Mercurial > repos > bgruening > infernal
comparison cmpress.xml @ 5:6e18e0b098cd draft
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86
author | bgruening |
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date | Sat, 21 Jan 2017 17:36:57 -0500 |
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children | c9e29ac5d099 |
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4:c47a7c52ac4f | 5:6e18e0b098cd |
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1 <tool id="infernal_cmpress" name="cmpress" version="@VERSION@.0"> | |
2 <description> Prepare a covariance model database for cmscan</description> | |
3 <macros> | |
4 <import>macros.xml</import> | |
5 </macros> | |
6 <expand macro="requirements" /> | |
7 <expand macro="stdio" /> | |
8 <command> | |
9 <![CDATA[ | |
10 ## CM file from the history or stored as database on disc | |
11 #if str($cm_opts.cm_opts_selector) == "db": | |
12 cmfile_path='$cm_opts.database.fields.path' | |
13 #else: | |
14 ##'$cm_opts.cmfile' | |
15 cmfile_path='$cmfile' | |
16 #end if | |
17 && | |
18 cmpress -F "\$cmfile_path" && | |
19 ##cmpress creates four files in the same directory of the cm file | |
20 cd `dirname "\$cmfile_path"` && | |
21 tar -cvf '$outfile' `basename "\$cmfile_path"`.i1* | |
22 ]]> | |
23 </command> | |
24 <inputs> | |
25 <conditional name="cm_opts"> | |
26 <param name="cm_opts_selector" type="select" label="Subject covariance models <cmdb> "> | |
27 <option value="db" >Locally installed covariance models</option> | |
28 <option value="histdb" selected="True">Covariance model from your history</option> | |
29 </param> | |
30 <when value="db"> | |
31 <param name="database" type="select" label="Covariance models"> | |
32 <options from_file="infernal.loc"> | |
33 <column name="value" index="0"/> | |
34 <column name="name" index="1"/> | |
35 <column name="path" index="2"/> | |
36 </options> | |
37 </param> | |
38 </when> | |
39 <when value="histdb"> | |
40 <param name="cmfile" type="data" format="cm" label="Covariance models file from the history."/> | |
41 </when> | |
42 </conditional> | |
43 | |
44 </inputs> | |
45 <outputs> | |
46 <data format="tar" name="outfile" label="cmpress on ${on_string}"/> | |
47 </outputs> | |
48 | |
49 <tests> | |
50 <test> | |
51 <conditional name="cm_opts"> | |
52 <param name="cm_opts_selector" value="histdb"/> | |
53 <param name="cmfile" value="cmpress_input_minifam.cm"/> | |
54 </conditional> | |
55 <assert_stdout> | |
56 <has_text text="Working... done."/> | |
57 </assert_stdout> | |
58 | |
59 </test> | |
60 | |
61 </tests> | |
62 <help> | |
63 <![CDATA[ | |
64 | |
65 | |
66 **What it does** | |
67 | |
68 Starting from a CM database <cmfile> in standard Infernal-1.1 format, construct binary compressed datafiles for cm- | |
69 scan. The cmpress step is required for cmscan to work. | |
70 | |
71 **Input format** | |
72 | |
73 The <cmfile> must be have already been calibrated with cmcalibrate for cmpress to work. | |
74 | |
75 **Output format** | |
76 | |
77 | |
78 | |
79 For further questions please refere to the Infernal `Userguide <http://eddylab.org/infernal/Userguide.pdf>`_. | |
80 | |
81 | |
82 ]]> | |
83 </help> | |
84 | |
85 <expand macro="citations" /> | |
86 | |
87 | |
88 </tool> |