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comparison cmv.xml @ 0:d6d7ca0df693 draft default tip

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/cmv commit 3bc676ca60e837f8aca261d0b7860128b3474a5c
author bgruening
date Fri, 20 Oct 2017 04:25:47 -0400
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1 <tool id="cmv" name="cmv" version="@VERSION@.1">
2 <description>
3 CMV is a tool for visualization of RNA family models, also known as covariance models (CM)
4 </description>
5 <macros>
6 <import>macros.xml</import>
7 </macros>
8
9 <expand macro="requirements" />
10
11 <expand macro="stdio" />
12
13 <expand macro="version" />
14 <command><![CDATA[
15 CMV
16 @COMMON_ARGS@
17 -m $model_filepath
18 ]]></command>
19
20 <inputs>
21 <param name="model_filepath" type="data" format="cm" label="Input model"/>
22 <section name="common" title="Common parameters">
23 <expand macro="common_parameters" />
24 </section>
25 </inputs>
26
27 <outputs>
28 <expand macro="vis_output"/>
29 </outputs>
30
31 <tests>
32 <test>
33 <param name="model_filepath" value="Hammerhead_HH9.cm" />
34 <param name="output_format" value="pdf" />
35 <param name="model_details" value="detailed" />
36 <param name="emission_layout" value="bar" />
37 <output_collection name="output_pdfs" type="list">
38 <element name="Hammerhead_HH9" file="Hammerhead_HH9.pdf" ftype="pdf" compare="sim_size" />
39 </output_collection>
40 </test>
41 </tests>
42 <help><![CDATA[
43 **CMV -- Visualisation of RNA family models**
44
45 **Input.**
46 Covariance Models in INFERNAL format.
47 Optionally a stockholm alignment for each input model can be provided.
48
49 **Output.**
50 Depending on the detail level, only nodes with index (minimal), nodes with node type and indices (simple)
51 or nodes with states, emission and transition probabilities are visualised. Nodes linked by input comparison data
52 between different families are highlighted with color labels.
53 File in pdf,svg,png,ps format.
54
55 For more information, see
56 .. __: https://github.com/eggzilla/cmv
57
58 ]]></help>
59 <expand macro="citations" />
60
61 </tool>