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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 16:38:05 -0400
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-1:000000000000 0:d6b4ae743405
1 <tool profile="16.07" id="mothur_make_files" name="Make.group" version="@WRAPPER_VERSION@.0">
2 <description>Make a group file</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 ## create symlinks to input datasets
10 ln -s "$fasta" fasta.dat &&
11 #for $i in $inputs:
12 ln -s "$i.fasta" fasta${inputs.index($i)}.dat &&
13 #end for
14
15 echo 'make.group(
16 fasta=fasta.dat#for $i in $inputs#-fasta${inputs.index($i)}.dat#end for#,
17 groups=${group}#for $i in $inputs#-${i.group}#end for#
18 )'
19 | sed 's/ //g' ## mothur trips over whitespace
20 | mothur
21 ]]></command>
22 <inputs>
23 <param name="fasta" type="data" format="fasta" label="fasta - Fasta to group"/>
24 <param name="group" type="text" label="group - Group name"/>
25 <repeat name="inputs" title="Additional">
26 <param name="fasta" type="data" format="fasta" label="fasta - Fasta to group"/>
27 <param name="group" type="text" label="group - Group name"/>
28 </repeat>
29 </inputs>
30 <outputs>
31 <expand macro="logfile-output"/>
32 <data name="output" format="mothur.groups" from_work_dir="fasta*groups" label="${tool.name} on ${on_string}: group"/>
33 </outputs>
34 <tests>
35 <test>
36 <param name="fasta" value="Mock_S280_L001_R1_001_small.trim.contigs.good.align_head"/>
37 <param name="group" value="testgroup"/>
38 <repeat name="inputs">
39 <param name="fasta" value="Mock_S280_L001_R1_001_small.trim.contigs.good.align_head"/>
40 <param name="group" value="testgroup2"/>
41 </repeat>
42 <output name="output" file="Mock_S280_L001_R1_001_small.trim.contigs.good.Mock_S280_L001_R1_001_small.trim.contigs.good.groups"/>
43 <expand macro="logfile-test"/>
44 </test>
45 </tests>
46 <help>
47 <![CDATA[
48
49 @MOTHUR_OVERVIEW@
50
51 **Command Documenation**
52
53 The make.group_ command reads a fasta file or series of fasta files and creates a group_ file.
54
55 .. _group: http://www.mothur.org/wiki/Group_file
56 .. _make.group: http://www.mothur.org/wiki/Make.group
57
58 ]]>
59 </help>
60 <expand macro="citations"/>
61 </tool>