Mercurial > repos > iuc > mothur_make_group

comparison make.group.xml @ 2:5b28532dfc0a draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
author iuc
date Wed, 14 Feb 2018 09:13:47 -0500
parents 1cf5a6a5eb05
children e1e0c8bb9aa8
comparison
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1:22dff2e08c84 2:5b28532dfc0a
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 #set fastas = '' 12 #set fastas = ''
13 #set groups = '' 13 #set groups = ''
14 #set count = 0 14 #set count = 0
15 15
16 #if $method.how == 'collection': 16 #if $method.how == 'collection':
17 #for $i in $method.fasta_collection: 17 #for $i in $method.fasta_collection:
18 ln -s '$i' fasta_${i.element_identifier}.dat && 18 ln -s '$i' fasta_${i.element_identifier}.dat &&
19 #set fastas+='fasta_'+$i.element_identifier+'.dat-' 19 #set fastas+='fasta_'+$i.element_identifier+'.dat-'
20 #set groups+=$i.element_identifier+'-' 20 #set groups+=$i.element_identifier+'-'
21 #end for 21 #end for
22 #else 22 #else
23 #for $i in $method.inputs: 23 #for $i in $method.inputs:
24 ln -s '$i.fasta' fasta_${count}.dat && 24 ln -s '$i.fasta' fasta_${count}.dat &&
25 #set fastas+='fasta_'+str($count)+'.dat-' 25 #set fastas+='fasta_'+str($count)+'.dat-'
26 #set groups+=str($i.group)+'-' 26 #set groups+=str($i.group)+'-'
27 #set count+=1 27 #set count+=1
28 #end for 28 #end for
29 #end if 29 #end if
30 30
31 echo 'make.group( 31 echo 'make.group(
32 fasta=${ str($fastas).rstrip('-') }, 32 fasta=${ str($fastas).rstrip('-') },
33 groups=${ str($groups).rstrip('-') } 33 groups=${ str($groups).rstrip('-') }
34 )' 34 )'
35 | sed 's/ //g' ## mothur trips over whitespace 35 | sed 's/ //g' ## mothur trips over whitespace
36 | mothur 36 | mothur
37 | tee mothur.out.log 37 | tee mothur.out.log
38
39 ]]></command> 38 ]]></command>
40 <inputs> 39 <inputs>
41 <conditional name="method"> 40 <conditional name="method">
42 <param name="how" type="select" label="Method to create group file"> 41 <param name="how" type="select" label="Method to create group file">
43 <option value="collection"> Automatically from collection </option> 42 <option value="collection"> Automatically from collection </option>
82 </param> 81 </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"/> 82 <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"/> 83 <expand macro="logfile-test"/>
85 </test> 84 </test>
86 </tests> 85 </tests>
87 <help> 86 <help><![CDATA[
88 <![CDATA[
89 87
90 @MOTHUR_OVERVIEW@ 88 @MOTHUR_OVERVIEW@
91 89
92 **Command Documentation** 90 **Command Documentation**
93 91
94 The make.group_ command reads a fasta file or series of fasta files and creates a group_ file. 92 The make.group_ command reads a fasta file or series of fasta files and creates a group_ file.
95 93
96 .. _group: https://www.mothur.org/wiki/Group_file 94 .. _group: https://www.mothur.org/wiki/Group_file
97 .. _make.group: https://www.mothur.org/wiki/Make.group 95 .. _make.group: https://www.mothur.org/wiki/Make.group
98 96
99 ]]> 97 ]]></help>
100 </help>
101 <expand macro="citations"/> 98 <expand macro="citations"/>
102 </tool> 99 </tool>