Mercurial > repos > iuc > mothur_heatmap_bin
comparison heatmap.bin.xml @ 2:ac2fa6a167ad draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
author | iuc |
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date | Tue, 20 Mar 2018 22:22:20 -0400 |
parents | b0718c06e329 |
children | 35a719cd08da |
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1:b08d51984da6 | 2:ac2fa6a167ad |
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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<designation>.*)\.bin\.svg"/> | 84 <discover_datasets pattern=".*?\.(?P<designation>.*)\.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> |