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comparison get.communitytype.xml @ 0:e86199dc2a7c 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 05:34:30 -0400
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children 92b64ed4e08b
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-1:000000000000 0:e86199dc2a7c
1 <tool profile="16.07" id="mothur_get_communitytype" name="Get.communitytype" version="@WRAPPER_VERSION@.0">
2 <description>description</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 ln -s '$otu' shared.dat &&
14
15 echo 'get.communitytype(
16 shared=shared.dat,
17 #if $label:
18 label=${ str($label).replace(",","-") },
19 #end if
20 #if $groups:
21 groups=${ str($groups).replace(",","-") },
22 #end if
23 method=$m.method,
24 #if $m.method == 'kmeans' or $m.method == 'pams':
25 calc=$m.calc,
26 iters=$m.iters,
27 #end if
28 #if int($subsample) == 0:
29 subsample=T,
30 #elif int($subsample) > 0:
31 subsample=$subsample,
32 #end if
33 minpartitions=$minpartitions,
34 maxpartitions=$maxpartitions,
35 optimizegap=$optimizegap,
36 processors='\${GALAXY_SLOTS:-8}'
37 )'
38 | sed 's/ //g' ## mothur trips over whitespace
39 | mothur
40 | tee mothur.out.log
41 ]]></command>
42 <inputs>
43 <param name="otu" type="data" format="mothur.shared" label="shared - Shared file"/>
44 <param name="label" type="select" label="label - OTU Labels" multiple="true" optional="true">
45 <expand macro="labeloptions"/>
46 </param>
47 <param name="groups" type="select" label="groups - Groups to consider" multiple="true" optional="true">
48 <options>
49 <filter type="data_meta" ref="otu" key="groups"/>
50 </options>
51 </param>
52 <conditional name="m">
53 <param name="method" type="select" label="method">
54 <option value="dmm" selected="true">dmm</option>
55 <option value="kmeans">k means</option>
56 <option value="pam">pam</option>
57 </param>
58 <when value="dmm"/>
59 <when value="kmeans">
60 <param name="calc" type="select" label="calc - Calculators (Uses defaults if none selected)">
61 <expand macro="calc-common"/>
62 <!-- set default option(s) -->
63 <option value="rjsd" selected="true">rjsd</option>
64 </param>
65 <param name="iters" type="integer" optional="true" value="" min="0" label="iters - number of iterations" help=""/>
66 </when>
67 <when value="pam">
68 <param name="calc" type="select" label="calc - Calculators (Uses defaults if none selected)">
69 <expand macro="calc-common"/>
70 <!-- set default option -->
71 <option value="rjsd" selected="true">rjsd</option>
72 </param>
73 <param name="iters" type="integer" optional="true" value="" min="0" label="iters - number of iterations" help=""/>
74 </when>
75 </conditional>
76 <param name="minpartitions" type="integer" value="5" min="0" label="minpartitions" help=""/>
77 <param name="maxpartitions" type="integer" value="10" min="0" label="minpartitions" help=""/>
78 <param name="optimizegap" type="integer" value="3" min="0" label="minpartitions" help=""/>
79 <param name="subsample" type="integer" value="-1" min="-1" label="subsample" help="Ignored if negative, when set to 0 it uses the size of your smallest group (subsample=T)"/>
80 </inputs>
81 <outputs>
82 <expand macro="logfile-output"/>
83 <data name="summary" format="tabular" from_work_dir="shared*.summary" label="${tool.name} on ${on_string}: summary">
84 <filter> m['method'] == 'dmm' </filter>
85 </data>
86 <data name="design" format="tabular" from_work_dir="shared*.design" label="${tool.name} on ${on_string}: design"/>
87 <data name="parameters" format="tabular" from_work_dir="shared*.parameters" label="${tool.name} on ${on_string}: parameters">
88 <filter> m['method'] == 'dmm' </filter>
89 </data>
90 <data name="fit" format="tabular" from_work_dir="shared*.fit" label="${tool.name} on ${on_string}: fit"/>
91 <collection name="relabund" type="list" label="${tool.name} on ${on_string}: relabund">
92 <discover_datasets pattern="shared\.(?P&lt;designation&gt;.*)\.relabund" format="mothur.relabund"/>
93 </collection>
94 <collection name="posterior" type="list" label="${tool.name} on ${on_string}: posterior">
95 <discover_datasets pattern="shared\.(?P&lt;designation&gt;.*)\.posterior" format="tabular"/>
96 </collection>
97 </outputs>
98 <tests>
99 <test><!-- test with defaults -->
100 <param name="otu" value="final.tx.1.subsample.1.pick.shared"/>
101 <output name="summary" md5="3e81c01da5f6c86b69516e204ad51610" ftype="tabular"/>
102 <output name="design" md5="df00e5ea21154669bbb85efa20a9661d" ftype="tabular"/>
103 <output name="parameters" md5="ef972523811b80b12d4343f0df472214" ftype="tabular"/>
104 <output name="fit" ftype="tabular">
105 <assert_contents>
106 <has_line_matching expression="K\tNLE\tlogDet\tBIC\tAIC\tLaplace"/>
107 </assert_contents>
108 </output>
109 <output_collection name="relabund" count="5">
110 <element name="1.dmm.1.mix" md5="9c338b1fb5aea4baae2dbf242331d27c" ftype="mothur.relabund"/>
111 </output_collection>
112 <output_collection name="posterior" count="5">
113 <element name="1.dmm.1.mix" md5="fae04096d53d6980d8eb712e6ec8b0d2" ftype="tabular"/>
114 </output_collection>
115 <expand macro="logfile-test"/>
116 </test>
117 <test><!-- test with all settings -->
118 <param name="otu" value="final.tx.1.subsample.1.pick.shared" ftype="mothur.shared"/>
119 <param name="label" value="1"/>
120 <param name="groups" value="F003D000,F003D002,F003D006,F003D008,F003D142"/>
121 <param name="method" value="kmeans"/>
122 <param name="iters" value="100"/>
123 <param name="calc" value="manhattan"/>
124 <param name="maxpartitions" value="4"/>
125 <param name="subsample" value="0"/>
126 <output name="design" ftype="tabular">
127 <assert_contents>
128 <has_text text="Partition_"/>
129 <has_text text="F003D000"/>
130 <has_text text="F003D142"/>
131 </assert_contents>
132 </output>
133 <output name="fit" ftype="tabular">
134 <assert_contents>
135 <has_line_matching expression="K\tCH\tF003D000\tF003D002\tF003D006\tF003D008\tF003D142"/>
136 </assert_contents>
137 </output>
138 <output_collection name="relabund" count="4">
139 <element name="1.kmeans.1.mix" md5="514780678b8d9413566df3355d427e27" ftype="mothur.relabund"/>
140 </output_collection>
141 <output_collection name="posterior" count="4">
142 <element name="1.kmeans.1.mix" md5="43f4dfc2bcd1cf20db4f89ee90b6041c" ftype="tabular"/>
143 </output_collection>
144 <expand macro="logfile-test"/>
145 </test>
146 </tests>
147 <help><![CDATA[
148 @MOTHUR_OVERVIEW@
149
150
151 **Command Documentation**
152
153
154 .. _get.communitytype: https://www.mothur.org/wiki/Get.communitytype
155 ]]></help>
156 <expand macro="citations"/>
157 </tool>