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comparison make.group.xml @ 0:1cf5a6a5eb05 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit ea40e3d84e7850eb4226d6c85f709dcad18d4ba9
author iuc
date Thu, 18 May 2017 18:14:05 -0400
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-1:000000000000 0:1cf5a6a5eb05
1 <tool profile="16.07" id="mothur_make_group" 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="stdio"/>
8 <expand macro="version_command"/>
9 <command><![CDATA[
10 @SHELL_OPTIONS@
11
12 #set fastas = ''
13 #set groups = ''
14 #set count = 0
15
16 #if $method.how == 'collection':
17 #for $i in $method.fasta_collection:
18 ln -s '$i' fasta_${i.element_identifier}.dat &&
19 #set fastas+='fasta_'+$i.element_identifier+'.dat-'
20 #set groups+=$i.element_identifier+'-'
21 #end for
22 #else
23 #for $i in $method.inputs:
24 ln -s '$i.fasta' fasta_${count}.dat &&
25 #set fastas+='fasta_'+str($count)+'.dat-'
26 #set groups+=str($i.group)+'-'
27 #set count+=1
28 #end for
29 #end if
30
31 echo 'make.group(
32 fasta=${ str($fastas).rstrip('-') },
33 groups=${ str($groups).rstrip('-') }
34 )'
35 | sed 's/ //g' ## mothur trips over whitespace
36 | mothur
37 | tee mothur.out.log
38
39 ]]></command>
40 <inputs>
41 <conditional name="method">
42 <param name="how" type="select" label="Method to create group file">
43 <option value="collection"> Automatically from collection </option>
44 <option value="manually"> Manually specify fasta files and group names</option>
45 </param>
46 <when value="collection">
47 <param name="fasta_collection" type="data_collection" collection_type="list" format="fasta" label="Collection with fasta files to group" help="group names will be named after the collection element names"/>
48 </when>
49 <when value="manually">
50 <repeat name="inputs" title="Additional">
51 <param name="fasta" type="data" format="fasta" label="fasta - Fasta to group"/>
52 <param name="group" type="text" label="group - Group name"/>
53 </repeat>
54 </when>
55 </conditional>
56 </inputs>
57 <outputs>
58 <expand macro="logfile-output"/>
59 <data name="output" format="mothur.groups" from_work_dir="*groups" label="${tool.name} on ${on_string}: group"/>
60 </outputs>
61 <tests>
62 <test> <!-- test manual groups creation -->
63 <param name="how" value="manually"/>
64 <repeat name="inputs">
65 <param name="fasta" value="Mock_S280_L001_R1_001_small.trim.contigs.good.align_head"/>
66 <param name="group" value="testgroup"/>
67 </repeat>
68 <repeat name="inputs">
69 <param name="fasta" value="Mock_S280_L001_R1_001_small.trim.contigs.good.align_head"/>
70 <param name="group" value="testgroup2"/>
71 </repeat>
72 <output name="output" file="Mock_S280_L001_R1_001_small.trim.contigs.good.Mock_S280_L001_R1_001_small.trim.contigs.good.groups"/>
73 <expand macro="logfile-test"/>
74 </test>
75 <test> <!-- test auto-creation from collection -->
76 <param name="how" value="collection"/>
77 <param name="fasta_collection">
78 <collection type="list">
79 <element name="testgroup" ftype="fasta" value="Mock_S280_L001_R1_001_small.trim.contigs.good.align_head" />
80 <element name="testgroup2" ftype="fasta" value="Mock_S280_L001_R1_001_small.trim.contigs.good.align_head" />
81 </collection>
82 </param>
83 <output name="output" file="Mock_S280_L001_R1_001_small.trim.contigs.good.Mock_S280_L001_R1_001_small.trim.contigs.good.groups"/>
84 <expand macro="logfile-test"/>
85 </test>
86 </tests>
87 <help>
88 <![CDATA[
89
90 @MOTHUR_OVERVIEW@
91
92 **Command Documentation**
93
94 The make.group_ command reads a fasta file or series of fasta files and creates a group_ file.
95
96 .. _group: https://www.mothur.org/wiki/Group_file
97 .. _make.group: https://www.mothur.org/wiki/Make.group
98
99 ]]>
100 </help>
101 <expand macro="citations"/>
102 </tool>