comparison hmmfetch.xml @ 0:62479bdcc059 draft

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
parents
children b5066aa77fea
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-1:000000000000 0:62479bdcc059
1 <?xml version="1.0"?>
2 <tool id="hmmer_hmmfetch" name="hmmfetch" version="@WRAPPER_VERSION@.0">
3 <description>retrieve profile HMM(s) from a file</description>
4 <macros>
5 <import>macros.xml</import>
6 </macros>
7 <expand macro="requirements"/>
8 <expand macro="stdio"/>
9 <command><![CDATA[
10 hmmfetch -f $hmmfile $keyfile > $output;
11 ]]></command>
12 <inputs>
13 <!-- TODO: implement auto-indexing -->
14 <expand macro="input_hmm" />
15 <param name="keyfile" type="data" format="tabular,txt" label="List of HMM names to extract"/>
16 </inputs>
17 <outputs>
18 <data format="hmmer3" name="output" label="Selected HMM Models from $hmmfile.name">
19 </data>
20 </outputs>
21 <tests>
22 <test>
23 <param name="hmmfile" value="fn3.hmm"/>
24 <param name="keyfile" value="fn3.keys"/>
25 <output name="output" file="fn3.hmm" lines_diff="4"/>
26 </test>
27 </tests>
28 <help><![CDATA[
29 @HELP_PRE@
30
31 Quickly retrieves one or more profile HMMs from an <hmmfile> (a large Pfam
32 database, for example). The profile names should be listed in a text file,
33 separated by newlines
34
35 By default, fetched HMMs are printed to standard output in HMMER3 format.
36
37 @ATTRIBUTION@
38 ]]></help>
39 <expand macro="citation"/>
40 </tool>