Mercurial > repos > rnateam > hmmcv
comparison hmmcv.xml @ 0:559e11a57c3e 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 04:34:18 -0400 |
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children | ef8be69b8e9e |
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1 <tool id="hmmcv" name="hmmcv" version="@VERSION@.1"> | |
2 <description> | |
3 HMMCV is a tool for visualization of comparisons between hidden markov models (HMM) | |
4 </description> | |
5 <macros> | |
6 <import>macros.xml</import> | |
7 </macros> | |
8 <expand macro="requirements" /> | |
9 <expand macro="stdio" /> | |
10 <expand macro="version" /> | |
11 <command detect_errors="aggressive"><![CDATA[ | |
12 HMMCV | |
13 @COMMON_ARGS@ | |
14 -m $model_filepath | |
15 -r $hmmcompare_file | |
16 ]]></command> | |
17 | |
18 <inputs> | |
19 <param name="model_filepath" type="data" format="hmm" label="Input model"/> | |
20 <param name="hmmcompare_file" type="data" format="hmmcompare" label="Input comparison"/> | |
21 <section name="common" title="Common parameters"> | |
22 <expand macro="common_parameters" /> | |
23 </section> | |
24 </inputs> | |
25 <outputs> | |
26 <expand macro="vis_output"/> | |
27 </outputs> | |
28 <tests> | |
29 <test> | |
30 <param name="model_filepath" value="hammerheadClan.hmm" /> | |
31 <param name="hmmcompare_file" value="input.hmmcompare" /> | |
32 <param name="output_format" value="pdf" /> | |
33 <param name="model_details" value="detailed" /> | |
34 <param name="emission_layout" value="bar" /> | |
35 <output_collection name="output_pdfs" type="list"> | |
36 <element name="Hammerhead_1" file="Hammerhead_1.pdf" ftype="pdf" compare="sim_size" delta="50000"/> | |
37 <element name="Hammerhead_3" file="Hammerhead_3.pdf" ftype="pdf" compare="sim_size" delta="50000" /> | |
38 </output_collection> | |
39 </test> | |
40 </tests> | |
41 <help><![CDATA[ **HMMCV -- Visualisation of Hidden Markov Models comparisons** | |
42 **Input.** | |
43 Hidden Markov Models in HMMER3 format, comparison file in hmmcompare format. | |
44 Optionally a stockholm alignment for each input model can be provided. | |
45 | |
46 **Output.** | |
47 Depending on the detail level, only nodes with index (minimal), nodes with emission probabilities and indices (simple) | |
48 or nodes with states, emission and transition probabilities is visualised. Nodes linked by input comparison data | |
49 between different families are highlighted with color labels. | |
50 File in pdf,svg,png,ps format. | |
51 | |
52 For more information, see | |
53 .. __: https://github.com/eggzilla/cmv | |
54 ]]> | |
55 </help> | |
56 <expand macro="citations" /> | |
57 </tool> |