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comparison make.design.xml @ 0:7f5f942a6862 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
author iuc
date Fri, 19 May 2017 04:58:48 -0400
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-1:000000000000 0:7f5f942a6862
1 <tool profile="16.07" id="mothur_make_design" name="Make Design" version="@WRAPPER_VERSION@.0">
2 <description>Assign groups to Sets</description>
3 <macros>
4 <import>macros.xml</import>
5 </macros>
6 <expand macro="requirements"/>
7 <expand macro="stdio"/>
8 <expand macro="version_command"/>
9 <command><![CDATA[
10 @SHELL_OPTIONS@
11
12 #for $grouping in $groupings:
13 #set grp_str = $grouping.groups.__str__
14 #if grp_str:
15 #for $grp in grp_str.split(','):
16 echo -e "$grp\t$grouping.name" >> $design;
17 #end for
18 #end if
19 #end for
20 ]]></command>
21 <inputs>
22 <param name="source" type="data" format="mothur.shared,mothur.groups" label="Source containing groups"/>
23 <repeat name="groupings" title="Grouping">
24 <param name="name" type="text" label="Name for a new combined grouping"/>
25 <param name="groups" type="select" multiple="true" label="Select groups for to include in this grouping">
26 <options>
27 <filter type="data_meta" ref="source" key="groups"/>
28 </options>
29 </param>
30 </repeat>
31 </inputs>
32 <outputs>
33 <data name="design" format="mothur.design" label="${tool.name} on ${on_string}: design"/>
34 </outputs>
35 <tests>
36 <test>
37 <param name="source" value="amazon.mothur.shared" ftype="mothur.shared"/>
38 <repeat name="groupings">
39 <param name="name" value="tardis"/>
40 <param name="groups" value="forest,pasture"/>
41 </repeat>
42 <repeat name="groupings">
43 <param name="name" value="dalek"/>
44 <param name="groups" value="pasture"/>
45 </repeat>
46 <output name="design" file="toymothur.design" ftype="mothur.design"/>
47 </test>
48 </tests>
49 <help>
50 <![CDATA[
51
52 @MOTHUR_OVERVIEW@
53
54 **Command Documentation**
55
56 Make Design creates a design file for use in mothur commands: merge.groups_, indicator_, and metastats_.
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
59 .. _merge.groups: https://www.mothur.org/wiki/Merge.groups
60 .. _indicator: https://www.mothur.org/wiki/Indicator
61 .. _metastats: https://www.mothur.org/wiki/Metastats
62 ]]>
63 </help>
64 <expand macro="citations"/>
65 </tool>