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comparison xmfa2gff3.xml @ 0:74093fb62bdf draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8
author iuc
date Wed, 17 Aug 2016 14:46:55 -0400
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1 <?xml version="1.0"?>
2 <tool id="xmfa2gff3" name="Convert XMFA to gapped GFF3" version="@WRAPPER_VERSION@.0">
3 <description></description>
4 <macros>
5 <import>macros.xml</import>
6 </macros>
7 <expand macro="requirements"/>
8 <expand macro="stdio"/>
9 <version_command>python xmfa2gff3.py --version</version_command>
10 <command interpreter="python"><![CDATA[
11 xmfa2gff3.py
12 $xmfa
13 --window_size $window_size
14 --relative_to $relative_to
15 --sequences
16 #for file in $sequences:
17 "${file}"
18 #end for
19 > $output
20
21 ]]></command>
22 <inputs>
23 <param type="data" format="xmfa" name="xmfa"
24 label="XMFA MSA" />
25
26 <param type="data" format="fasta" name="sequences" multiple="True"
27 label="Select sequences used in progressiveMauve alignment"
28 help="Should be provided in the same order as in original progressiveMauve run"/>
29
30 <param type="integer" label="Window Size" value="100" name="window_size"
31 help="maximum length of a match_part feature. Lower number = larger GFF output" />
32
33 <param type="integer" label="Generate relative to Nth sequence in XMFA file" value="1" name="relative_to"
34 help="progressiveMauve (un)helpfully strips original sequence IDs and replaces with integer numbers. This option lets you generate the alignment relative to e.g. the second genome if you wished to display against that base sequence" />
35 </inputs>
36 <outputs>
37 <data format="gff3" name="output">
38 </data>
39 </outputs>
40 <tests>
41 <test>
42 <param name="xmfa" value="1.xmfa"/>
43 <param name="sequences" value="karma.fa,phagey.fa" />
44 <param name="window_size" value="10" />
45 <param name="relative_to" value="1" />
46 <output name="output" file="1.gff3"/>
47 </test>
48 </tests>
49 <help><![CDATA[
50 What it does
51 ============
52
53 XMFA Alignments are great, but now you need a way to visualize this data!
54
55 This tool provides a conversion step to GFF3 formatted output consiting of
56 ``match``es and ``match_part``s with scores indicating percent identity over
57 that chunk of sequence.
58
59 A rendering of the output GFF3 file in JBrowse is shown below:
60
61 .. image:: $PATH_TO_IMAGES/xmfa2gff3.png
62
63 ]]></help>
64 <citations>
65 </citations>
66 </tool>