">
94 <filter>groupnames['source'] == 'other' and groupnames['taxonomy_in']</filter>
95 </data>
96 <collection name="list_out" type="list" label="${tool.name} on ${on_string}: pick.list">
97 <filter>groupnames['source'] == 'other' and groupnames['list_in']</filter>
98 <discover_datasets pattern=".*?\.(?P&lt;designation&gt;.*)\.pick\.dat" format="mothur.list"/>
99 </collection>
100 <collection name="shared_out" type="list" label="${tool.name} on ${on_string}: pick.shared">
101 <filter>groupnames['source'] == 'shared'</filter>
102 <discover_datasets pattern=".*?\.(?P&lt;designation&gt;.*)\.pick\.dat" format="mothur.shared"/>
103 </collection>
104 </outputs>
105 <tests>
106 <test><!-- test with shared file -->
107 <param name="source" value="shared"/>
108 <param name="shared_in" value="amazon.an.shared"/>
109 <param name="groups" value="pasture"/>
110 <output_collection name="shared_out" count="36">
111 <element name="0.26" md5="c5043237225f0292ce1bfbd2766b96ea" ftype="mothur.shared"/>
112 </output_collection>
113 <expand macro="logfile-test"/>
114 </test>
115 <test><!-- test with group file and fasta/names/list/taxonomy files -->
116 <param name="source" value="other"/>
117 <param name="group_in" value="amazon.groups" ftype="mothur.groups"/>
118 <param name="fasta_in" value="amazon.fasta" ftype="fasta"/>
119 <param name="name_in" value="amazon.names" ftype="mothur.names"/>
120 <param name="list_in" value="amazon.an.list" ftype="mothur.list"/>
121 <param name="taxonomy_in" value="amazon.wang.wang.taxonomy" ftype="mothur.seq.taxonomy"/>
122 <param name="groups" value="pasture"/>
123 <output name="fasta_out" md5="f0e662d1d82e96b4977864925493dbf5" ftype="fasta"/>
124 <output name="taxonomy_out" md5="8fcaadcb5ad40873e270ad7e2cebe7fa" ftype="mothur.seq.taxonomy"/>
125 <output name="group_out" md5="6d689ead98f3eb1af41f1a78386d0b50" ftype="mothur.groups"/>
126 <output name="name_out" md5="55dbcadbb414d95bae8a282a93c10e63" ftype="mothur.names"/>
127 <output_collection name="list_out" count="36">
128 <element name="0.26" md5="71282909924de5f43452f1a5dbf623e8" ftype="mothur.list"/>
129 </output_collection>
130 <expand macro="logfile-test"/>
131 </test>
132 </tests>
133 <help><![CDATA[
134
135 @MOTHUR_OVERVIEW@
136
137 **Command Documentation**
138
139 The remove.groups_ command removes sequences from a specific group or set of groups from the following file types: fasta, name_, group_, list_, taxonomy_.
140
141 .. _name: https://www.mothur.org/wiki/Name_file
142 .. _group: https://www.mothur.org/wiki/Group_file
143 .. _list: https://www.mothur.org/wiki/List_file
144 .. _taxonomy: https://www.mothur.org/wiki/Taxonomy_outline
145 .. _remove.groups: https://www.mothur.org/wiki/Remove.groups
146
147 ]]>
148 </help>
149 <expand macro="citations"/>
150 </tool>