Mercurial > repos > iuc > mothur_make_design

comparison make.design.xml @ 2:afa78efd7056 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 22:23:04 -0400
parents 7f5f942a6862
children 7a6b209a7bd7
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1:22e5a53596b6 2:afa78efd7056
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" >> $design;
17 #end for
18 #end if
19 #end for 17 #end for
18 #end if
19 #end for
20 ]]></command> 20 ]]></command>
21 <inputs> 21 <inputs>
22 <param name="source" type="data" format="mothur.shared,mothur.groups" label="Source containing groups"/> 22 <param name="source" type="data" format="mothur.shared,mothur.groups" label="Source containing groups"/>
23 <repeat name="groupings" title="Grouping"> 23 <repeat name="groupings" title="Grouping">
24 <param name="name" type="text" label="Name for a new combined grouping"/> 24 <param name="name" type="text" label="Name for a new combined grouping"/>
26 <options> 26 <options>
27 <filter type="data_meta" ref="source" key="groups"/> 27 <filter type="data_meta" ref="source" key="groups"/>
28 </options> 28 </options>
29 </param> 29 </param>
30 </repeat> 30 </repeat>
31 <expand macro="param-savelog"/>
31 </inputs> 32 </inputs>
32 <outputs> 33 <outputs>
33 <data name="design" format="mothur.design" label="${tool.name} on ${on_string}: design"/> 34 <data name="design" format="mothur.design" label="${tool.name} on ${on_string}: design"/>
34 </outputs> 35 </outputs>
35 <tests> 36 <tests>
44 <param name="groups" value="pasture"/> 45 <param name="groups" value="pasture"/>
45 </repeat> 46 </repeat>
46 <output name="design" file="toymothur.design" ftype="mothur.design"/> 47 <output name="design" file="toymothur.design" ftype="mothur.design"/>
47 </test> 48 </test>
48 </tests> 49 </tests>
49 <help> 50 <help><![CDATA[
50 <![CDATA[
51 51
52 @MOTHUR_OVERVIEW@ 52 @MOTHUR_OVERVIEW@
53 53
54 **Command Documentation** 54 **Command Documentation**
55 55
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. 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.
58 58
59 .. _merge.groups: https://www.mothur.org/wiki/Merge.groups 59 .. _merge.groups: https://www.mothur.org/wiki/Merge.groups
60 .. _indicator: https://www.mothur.org/wiki/Indicator 60 .. _indicator: https://www.mothur.org/wiki/Indicator
61 .. _metastats: https://www.mothur.org/wiki/Metastats 61 .. _metastats: https://www.mothur.org/wiki/Metastats
62 ]]> 62
63 </help> 63 ]]></help>
64 <expand macro="citations"/> 64 <expand macro="citations"/>
65 </tool> 65 </tool>