Mercurial > repos > iuc > mothur_heatmap_bin

comparison heatmap.bin.xml @ 4:1cc0526b5a0f draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
author iuc
date Wed, 14 Feb 2018 09:28:56 -0500
parents 70cd6357502a
children 9ab1c6d9f002
comparison
equal deleted inserted replaced
3:6909adf6cb59 4:1cc0526b5a0f
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>
114 <element name="0.26.heatmap" md5="b46ed47e441a30588f60e1554ff703bb"/> 114 <element name="0.26.heatmap" md5="b46ed47e441a30588f60e1554ff703bb"/>
115 </output_collection> 115 </output_collection>
116 <expand macro="logfile-test"/> 116 <expand macro="logfile-test"/>
117 </test> 117 </test>
118 </tests> 118 </tests>
119 <help> 119 <help><![CDATA[
120 <![CDATA[
121 120
122 @MOTHUR_OVERVIEW@ 121 @MOTHUR_OVERVIEW@
123 122
124 123
125 **Command Documentation** 124 **Command Documentation**
129 .. _list: https://www.mothur.org/wiki/List_file 128 .. _list: https://www.mothur.org/wiki/List_file
130 .. _shared: https://www.mothur.org/wiki/Shared_file 129 .. _shared: https://www.mothur.org/wiki/Shared_file
131 .. _heatmap.bin: https://www.mothur.org/wiki/Heatmap.bin 130 .. _heatmap.bin: https://www.mothur.org/wiki/Heatmap.bin
132 131
133 v.1.21.0: Updated to Mothur 1.33 132 v.1.21.0: Updated to Mothur 1.33
134 ]]> 133
135 </help> 134 ]]></help>
136 <expand macro="citations"/> 135 <expand macro="citations"/>
137 </tool> 136 </tool>