Mercurial > repos > iuc > mothur_heatmap_bin

comparison heatmap.bin.xml @ 2:ac2fa6a167ad 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 22:22:20 -0400
parents b0718c06e329
children
comparison
equal deleted inserted replaced
1:b08d51984da6 2:ac2fa6a167ad
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 "$input.otu" input_otu.dat && 13 ln -s '$input.otu' input_otu.dat &&
14 14
15 echo 'heatmap.bin( 15 echo 'heatmap.bin(
16 #if $input.otu.is_of_type("mothur.rabund"): 16 #if $input.otu.is_of_type("mothur.rabund"):
17 rabund=input_otu.dat, 17 rabund=input_otu.dat,
18 #elif $input.otu.is_of_type("mothur.sabund"): 18 #elif $input.otu.is_of_type("mothur.sabund"):
19 sabund=input_otu.dat, 19 sabund=input_otu.dat,
20 #elif $input.otu.is_of_type("mothur.list"): 20 #elif $input.otu.is_of_type("mothur.list"):
21 list=input_otu.dat, 21 list=input_otu.dat,
22 #elif $input.otu.is_of_type("mothur.relabund"): 22 #elif $input.otu.is_of_type("mothur.relabund"):
23 relabund=input_otu.dat, 23 relabund=input_otu.dat,
24 #elif $input.otu.is_of_type("mothur.shared"): 24 #elif $input.otu.is_of_type("mothur.shared"):
25 shared=input_otu.dat, 25 shared=input_otu.dat,
26 #end if 26 #end if
27 #if $input.has_groups == 'yes' and $input.groups: 27 #if $input.has_groups == 'yes' and $input.groups:
28 groups=${ str($input.groups).replace(",","-") }, 28 groups=${ str($input.groups).replace(",","-") },
29 #end if 29 #end if
30 #if $input.label: 30 #if $input.label:
31 label=${ str($input.label).replace(",","-") }, 31 label=${ str($input.label).replace(",","-") },
32 #end if 32 #end if
33 scale=$scale, 33 scale=$scale,
34 sorted=$sorted, 34 sorted=$sorted,
35 numotu=$numotu, 35 numotu=$numotu,
36 fontsize=$fontsize 36 fontsize=$fontsize
37 )' 37 )'
38 | sed 's/ //g' ## mothur trips over whitespace 38 | sed 's/ //g' ## mothur trips over whitespace
39 | mothur 39 | mothur
40 | tee mothur.out.log 40 | tee mothur.out.log
41 ]]></command> 41 ]]></command>
42 <inputs> 42 <inputs>
43 <conditional name="input"> 43 <conditional name="input">
44 <param name="has_groups" type="select" label="Generate Heatmap for"> 44 <param name="has_groups" type="select" label="Generate Heatmap for">
45 <option value="no">list, rabund, sabund</option> 45 <option value="no">list, rabund, sabund</option>
74 <option value="topotu">By Total OTUs</option> 74 <option value="topotu">By Total OTUs</option>
75 <option value="topgroup">By Total Groups</option> 75 <option value="topgroup">By Total Groups</option>
76 </param> 76 </param>
77 <param name="numotu" type="integer" value="0" min="0" label="numotu - Limit the number of OTUs displayed (ignored if 0)"/> 77 <param name="numotu" type="integer" value="0" min="0" label="numotu - Limit the number of OTUs displayed (ignored if 0)"/>
78 <param name="fontsize" type="integer" value="24" min="0" max="100" label="fontsize - Fontsize (default is 24)"/> 78 <param name="fontsize" type="integer" value="24" min="0" max="100" label="fontsize - Fontsize (default is 24)"/>
79 <expand macro="param-savelog"/>
79 </inputs> 80 </inputs>
80 <outputs> 81 <outputs>
81 <expand macro="logfile-output"/> 82 <expand macro="logfile-output"/>
82 <collection name="heatmaps" type="list" label="${tool.name} on ${on_string}: Heatmaps"> 83 <collection name="heatmaps" type="list" label="${tool.name} on ${on_string}: Heatmaps">
83 <discover_datasets pattern=".*?\.(?P&lt;designation&gt;.*)\.bin\.svg"/> 84 <discover_datasets pattern=".*?\.(?P&lt;designation&gt;.*)\.bin\.svg"/>
88 <param name="otu" value="amazon.an.list" ftype="mothur.list"/> 89 <param name="otu" value="amazon.an.list" ftype="mothur.list"/>
89 <param name="has_groups" value="no"/> 90 <param name="has_groups" value="no"/>
90 <output_collection name="heatmaps" count="36"> 91 <output_collection name="heatmaps" count="36">
91 <element name="0.26.heatmap" md5="8f0d5cb95808115e50729e6df60629cc"/> 92 <element name="0.26.heatmap" md5="8f0d5cb95808115e50729e6df60629cc"/>
92 </output_collection> 93 </output_collection>
94 <param name="savelog" value="true"/>
93 <expand macro="logfile-test"/> 95 <expand macro="logfile-test"/>
94 </test> 96 </test>
95 <test> 97 <test>
96 <param name="otu" value="amazon.an.relabund" ftype="mothur.relabund"/> 98 <param name="otu" value="amazon.an.relabund" ftype="mothur.relabund"/>
97 <param name="has_groups" value="yes"/> 99 <param name="has_groups" value="yes"/>
98 <param name="groups" value="forest"/> 100 <param name="groups" value="forest"/>
99 <param name="label" value="0.26"/> 101 <param name="label" value="0.26"/>
100 <output_collection name="heatmaps" count="1"> 102 <output_collection name="heatmaps" count="1">
101 <element name="0.26.heatmap" md5="b2b46b7e55f55e2b260cd6dc6ccb4485"/> 103 <element name="0.26.heatmap" md5="b2b46b7e55f55e2b260cd6dc6ccb4485"/>
102 </output_collection> 104 </output_collection>
105 <param name="savelog" value="true"/>
103 <expand macro="logfile-test"/> 106 <expand macro="logfile-test"/>
104 </test> 107 </test>
105 <test> 108 <test>
106 <param name="otu" value="amazon.an.shared" ftype="mothur.shared"/> 109 <param name="otu" value="amazon.an.shared" ftype="mothur.shared"/>
107 <param name="has_groups" value="yes"/> 110 <param name="has_groups" value="yes"/>
111 <param name="scale" value="linear"/> 114 <param name="scale" value="linear"/>
112 <param name="sorted" value="none"/> 115 <param name="sorted" value="none"/>
113 <output_collection name="heatmaps" count="3"> 116 <output_collection name="heatmaps" count="3">
114 <element name="0.26.heatmap" md5="b46ed47e441a30588f60e1554ff703bb"/> 117 <element name="0.26.heatmap" md5="b46ed47e441a30588f60e1554ff703bb"/>
115 </output_collection> 118 </output_collection>
119 <param name="savelog" value="true"/>
116 <expand macro="logfile-test"/> 120 <expand macro="logfile-test"/>
117 </test> 121 </test>
118 </tests> 122 </tests>
119 <help> 123 <help><![CDATA[
120 <![CDATA[
121 124
122 @MOTHUR_OVERVIEW@ 125 @MOTHUR_OVERVIEW@
123 126
124 127
125 **Command Documentation** 128 **Command Documentation**
129 .. _list: https://www.mothur.org/wiki/List_file 132 .. _list: https://www.mothur.org/wiki/List_file
130 .. _shared: https://www.mothur.org/wiki/Shared_file 133 .. _shared: https://www.mothur.org/wiki/Shared_file
131 .. _heatmap.bin: https://www.mothur.org/wiki/Heatmap.bin 134 .. _heatmap.bin: https://www.mothur.org/wiki/Heatmap.bin
132 135
133 v.1.21.0: Updated to Mothur 1.33 136 v.1.21.0: Updated to Mothur 1.33
134 ]]> 137
135 </help> 138 ]]></help>
136 <expand macro="citations"/> 139 <expand macro="citations"/>
137 </tool> 140 </tool>