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comparison hmmconvert.xml @ 0:62479bdcc059 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569
author iuc
date Tue, 12 May 2015 15:04:26 -0400
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1 <?xml version="1.0"?>
2 <tool id="hmmer_hmmconvert" name="hmmconvert" version="@WRAPPER_VERSION@.0">
3 <description>convert profile file to a HMMER format</description>
4 <macros>
5 <import>macros.xml</import>
6 </macros>
7 <expand macro="requirements"/>
8 <expand macro="stdio"/>
9 <command><![CDATA[
10 hmmconvert
11 $format
12 $hmmfile > $output
13 ]]></command>
14 <inputs>
15 <expand macro="input_hmm" />
16 <param type="select" label="Output Format" name="format">
17 <option value="-a" selected="true">output models in HMMER3 ASCII format</option>
18 <!--<option value="-b">output models in HMMER3 binary format</option>-->
19 <option value="-2">backward compatible HMMER2 ASCII format</option>
20 </param>
21 </inputs>
22 <outputs>
23 <data format="hmmer3" name="output" label="$msafile.name">
24 <change_format>
25 <when input="format" value="-a" format="hmmer3"/>
26 <when input="format" value="-2" format="hmmer2"/>
27 </change_format>
28 </data>
29 </outputs>
30 <tests>
31 <test>
32 <param name="msafile" value="globins4.hmm"/>
33 <param name="format" value="-2"/>
34 <output name="output" file="globins4.hmm2"/>
35 </test>
36 </tests>
37 <help><![CDATA[
38 @HELP_PRE@
39
40 The hmmconvert utility converts an input profile file to different HMMER formats.
41
42 By default, the input profile can be in any HMMER format, including
43 old/obsolete formats from HMMER2, ASCII or binary; the output profile is a
44 current HMMER3 ASCII format.
45
46 @ATTRIBUTION@
47 ]]></help>
48 <expand macro="citation"/>
49 </tool>