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comparison xmfa2gff3.xml @ 1:bca52822843e draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit e0cd7ae10ce97bed51594e7cc0b969a803d698b7
author iuc
date Fri, 07 Sep 2018 11:30:11 -0400
parents 74093fb62bdf
children 97a43bcbf44d
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0:74093fb62bdf 1:bca52822843e
2 <tool id="xmfa2gff3" name="Convert XMFA to gapped GFF3" version="@WRAPPER_VERSION@.0"> 2 <tool id="xmfa2gff3" name="Convert XMFA to gapped GFF3" version="@WRAPPER_VERSION@.0">
3 <description></description> 3 <description></description>
4 <macros> 4 <macros>
5 <import>macros.xml</import> 5 <import>macros.xml</import>
6 </macros> 6 </macros>
7 <expand macro="requirements"/> 7 <requirements>
8 <requirement type="package" version="2.7">python</requirement>
9 <requirement type="package" version="1.72">biopython</requirement>
10 <requirement type="package" version="0.6.4">bcbiogff</requirement>
11 </requirements>
8 <expand macro="stdio"/> 12 <expand macro="stdio"/>
9 <version_command>python xmfa2gff3.py --version</version_command> 13 <version_command>python xmfa2gff3.py --version</version_command>
10 <command interpreter="python"><![CDATA[ 14 <command><![CDATA[
11 xmfa2gff3.py 15 python '${__tool_directory__}/xmfa2gff3.py'
12 $xmfa 16 $xmfa
13 --window_size $window_size 17 --window_size $window_size
14 --relative_to $relative_to 18 --relative_to $relative_to
15 --sequences 19 --sequences
16 #for file in $sequences: 20 #for file in $sequences:
17 "${file}" 21 '${file}'
18 #end for 22 #end for
19 > $output 23 > '$output'
20 24
21 ]]></command> 25 ]]></command>
22 <inputs> 26 <inputs>
23 <param type="data" format="xmfa" name="xmfa" 27 <param type="data" format="xmfa" name="xmfa"
24 label="XMFA MSA" /> 28 label="XMFA MSA" />
37 <data format="gff3" name="output"> 41 <data format="gff3" name="output">
38 </data> 42 </data>
39 </outputs> 43 </outputs>
40 <tests> 44 <tests>
41 <test> 45 <test>
42 <param name="xmfa" value="1.xmfa"/> 46 <param name="xmfa" value="2.xmfa"/>
43 <param name="sequences" value="karma.fa,phagey.fa" /> 47 <param name="sequences" value="karma.fa,phagey.fa" />
44 <param name="window_size" value="10" /> 48 <param name="window_size" value="10" />
45 <param name="relative_to" value="1" /> 49 <param name="relative_to" value="1" />
46 <output name="output" file="1.gff3"/> 50 <output name="output" file="1.gff3"/>
47 </test> 51 </test>