Mercurial > repos > iuc > mothur_make_design

comparison make.design.xml @ 3:e98fb3b14c12 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
author iuc
date Wed, 14 Feb 2018 10:07:16 -0500
parents 840ac4688cf5
children 717ab045706c
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2:4055bc0b0d2d 3:e98fb3b14c12
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 #for $grouping in $groupings: 12 #for $grouping in $groupings:
13 #set grp_str = $grouping.groups.__str__ 13 #set grp_str = $grouping.groups.__str__
14 #if grp_str: 14 #if grp_str:
15 #for $grp in grp_str.split(','): 15 #for $grp in grp_str.split(','):
16 echo -e "$grp\t$grouping.name" >> $design; 16 echo -e "$grp\t$grouping.name" >> $design;
17 #end for
18 #end if
19 #end for 17 #end for
18 #end if
19 #end for
20 ]]></command> 20 ]]></command>
21 <inputs> 21 <inputs>
22 <param name="source" type="data" format="mothur.shared,mothur.groups" label="Source containing groups"/> 22 <param name="source" type="data" format="mothur.shared,mothur.groups" label="Source containing groups"/>
23 <repeat name="groupings" title="Grouping"> 23 <repeat name="groupings" title="Grouping">
24 <param name="name" type="text" label="Name for a new combined grouping"/> 24 <param name="name" type="text" label="Name for a new combined grouping"/>
44 <param name="groups" value="pasture"/> 44 <param name="groups" value="pasture"/>
45 </repeat> 45 </repeat>
46 <output name="design" file="toymothur.design" ftype="mothur.design"/> 46 <output name="design" file="toymothur.design" ftype="mothur.design"/>
47 </test> 47 </test>
48 </tests> 48 </tests>
49 <help> 49 <help><![CDATA[
50 <![CDATA[
51 50
52 @MOTHUR_OVERVIEW@ 51 @MOTHUR_OVERVIEW@
53 52
54 **Command Documentation** 53 **Command Documentation**
55 54
57 A design file looks like the group file. It is a 2 column tab delimited file, where the first column is the group name and the second column is the set the group belongs to. 56 A design file looks like the group file. It is a 2 column tab delimited file, where the first column is the group name and the second column is the set the group belongs to.
58 57
59 .. _merge.groups: https://www.mothur.org/wiki/Merge.groups 58 .. _merge.groups: https://www.mothur.org/wiki/Merge.groups
60 .. _indicator: https://www.mothur.org/wiki/Indicator 59 .. _indicator: https://www.mothur.org/wiki/Indicator
61 .. _metastats: https://www.mothur.org/wiki/Metastats 60 .. _metastats: https://www.mothur.org/wiki/Metastats
62 ]]> 61
63 </help> 62 ]]></help>
64 <expand macro="citations"/> 63 <expand macro="citations"/>
65 </tool> 64 </tool>