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comparison get.sharedseqs.xml @ 0:d20133cb8909 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 16:39:36 -0400
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children e4e0bfb92a94
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-1:000000000000 0:d20133cb8909
1 <tool profile="16.07" id="mothur_get_sharedseqs" name="Get.sharedseqs" version="@WRAPPER_VERSION@.0">
2 <description>Get shared sequences at each distance from list and group</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 "$infile.otu" infile_otu.dat &&
11 #if $infile.intype == "in_listgroup":
12 ln -s "$infile.group" infile.group.dat &&
13 ln -s "$infile.fasta" infile_fasta.dat &&
14 #end if
15
16 echo 'get.sharedseqs(
17 #if $infile.intype == "in_listgroup":
18 list=infile_otu.dat
19 ,group=infile.group.dat
20 #if $infile.fasta:
21 ,fasta=infile_fasta.dat
22 #end if
23 #else
24 shared=infile_otu.dat
25 #end if
26 #if $infile.label:
27 ,label=${ str($infile.label).replace(",","-") }
28 #end if
29 #if $infile.seqsfrom.selection == "unique" and $infile.seqsfrom.groups:
30 ,uniquegroups=${ str($infile.seqsfrom.groups).replace(",","-") }
31 #end if
32 #if $infile.seqsfrom.selection == "shared" and $infile.seqsfrom.groups:
33 ,sharedgroups=${ str($infile.seqsfrom.groups).replace(",","-") }
34 #end if
35 #if $output:
36 ,output=$output
37 #end if
38 )'
39 | sed 's/ //g' ## mothur trips over whitespace
40 | mothur
41 ]]></command>
42 <inputs>
43 <conditional name="infile">
44 <param name="intype" type="select" label="Will you be supplying a shared file or a list and group file?" help="">
45 <option value="in_shared">Shared file</option>
46 <option value="in_listgroup">OTU list and group file</option>
47 </param>
48 <when value="in_shared">
49 <param name="otu" type="data" format="mothur.shared" label="list - OTU List or shared file"/>
50 <param name="label" type="select" optional="true" label="label - Select OTU Labels to include" multiple="true" help="By default all are included if no selection is made.">
51 <options>
52 <filter type="data_meta" ref="otu" key="labels"/>
53 </options>
54 </param>
55 <conditional name="seqsfrom">
56 <param name="selection" type="select" label="Select Groups" help="">
57 <option value="all" selected="true">None (use all groups)</option>
58 <option value="unique">OTUs that contain ONLY sequences from the selected groups</option>
59 <option value="shared">OTUs that contain sequences from the selected groups</option>
60 </param>
61 <when value="unique">
62 <param name="groups" type="select" multiple="true" label="unique - Group to analyze">
63 <options>
64 <filter type="data_meta" ref="otu" key="groups"/>
65 </options>
66 </param>
67 </when>
68 <when value="shared">
69 <param name="groups" type="select" multiple="true" label="shared - Groups to analyze">
70 <options>
71 <filter type="data_meta" ref="otu" key="groups"/>
72 </options>
73 </param>
74 </when>
75 <when value="all"/>
76 </conditional>
77 </when>
78 <when value="in_listgroup">
79 <param name="otu" type="data" format="mothur.list" label="list - OTU List or shared file"/>
80 <param name="label" type="select" optional="true" multiple="true" label="label - Select OTU Labels to include" help="By default all are included if no selection is made">
81 <options>
82 <filter type="data_meta" ref="otu" key="labels"/>
83 </options>
84 </param>
85 <param name="group" type="data" format="mothur.groups" optional="true" label="group - not required if using a shared file"/>
86 <param name="fasta" type="data" format="fasta" optional="true" label="fasta - Dataset" help="will output a fasta file for each distance level containing only the sequences that are in OTUs shared by the groups specified"/>
87 <conditional name="seqsfrom">
88 <param name="selection" type="select" label="Select Groups" help="">
89 <option value="all" selected="true">None (use all groups)</option>
90 <option value="unique">OTUs that contain ONLY sequences from the selected groups</option>
91 <option value="shared">OTUs that contain sequences from the selected groups</option>
92 </param>
93 <when value="unique">
94 <param name="groups" type="select" multiple="true" label="unique - Group to analyze">
95 <options>
96 <filter type="data_meta" ref="group" key="groups"/>
97 </options>
98 </param>
99 </when>
100 <when value="shared">
101 <param name="groups" type="select" multiple="true" label="shared - Groups to analyze">
102 <options>
103 <filter type="data_meta" ref="group" key="groups"/>
104 </options>
105 </param>
106 </when>
107 <when value="all"/>
108 </conditional>
109 </when>
110 </conditional>
111 <param name="output" type="select" label="output - select the output format" help="accnos can be used with get.seqs, list.seqs and remove.seqs">
112 <option value="" selected="true">default: (name group bin_number)</option>
113 <option value="accnos">accnos (name)</option>
114 </param>
115 </inputs>
116 <outputs>
117 <expand macro="logfile-output"/>
118 <collection name="sharedseqs" type="list" label="${tool.name} on ${on_string}: shared.seqs">
119 <discover_datasets pattern=".*?\.(?P&lt;designation&gt;.*)\.shared\.seqs" format="tabular"/>
120 <filter>output != 'accnos'</filter>
121 </collection>
122 <collection name="sharedaccnos" type="list" label="${tool.name} on ${on_string}: shared.accnos">
123 <discover_datasets pattern=".*?\.(?P&lt;designation&gt;.*)\.accnos" format="mothur.accnos"/>
124 <filter>output == 'accnos'</filter>
125 </collection>
126 <collection name="sharedfastas" type="list" label="${tool.name} on ${on_string}: shared.fastas">
127 <discover_datasets pattern=".*?\.(?P&lt;designation&gt;.*)\.shared\.fasta" format="fasta"/>
128 <filter>infile['fasta']</filter>
129 </collection>
130 </outputs>
131 <tests>
132 <test><!-- test with shared file -->
133 <param name="intype" value="in_shared"/>
134 <param name="otu" value="amazon.an.shared" ftype="mothur.shared"/>
135 <param name="selection" value="shared"/>
136 <output_collection name="sharedseqs" count="35">
137 <element name="0.41.unique.forest-pasture" md5="e07fe8acfa12d6f61a9efee88d91be54" ftype="tabular"/>
138 </output_collection>
139 <expand macro="logfile-test"/>
140 </test>
141 <test><!-- test with list and group file -->
142 <param name="intype" value="in_listgroup"/>
143 <param name="otu" value="amazon.an.list" ftype="mothur.list"/>
144 <param name="group" value="amazon.groups" ftype="mothur.groups"/>
145 <output_collection name="sharedseqs" count="35">
146 <element name="0.41.unique.forest-pasture" md5="ceb32c3dc2c99055efdaa6ef6aaed7f0" ftype="tabular"/>
147 </output_collection>
148 <expand macro="logfile-test"/>
149 </test>
150 <test><!-- test with shared seqs and subset of labels -->
151 <param name="intype" value="in_shared"/>
152 <param name="otu" value="amazon.an.shared" ftype="mothur.shared"/>
153 <param name="selection" value="shared"/>
154 <param name="groups" value="forest,pasture"/>
155 <param name="label" value="0.03,0.33,0.41"/>
156 <output_collection name="sharedseqs" count="3">
157 <element name="0.41.forest-pasture" md5="e07fe8acfa12d6f61a9efee88d91be54" ftype="tabular"/>
158 </output_collection>
159 <expand macro="logfile-test"/>
160 </test>
161 <test><!-- test with unique seqs and subset of groups -->
162 <param name="intype" value="in_shared"/>
163 <param name="otu" value="amazon.an.shared" ftype="mothur.shared"/>
164 <param name="selection" value="unique"/>
165 <param name="groups" value="pasture"/>
166 <output_collection name="sharedseqs" count="34">
167 <element name="0.41.unique.pasture" md5="f4735f56d96d13cd603ca0b11c4bc231" ftype="tabular"/>
168 </output_collection>
169 <expand macro="logfile-test"/>
170 </test>
171 <test><!-- test with accnos output -->
172 <param name="intype" value="in_shared"/>
173 <param name="otu" value="amazon.an.shared" ftype="mothur.shared"/>
174 <param name="output" value="accnos"/>
175 <output_collection name="sharedaccnos" count="35">
176 <element name="0.41.unique.forest-pasture" md5="0e0dcf8a91c03e1cc6adbf2593addf20" ftype="mothur.accnos"/>
177 </output_collection>
178 <expand macro="logfile-test"/>
179 </test>
180 <test><!-- test with fasta input and output -->
181 <param name="intype" value="in_listgroup"/>
182 <param name="otu" value="amazon.an.list" ftype="mothur.list"/>
183 <param name="group" value="amazon.groups" ftype="mothur.groups"/>
184 <param name="fasta" value="amazon.fasta" ftype="fasta"/>
185 <output_collection name="sharedseqs" count="35">
186 <element name="0.41.unique.forest-pasture" md5="ceb32c3dc2c99055efdaa6ef6aaed7f0" ftype="tabular"/>
187 </output_collection>
188 <output_collection name="sharedfastas" count="35">
189 <element name="0.41.unique.forest-pasture" md5="fd4265d7c139d2d3acf8e19e6337ee28" ftype="fasta"/>
190 </output_collection>
191 <expand macro="logfile-test"/>
192 </test>
193 </tests>
194 <help>
195 <![CDATA[
196
197 @MOTHUR_OVERVIEW@
198
199 **Command Documenation**
200
201 The get.sharedseqs_ command takes a list and group file and outputs a .shared.seqs file for each distance. This is useful for those cases where you might be interested in identifying sequences that are either unique or shared by specific groups, which you could then classify.
202
203 .. _get.sharedseqs: http://www.mothur.org/wiki/Get.sharedseqs
204
205 v1.21.0: Updated to Mothur 1.33, added shared file option
206 ]]>
207 </help>
208 <expand macro="citations"/>
209 </tool>