Mercurial > repos > iuc > mummer_nucmer

comparison nucmer.xml @ 1:5b0b49b5421c draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 96608e94742d17cb73d57201099ff5f5abbef276"
author iuc
date Fri, 24 Jan 2020 15:56:52 -0500
parents a18fb4f826fc
children e18267f90096
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0:a18fb4f826fc 1:5b0b49b5421c
1 <tool id="mummer_nucmer" name="Nucmer" version="@MUMMER_VERSION@"> 1 <tool id="mummer_nucmer" name="Nucmer" version="@MUMMER_VERSION@@WRAPPER_VERSION@">
2 <description>Align two or more sequences</description> 2 <description>Align two or more sequences</description>
3 <macros> 3 <macros>
4 <import>macros.xml</import> 4 <import>macros.xml</import>
5 </macros> 5 </macros>
6 <expand macro="requirements"> 6 <expand macro="requirements">
7 <requirement type="package" version="5.2.3">gnuplot</requirement> 7 <expand macro="gnuplot_requirement"/>
8 </expand> 8 </expand>
9 <command detect_errors="exit_code"> 9 <command detect_errors="exit_code">
10 <![CDATA[ 10 <![CDATA[
11 ln -s $reference_sequence reference.fa && 11 ln -s $reference_sequence reference.fa &&
12 ln -s $query_sequence query.fa && 12 ln -s $query_sequence query.fa &&
54 #if $mumplot.range.custom == 'yes': 54 #if $mumplot.range.custom == 'yes':
55 -x [$mumplot.range.min_x:$mumplot.range.max_x] 55 -x [$mumplot.range.min_x:$mumplot.range.max_x]
56 -y [$mumplot.range.min_y:$mumplot.range.max_y] 56 -y [$mumplot.range.min_y:$mumplot.range.max_y]
57 #end if 57 #end if
58 'out.delta' 58 'out.delta'
59 @MUMMER_GNUPLOT_MANUAL@
59 #end if 60 #end if
60 ]]> 61 ]]>
61 </command> 62 </command>
62 <inputs> 63 <inputs>
63 <param name="reference_sequence" type="data" format="fasta" label="Reference Sequence" help="FastA or multi-FastA" /> 64 <param name="reference_sequence" type="data" format="fasta" label="Reference Sequence" help="FastA or multi-FastA" />
64 <param name="query_sequence" type="data" format="fasta" label="Query Sequence" help="FastA or multi-FastA" /> 65 <param name="query_sequence" type="data" format="fasta" label="Query Sequence" help="FastA or multi-FastA" />
65 <param name="anchoring" type="select" label="Anchoring" help="Choose a match anchoring strategy"> 66 <param name="anchoring" type="select" label="Anchoring" help="Choose a match anchoring strategy">