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comparison get.groups.xml @ 2:1715be05e718 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
author iuc
date Tue, 20 Mar 2018 22:15:38 -0400
parents e2b43f377f7d
children
comparison
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1:1ce4fb8667ea 2:1715be05e718
5 </macros> 5 </macros>
6 <expand macro="requirements"/> 6 <expand macro="requirements"/>
7 <expand macro="stdio"/> 7 <expand macro="stdio"/>
8 <expand macro="version_command"/> 8 <expand macro="version_command"/>
9 <command><![CDATA[ 9 <command><![CDATA[
10 @SHELL_OPTIONS@ 10 @SHELL_OPTIONS@
11 11
12 ## create symlinks to input datasets 12 ## create symlinks to input datasets
13 ln -s "$group_in" group_in.dat && 13 ln -s '$group_in' group_in.dat &&
14 ln -s "$fasta_in" fasta_in.dat && 14 ln -s '$fasta_in' fasta_in.dat &&
15 ln -s "$name_in" name_in.dat && 15 ln -s '$name_in' name_in.dat &&
16 ln -s "$list_in" list_in.dat && 16 ln -s '$list_in' list_in.dat &&
17 ln -s "$shared_in" shared_in.dat && 17 ln -s '$shared_in' shared_in.dat &&
18 ln -s "$taxonomy_in" taxonomy_in.dat && 18 ln -s '$taxonomy_in' taxonomy_in.dat &&
19 ln -s "$design_in" design_in.dat && 19 ln -s '$design_in' design_in.dat &&
20 #if $groupnames.source == 'accnos': 20 ln -s '$column_in' column_in.dat &&
21 ln -s "$groupnames.accnos" groupnames.accnos.dat && 21 ln -s '$phylip_in' phylip_in.dat &&
22 #if $groupnames.source == 'accnos':
23 ln -s '$groupnames.accnos' groupnames.accnos.dat &&
24 #end if
25
26 echo 'get.groups(
27 #if $group_in.is_of_type("mothur.groups"):
28 group=group_in.dat
29 #else
30 count=group_in.dat
31 #end if
32 #if $groupnames.source == 'groups':
33 #if $groupnames.groups:
34 ,groups=${ str($groupnames.groups).replace(",","-") }
22 #end if 35 #end if
23 36 #else
24 echo 'get.groups( 37 ,accnos=groupnames.accnos.dat
25 #if $group_in.is_of_type("mothur.groups"): 38 #end if
26 group=group_in.dat 39 #if $fasta_in:
27 #else 40 ,fasta=fasta_in.dat
28 count=group_in.dat 41 #end if
29 #end if 42 #if $name_in:
30 #if $groupnames.source == 'groups': 43 ,name=name_in.dat
31 #if $groupnames.groups: 44 #end if
32 ,groups=${ str($groupnames.groups).replace(",","-") } 45 #if $list_in:
33 #end if 46 ,list=list_in.dat
34 #else 47 #end if
35 ,accnos=groupnames.accnos.dat 48 #if $shared_in:
36 #end if 49 ,shared=shared_in.dat
37 #if $fasta_in: 50 #end if
38 ,fasta=fasta_in.dat 51 #if $taxonomy_in:
39 #end if 52 ,taxonomy=taxonomy_in.dat
40 #if $name_in: 53 #end if
41 ,name=name_in.dat 54 #if $design_in:
42 #end if 55 ,design=design_in.dat
43 #if $list_in: 56 #end if
44 ,list=list_in.dat 57 #if $column_in:
45 #end if 58 ,column=column_in.dat
46 #if $shared_in: 59 #end if
47 ,shared=shared_in.dat 60 #if $phylip_in:
48 #end if 61 ,phylip=phylip_in.dat
49 #if $taxonomy_in: 62 #end if
50 ,taxonomy=taxonomy_in.dat 63 )'
51 #end if 64 | sed 's/ //g' ## mothur trips over whitespace
52 #if $design_in: 65 | mothur
53 ,design=design_in.dat 66 | tee mothur.out.log
54 #end if
55 )'
56 | sed 's/ //g' ## mothur trips over whitespace
57 | mothur
58 | tee mothur.out.log
59 ]]></command> 67 ]]></command>
60 <inputs> 68 <inputs>
61 <param name="group_in" type="data" format="mothur.groups,mothur.count_table" label="group or count_table file"/> 69 <param name="group_in" type="data" format="mothur.groups,mothur.count_table" optional="true" label="group or count_table file"/>
70 <param name="shared_in" type="data" format="mothur.shared" optional="true" label="shared - OTU Shared"/>
71 <param name="design_in" type="data" format="tabular" optional="true" label="design - assign groups to new grouping"
72 help="design has 2 columns: group(col 1) and grouping(col 2) (separated by a TAB character) use make.design"/>
62 <conditional name="groupnames"> 73 <conditional name="groupnames">
63 <param name="source" type="select" label="Select Group Names from"> 74 <param name="source" type="select" label="Select Group Names from">
64 <option value="groups">A List of Group Names</option> 75 <option value="groups">A List of Group Names</option>
65 <option value="accnos">A History Group Name Accnos Dataset</option> 76 <option value="accnos">A History Group Name Accnos Dataset</option>
66 </param> 77 </param>
76 </when> 87 </when>
77 </conditional> 88 </conditional>
78 <param name="fasta_in" type="data" format="fasta,mothur.align" optional="true" label="fasta - Fasta Sequences"/> 89 <param name="fasta_in" type="data" format="fasta,mothur.align" optional="true" label="fasta - Fasta Sequences"/>
79 <param name="name_in" type="data" format="mothur.names" optional="true" label="name - Sequences Name reference"/> 90 <param name="name_in" type="data" format="mothur.names" optional="true" label="name - Sequences Name reference"/>
80 <param name="list_in" type="data" format="mothur.list" optional="true" label="list - OTU List"/> 91 <param name="list_in" type="data" format="mothur.list" optional="true" label="list - OTU List"/>
81 <param name="shared_in" type="data" format="mothur.shared" optional="true" label="shared - OTU Shared"/>
82 <param name="taxonomy_in" type="data" format="mothur.seq.taxonomy" optional="true" label="taxonomy - Taxonomy"/> 92 <param name="taxonomy_in" type="data" format="mothur.seq.taxonomy" optional="true" label="taxonomy - Taxonomy"/>
83 <param name="design_in" type="data" format="tabular" optional="true" label="design - assign groups to new grouping" help="design has 2 columns: group(col 1) and grouping(col 2) (separated by a TAB character) use make.design"/> 93 <param name="phylip_in" type="data" format="mothur.lower.dist,mothur.square.dist" optional="true" label="phylip - Distance Matrix you would like to select distances from"
94 help="must be a phylip-formatted distance matrix"/>
95 <param name="column_in" type="data" format="mothur.pair.dist" optional="true" label="column - Distance Matrix you would like to select distances from"
96 help="must be a column-formatted distance matrix"/>
97 <expand macro="param-savelog"/>
84 </inputs> 98 </inputs>
85 <outputs> 99 <outputs>
86 <expand macro="logfile-output"/> 100 <expand macro="logfile-output"/>
87 <data name="group_out" format="mothur.groups" from_work_dir="group_in*.pick.*" label="${tool.name} on ${on_string}: pick.groups"> 101 <data name="group_out" format="mothur.groups" from_work_dir="group_in*.pick.*" label="${tool.name} on ${on_string}: pick.groups">
88 <filter>group_in.ext == "mothur.groups"</filter> 102 <filter>group_in.ext == "mothur.groups"</filter>
108 <filter>taxonomy_in</filter> 122 <filter>taxonomy_in</filter>
109 </data> 123 </data>
110 <data name="design_out" format="mothur.design" from_work_dir="design_in*.pick.*" label="${tool.name} on ${on_string}: pick.design"> 124 <data name="design_out" format="mothur.design" from_work_dir="design_in*.pick.*" label="${tool.name} on ${on_string}: pick.design">
111 <filter>design_in</filter> 125 <filter>design_in</filter>
112 </data> 126 </data>
127 <data name="phylip_out" format_source="phylip_in" from_work_dir="phylip_in*.pick.*" label="${tool.name} on ${on_string}: pick.phylip">
128 <filter>phylip_in</filter>
129 </data>
130 <data name="column_out" format="mothur.pair.dist" from_work_dir="column_in*.pick.*" label="${tool.name} on ${on_string}: pick.column">
131 <filter>column_in</filter>
132 </data>
113 </outputs> 133 </outputs>
114 <tests> 134 <tests>
115 <test><!-- test with group file --> 135 <test><!-- test with group file -->
116 <param name="group_in" value="amazon.groups" ftype="mothur.groups"/> 136 <param name="group_in" value="amazon.groups" ftype="mothur.groups"/>
117 <param name="source" value="groups"/> 137 <param name="source" value="groups"/>
118 <param name="groups" value="forest,pasture"/> 138 <param name="groups" value="forest,pasture"/>
119 <output name="group_out" md5="fb60628ae445e7b06f9833f632b2cd0c" ftype="mothur.groups"/> 139 <output name="group_out" md5="fb60628ae445e7b06f9833f632b2cd0c" ftype="mothur.groups"/>
140 <param name="savelog" value="true"/>
120 <expand macro="logfile-test"/> 141 <expand macro="logfile-test"/>
121 </test> 142 </test>
122 <test><!-- test with accnos file --> 143 <test><!-- test with accnos file -->
123 <param name="group_in" value="amazon.groups" ftype="mothur.groups"/> 144 <param name="group_in" value="amazon.groups" ftype="mothur.groups"/>
124 <param name="source" value="accnos"/> 145 <param name="source" value="accnos"/>
125 <param name="accnos" value="amazon.groupaccnos" ftype="mothur.accnos"/> 146 <param name="accnos" value="amazon.groupaccnos" ftype="mothur.accnos"/>
126 <output name="group_out" md5="fb60628ae445e7b06f9833f632b2cd0c" ftype="mothur.groups"/> 147 <output name="group_out" md5="fb60628ae445e7b06f9833f632b2cd0c" ftype="mothur.groups"/>
148 <param name="savelog" value="true"/>
127 <expand macro="logfile-test"/> 149 <expand macro="logfile-test"/>
128 </test> 150 </test>
129 <test><!-- test with accnos file and most extra files--> 151 <test><!-- test with accnos file and most extra files-->
130 <param name="group_in" value="amazon.groups" ftype="mothur.groups"/> 152 <param name="group_in" value="amazon.groups" ftype="mothur.groups"/>
131 <param name="source" value="accnos"/> 153 <param name="source" value="accnos"/>
141 <element name="0.38" md5="49878dfbe53d5144f3bd885c629de822" ftype="mothur.list"/> 163 <element name="0.38" md5="49878dfbe53d5144f3bd885c629de822" ftype="mothur.list"/>
142 </output_collection> 164 </output_collection>
143 <output_collection name="sharedfiles" count="36"> 165 <output_collection name="sharedfiles" count="36">
144 <element name="0.38" md5="3c78742e0a480ca3353f9b591fc9bf36" ftype="mothur.shared"/> 166 <element name="0.38" md5="3c78742e0a480ca3353f9b591fc9bf36" ftype="mothur.shared"/>
145 </output_collection> 167 </output_collection>
168 <param name="savelog" value="true"/>
169 <expand macro="logfile-test"/>
170 </test>
171 <test><!-- test with distance matrix -->
172 <param name="group_in" value="amazon_withgroups.count_table" ftype="mothur.count_table"/>
173 <param name="source" value="accnos"/>
174 <param name="accnos" value="amazon.groupaccnos" ftype="mothur.accnos"/>
175 <param name="column_in" value="amazon.pair.dist" ftype="mothur.pair.dist"/>
176 <param name="phylip_in" value="amazon.dist" ftype="mothur.square.dist"/>
177 <output name="column_out" ftype="mothur.pair.dist">
178 <assert_contents>
179 <expand macro="test-column-format"/>
180 <has_text text="U68589"/>
181 </assert_contents>
182 </output>
183 <output name="phylip_out" ftype="mothur.square.dist">
184 <assert_contents>
185 <expand macro="test-dist-format"/>
186 <has_text text="U68589"/>
187 </assert_contents>
188 </output>
189 <param name="savelog" value="true"/>
146 <expand macro="logfile-test"/> 190 <expand macro="logfile-test"/>
147 </test> 191 </test>
148 </tests> 192 </tests>
149 <help> 193 <help><![CDATA[
150 <![CDATA[
151 194
152 @MOTHUR_OVERVIEW@ 195 @MOTHUR_OVERVIEW@
153 196
154 197
155 **Command Documentation** 198 **Command Documentation**
160 .. _group: https://www.mothur.org/wiki/Group_file 203 .. _group: https://www.mothur.org/wiki/Group_file
161 .. _list: https://www.mothur.org/wiki/List_file 204 .. _list: https://www.mothur.org/wiki/List_file
162 .. _taxonomy: https://www.mothur.org/wiki/Taxonomy_outline 205 .. _taxonomy: https://www.mothur.org/wiki/Taxonomy_outline
163 .. _get.groups: https://www.mothur.org/wiki/Get.groups 206 .. _get.groups: https://www.mothur.org/wiki/Get.groups
164 207
165 ]]> 208 ]]></help>
166 </help>
167 <expand macro="citations"/> 209 <expand macro="citations"/>
168 </tool> 210 </tool>