Mercurial > repos > rnateam > cmv
comparison cmv.xml @ 0:6baa763b77ba draft
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/cmv commit 3bc676ca60e837f8aca261d0b7860128b3474a5c
author | rnateam |
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date | Fri, 20 Oct 2017 04:26:28 -0400 |
parents | |
children | 6e36667f1729 |
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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> |