Mercurial > repos > iuc > mothur_venn
comparison venn.xml @ 0:af481cd93ede draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
author | iuc |
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date | Fri, 19 May 2017 05:57:45 -0400 |
parents | |
children | 8bfc093999ff |
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-1:000000000000 | 0:af481cd93ede |
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1 <tool profile="16.07" id="mothur_venn" name="Venn" version="@WRAPPER_VERSION@.0"> | |
2 <description>Generate Venn diagrams for groups </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 "$input.otu" input_otu.dat && | |
14 | |
15 echo 'venn( | |
16 #if $input.source == "shared": | |
17 shared=input_otu.dat, | |
18 nseqs=$nseqs, | |
19 permute=$permute, | |
20 #if $input.groups: | |
21 groups=${ str($input.groups).replace(",","-") }, | |
22 #end if | |
23 #elif $input.source == "similarity": | |
24 list=input_otu.dat, | |
25 abund=$input.abund, | |
26 #end if | |
27 #if $input.label: | |
28 label=${ str($input.label).replace(",","-") }, | |
29 #end if | |
30 #if $input.calc: | |
31 calc=${ str($input.calc).replace(",","-") }, | |
32 #end if | |
33 fontsize=$fontsize, | |
34 sharedotus=$sharedotus | |
35 )' | |
36 | sed 's/ //g' ## mothur trips over whitespace | |
37 | mothur | |
38 | tee mothur.out.log | |
39 ]]></command> | |
40 <inputs> | |
41 <conditional name="input"> | |
42 <param name="source" type="select" label="Generate Heatmap for"> | |
43 <option value="shared">OTU Shared</option> | |
44 <option value="similarity">OTU list</option> | |
45 </param> | |
46 <when value="shared"> | |
47 <param name="otu" type="data" format="mothur.shared" label="shared - OTU Shared"/> | |
48 <param name="calc" type="select" multiple="true" label="calc - Calculators (Uses defaults if none selected)"> | |
49 <option value="sharedsobs">Shared Sobs</option> | |
50 <option value="sharedchao">Shared Chao</option> | |
51 <option value="sharedace">Shared Ace</option> | |
52 </param> | |
53 <param name="label" type="select" multiple="true" label="label - OTU Labels"> | |
54 <expand macro="labeloptions"/> | |
55 </param> | |
56 <param name="groups" type="select" multiple="true" label="groups - Groups to consider"> | |
57 <options> | |
58 <filter type="data_meta" ref="otu" key="groups"/> | |
59 </options> | |
60 </param> | |
61 </when> | |
62 <when value="similarity"> | |
63 <param name="otu" type="data" format="mothur.list" label="list - OTU List"/> | |
64 <param name="calc" type="select" multiple="true" label="calc - Calculators (Uses defaults if none selected)"> | |
65 <option value="sobs">Sobs</option> | |
66 <option value="chao">Chao</option> | |
67 <option value="ace">Ace</option> | |
68 </param> | |
69 <param name="abund" type="integer" value="10" min="5" label="abund - Abundance when using the ace calculator ( >= 5 )"/> | |
70 <param name="label" type="select" multiple="true" label="label - OTU Labels"> | |
71 <expand macro="labeloptions"/> | |
72 </param> | |
73 </when> | |
74 </conditional> | |
75 <param name="nseqs" type="boolean" falsevalue="false" truevalue="true" checked="false" label="nseqs - Output the number of sequences represented by the otus in the picture"/> | |
76 <param name="permute" type="select" label="permute - Create pictures with all possible 4-way permutations of groups"> | |
77 <option value="1">1</option> | |
78 <option value="2">2</option> | |
79 <option value="3">3</option> | |
80 <option value="4" selected="true">4</option> | |
81 <option value="true">true</option> | |
82 </param> | |
83 <param name="fontsize" type="integer" value="24" label="fontsize - Fontsize (default is 24)"/> | |
84 <param name="sharedotus" type="boolean" falsevalue="false" truevalue="true" checked="true" label="sharedotus - This parameter can be used with the sharedsobs calculator to get the names of the OTUs in each section of the venn diagram. Default=T"/> | |
85 </inputs> | |
86 <outputs> | |
87 <collection name="sharedotus_out" type="list" label="${tool.name} on ${on_string}: sharedotus"> | |
88 <filter>sharedotus</filter> | |
89 <discover_datasets pattern=".*?\.(?P<designation>.*)\.sharedotus" format="tabular"/> | |
90 </collection> | |
91 <collection name="svgs_out" type="list" label="${tool.name} on ${on_string}: svg"> | |
92 <discover_datasets pattern=".*?\.(?P<designation>.*)\.svg"/> | |
93 </collection> | |
94 <expand macro="logfile-output"/> | |
95 </outputs> | |
96 <tests> | |
97 <test><!-- test with shared file --> | |
98 <param name="source" value="shared"/> | |
99 <param name="otu" value="amazon.an.shared" ftype="mothur.shared"/> | |
100 <param name="calc" value="sharedsobs,sharedchao"/> | |
101 <param name="groups" value="forest,pasture"/> | |
102 <output_collection name="sharedotus_out" count="35"> | |
103 <element name="0.05.sharedsobs.forest-pasture" md5="7513c9df64477a08b69f0d4665011e80" ftype="tabular"/> | |
104 </output_collection> | |
105 <output_collection name="svgs_out" count="72"> | |
106 <element name="0.05.sharedsobs.forest-pasture" md5="b3c6eba426e2e2b9002699e5e62cb71d"/> | |
107 </output_collection> | |
108 <expand macro="logfile-test"/> | |
109 </test> | |
110 <test><!-- test with list file --> | |
111 <param name="source" value="similarity"/> | |
112 <param name="otu" value="amazon.an.list" ftype="mothur.list"/> | |
113 <param name="calc" value="sobs,chao,ace"/> | |
114 <param name="groups" value="forest,pasture"/> | |
115 <output_collection name="svgs_out" count="108"> | |
116 <element name=".0.45.ace" md5="d69778f507939bc2f5d2bbc3a0088f21"/> | |
117 </output_collection> | |
118 <expand macro="logfile-test"/> | |
119 </test> | |
120 </tests> | |
121 <help> | |
122 <![CDATA[ | |
123 | |
124 @MOTHUR_OVERVIEW@ | |
125 | |
126 **Command Documentation** | |
127 | |
128 The venn_ command generates Venn diagrams to compare the richness shared among 2, 3, or 4 groups. For calc parameter choices see: https://www.mothur.org/wiki/Calculators | |
129 | |
130 .. _venn: https://www.mothur.org/wiki/Venn | |
131 | |
132 ]]> | |
133 </help> | |
134 <expand macro="citations"/> | |
135 </tool> |