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comparison alignment.xml @ 5:e8401372796a draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit 78d01e165304e0be6e6fd017b7314465492d7542
author iuc
date Thu, 17 Dec 2015 12:51:04 -0500
parents 24e4f42410e5
children 50cc0d99b800
comparison
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4:eb4910c5de12 5:e8401372796a
1 <tool id="vsearch_alignment" name="VSearch alignment" version="@VERSION@.0"> 1 <tool id="vsearch_alignment" name="VSearch alignment" version="@VERSION@.1">
2 <description></description> 2 <description></description>
3 <macros> 3 <macros>
4 <import>vsearch_macros.xml</import> 4 <import>vsearch_macros.xml</import>
5 </macros> 5 </macros>
6 <expand macro="requirements" /> 6 <expand macro="requirements" />
9 <command> 9 <command>
10 <![CDATA[ 10 <![CDATA[
11 vsearch 11 vsearch
12 @GENERAL@ 12 @GENERAL@
13 $acceptall 13 $acceptall
14 --id $id 14 --id "${id}"
15 --iddef $iddef 15 --iddef "${iddef}"
16 --allpairs_global "$infile" 16 --allpairs_global "${infile}"
17 --alnout $outfile 17 --alnout "${outfile}"
18 --query_cov $query_cov 18 #if str( $query_cov ):
19 --query_cov "${query_cov}"
20 #end if
19 @USERFIELDS@ 21 @USERFIELDS@
20 ]]> 22 ]]>
21 </command> 23 </command>
22 <inputs> 24 <inputs>
23 <param name="infile" type="data" format="fasta" label="Select your FASTA file" help="(--allpairs_global)" /> 25 <param name="infile" type="data" format="fasta" label="Select your FASTA file" help="(--allpairs_global)" />
53 --alnout FILENAME filename for human-readable alignment output 55 --alnout FILENAME filename for human-readable alignment output
54 --acceptall output all pairwise alignments 56 --acceptall output all pairwise alignments
55 57
56 @EXTERNAL_DOCUMENTATION@ 58 @EXTERNAL_DOCUMENTATION@
57 59
58 -------
59
60 @REFERENCES@
61
62 60
63 ]]> 61 ]]>
64 </help> 62 </help>
65 <expand macro="citations" /> 63 <expand macro="citations" />
66 </tool> 64 </tool>