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comparison make.design.xml @ 0:78dcf76823de draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
author iuc
date Fri, 24 Jun 2016 16:37:34 -0400
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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="version_command"/>
8 <command detect_errors="aggressive"><![CDATA[
9 #for $grouping in $groupings:
10 #set grp_str = $grouping.groups.__str__
11 #if grp_str:
12 #for $grp in grp_str.split(','):
13 echo -e "$grp\t$grouping.name" >> $design;
14 #end for
15 #end if
16 #end for
17 ]]></command>
18 <inputs>
19 <param name="source" type="data" format="mothur.shared,mothur.groups" label="Source containing groups"/>
20 <repeat name="groupings" title="Grouping">
21 <param name="name" type="text" label="Name for a new combined grouping"/>
22 <param name="groups" type="select" multiple="true" label="Select groups for to include in this grouping">
23 <options>
24 <filter type="data_meta" ref="source" key="groups"/>
25 </options>
26 </param>
27 </repeat>
28 </inputs>
29 <outputs>
30 <data name="design" format="mothur.design" label="${tool.name} on ${on_string}: design"/>
31 </outputs>
32 <tests>
33 <test>
34 <param name="source" value="amazon.mothur.shared" ftype="mothur.shared"/>
35 <repeat name="groupings">
36 <param name="name" value="tardis"/>
37 <param name="groups" value="forest,pasture"/>
38 </repeat>
39 <repeat name="groupings">
40 <param name="name" value="dalek"/>
41 <param name="groups" value="pasture"/>
42 </repeat>
43 <output name="design" file="toymothur.design" ftype="mothur.design"/>
44 </test>
45 </tests>
46 <help>
47 <![CDATA[
48
49 @MOTHUR_OVERVIEW@
50
51 **Command Documenation**
52
53 Make Design creates a design file for use in mothur commands: merge.groups_, indicator_, and metastats_.
54 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.
55
56 .. _merge.groups: http://www.mothur.org/wiki/Merge.groups
57 .. _indicator: http://www.mothur.org/wiki/Indicator
58 .. _metastats: http://www.mothur.org/wiki/Metastats
59 ]]>
60 </help>
61 <expand macro="citations"/>
62 </tool>