Mercurial > repos > rnateam > cmcv

annotate cmcv.xml @ 1:8405fa59c2b2 draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/cmv commit 108e83ea251bee3b952cb49ef758e69294608c1d
author rnateam
date Wed, 02 Jan 2019 10:12:15 -0500
parents fccb17c9e7ef
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
1
8405fa59c2b2 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/cmv commit 108e83ea251bee3b952cb49ef758e69294608c1d
rnateam
parents: 0
diff changeset
1 <tool id="cmcv" name="CMCV" version="@VERSION@">
0
fccb17c9e7ef planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/cmv commit 3bc676ca60e837f8aca261d0b7860128b3474a5c
rnateam
parents:
diff changeset
2 <description>visualization of comparisons between RNA family models (CM)</description>
fccb17c9e7ef planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/cmv commit 3bc676ca60e837f8aca261d0b7860128b3474a5c
rnateam
parents:
diff changeset
3 <macros>
fccb17c9e7ef planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/cmv commit 3bc676ca60e837f8aca261d0b7860128b3474a5c
rnateam
parents:
diff changeset
4 <import>macros.xml</import>
fccb17c9e7ef planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/cmv commit 3bc676ca60e837f8aca261d0b7860128b3474a5c
rnateam
parents:
diff changeset
5 </macros>
fccb17c9e7ef planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/cmv commit 3bc676ca60e837f8aca261d0b7860128b3474a5c
rnateam
parents:
diff changeset
6 <expand macro="requirements" />
fccb17c9e7ef planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/cmv commit 3bc676ca60e837f8aca261d0b7860128b3474a5c
rnateam
parents:
diff changeset
7 <expand macro="stdio" />
fccb17c9e7ef planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/cmv commit 3bc676ca60e837f8aca261d0b7860128b3474a5c
rnateam
parents:
diff changeset
8 <expand macro="version" />
fccb17c9e7ef planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/cmv commit 3bc676ca60e837f8aca261d0b7860128b3474a5c
rnateam
parents:
diff changeset
9 <command><![CDATA[
fccb17c9e7ef planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/cmv commit 3bc676ca60e837f8aca261d0b7860128b3474a5c
rnateam
parents:
diff changeset
10 CMCV
fccb17c9e7ef planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/cmv commit 3bc676ca60e837f8aca261d0b7860128b3474a5c
rnateam
parents:
diff changeset
11 @COMMON_ARGS@
fccb17c9e7ef planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/cmv commit 3bc676ca60e837f8aca261d0b7860128b3474a5c
rnateam
parents:
diff changeset
12 -m $model_filepath
fccb17c9e7ef planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/cmv commit 3bc676ca60e837f8aca261d0b7860128b3474a5c
rnateam
parents:
diff changeset
13 -r $cmcompare_file
fccb17c9e7ef planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/cmv commit 3bc676ca60e837f8aca261d0b7860128b3474a5c
rnateam
parents:
diff changeset
14 ]]></command>
fccb17c9e7ef planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/cmv commit 3bc676ca60e837f8aca261d0b7860128b3474a5c
rnateam
parents:
diff changeset
15
fccb17c9e7ef planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/cmv commit 3bc676ca60e837f8aca261d0b7860128b3474a5c
rnateam
parents:
diff changeset
16 <inputs>
fccb17c9e7ef planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/cmv commit 3bc676ca60e837f8aca261d0b7860128b3474a5c
rnateam
parents:
diff changeset
17 <param name="model_filepath" type="data" format="cm" label="Input model"/>
fccb17c9e7ef planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/cmv commit 3bc676ca60e837f8aca261d0b7860128b3474a5c
rnateam
parents:
diff changeset
18 <param name="cmcompare_file" type="data" format="cmcompare" label="Input comparison"/>
fccb17c9e7ef planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/cmv commit 3bc676ca60e837f8aca261d0b7860128b3474a5c
rnateam
parents:
diff changeset
19 <section name="common" title="Common parameters">
fccb17c9e7ef planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/cmv commit 3bc676ca60e837f8aca261d0b7860128b3474a5c
rnateam
parents:
diff changeset
20 <expand macro="common_parameters" />
fccb17c9e7ef planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/cmv commit 3bc676ca60e837f8aca261d0b7860128b3474a5c
rnateam
parents:
diff changeset
21 </section>
fccb17c9e7ef planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/cmv commit 3bc676ca60e837f8aca261d0b7860128b3474a5c
rnateam
parents:
diff changeset
22 </inputs>
fccb17c9e7ef planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/cmv commit 3bc676ca60e837f8aca261d0b7860128b3474a5c
rnateam
parents:
diff changeset
23 <outputs>
fccb17c9e7ef planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/cmv commit 3bc676ca60e837f8aca261d0b7860128b3474a5c
rnateam
parents:
diff changeset
24 <expand macro="vis_output"/>
fccb17c9e7ef planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/cmv commit 3bc676ca60e837f8aca261d0b7860128b3474a5c
rnateam
parents:
diff changeset
25 </outputs>
fccb17c9e7ef planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/cmv commit 3bc676ca60e837f8aca261d0b7860128b3474a5c
rnateam
parents:
diff changeset
26 <tests>
fccb17c9e7ef planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/cmv commit 3bc676ca60e837f8aca261d0b7860128b3474a5c
rnateam
parents:
diff changeset
27 <test>
fccb17c9e7ef planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/cmv commit 3bc676ca60e837f8aca261d0b7860128b3474a5c
rnateam
parents:
diff changeset
28 <param name="model_filepath" value="hammerheadClan.cm" />
fccb17c9e7ef planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/cmv commit 3bc676ca60e837f8aca261d0b7860128b3474a5c
rnateam
parents:
diff changeset
29 <param name="cmcompare_file" value="input.cmcompare" />
fccb17c9e7ef planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/cmv commit 3bc676ca60e837f8aca261d0b7860128b3474a5c
rnateam
parents:
diff changeset
30 <param name="output_format" value="pdf" />
fccb17c9e7ef planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/cmv commit 3bc676ca60e837f8aca261d0b7860128b3474a5c
rnateam
parents:
diff changeset
31 <param name="model_details" value="detailed" />
fccb17c9e7ef planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/cmv commit 3bc676ca60e837f8aca261d0b7860128b3474a5c
rnateam
parents:
diff changeset
32 <param name="emission_layout" value="bar" />
fccb17c9e7ef planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/cmv commit 3bc676ca60e837f8aca261d0b7860128b3474a5c
rnateam
parents:
diff changeset
33 <output_collection name="output_pdfs" type="list">
fccb17c9e7ef planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/cmv commit 3bc676ca60e837f8aca261d0b7860128b3474a5c
rnateam
parents:
diff changeset
34 <element name="Hammerhead_II" file="Hammerhead_II.pdf" ftype="pdf" compare="sim_size" delta="50000"/>
fccb17c9e7ef planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/cmv commit 3bc676ca60e837f8aca261d0b7860128b3474a5c
rnateam
parents:
diff changeset
35 <element name="Hammerhead_HH10" file="Hammerhead_HH10.pdf" ftype="pdf" compare="sim_size" delta="50000"/>
fccb17c9e7ef planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/cmv commit 3bc676ca60e837f8aca261d0b7860128b3474a5c
rnateam
parents:
diff changeset
36 </output_collection>
fccb17c9e7ef planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/cmv commit 3bc676ca60e837f8aca261d0b7860128b3474a5c
rnateam
parents:
diff changeset
37 </test>
fccb17c9e7ef planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/cmv commit 3bc676ca60e837f8aca261d0b7860128b3474a5c
rnateam
parents:
diff changeset
38 </tests>
fccb17c9e7ef planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/cmv commit 3bc676ca60e837f8aca261d0b7860128b3474a5c
rnateam
parents:
diff changeset
39 <help><![CDATA[
fccb17c9e7ef planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/cmv commit 3bc676ca60e837f8aca261d0b7860128b3474a5c
rnateam
parents:
diff changeset
40 **CMCV -- Visualisation of RNA family model comparison**
fccb17c9e7ef planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/cmv commit 3bc676ca60e837f8aca261d0b7860128b3474a5c
rnateam
parents:
diff changeset
41
fccb17c9e7ef planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/cmv commit 3bc676ca60e837f8aca261d0b7860128b3474a5c
rnateam
parents:
diff changeset
42 **Input.**
fccb17c9e7ef planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/cmv commit 3bc676ca60e837f8aca261d0b7860128b3474a5c
rnateam
parents:
diff changeset
43 Covariance Models in INFERNAL format, comparison file in cmcompare format.
fccb17c9e7ef planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/cmv commit 3bc676ca60e837f8aca261d0b7860128b3474a5c
rnateam
parents:
diff changeset
44
fccb17c9e7ef planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/cmv commit 3bc676ca60e837f8aca261d0b7860128b3474a5c
rnateam
parents:
diff changeset
45 **Output.**
fccb17c9e7ef planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/cmv commit 3bc676ca60e837f8aca261d0b7860128b3474a5c
rnateam
parents:
diff changeset
46 Depending on the detail level, only nodes with index (minimal), nodes with node type and indices (simple)
fccb17c9e7ef planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/cmv commit 3bc676ca60e837f8aca261d0b7860128b3474a5c
rnateam
parents:
diff changeset
47 or nodes with states, emission and transition probabilities are visualised. Nodes linked by input comparison data
fccb17c9e7ef planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/cmv commit 3bc676ca60e837f8aca261d0b7860128b3474a5c
rnateam
parents:
diff changeset
48 between different families are highlighted with color labels.
fccb17c9e7ef planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/cmv commit 3bc676ca60e837f8aca261d0b7860128b3474a5c
rnateam
parents:
diff changeset
49 File in pdf,svg,png,ps format.
fccb17c9e7ef planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/cmv commit 3bc676ca60e837f8aca261d0b7860128b3474a5c
rnateam
parents:
diff changeset
50
fccb17c9e7ef planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/cmv commit 3bc676ca60e837f8aca261d0b7860128b3474a5c
rnateam
parents:
diff changeset
51 For more information, see
fccb17c9e7ef planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/cmv commit 3bc676ca60e837f8aca261d0b7860128b3474a5c
rnateam
parents:
diff changeset
52 .. __: https://github.com/eggzilla/cmv
fccb17c9e7ef planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/cmv commit 3bc676ca60e837f8aca261d0b7860128b3474a5c
rnateam
parents:
diff changeset
53
fccb17c9e7ef planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/cmv commit 3bc676ca60e837f8aca261d0b7860128b3474a5c
rnateam
parents:
diff changeset
54 ]]></help>
fccb17c9e7ef planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/cmv commit 3bc676ca60e837f8aca261d0b7860128b3474a5c
rnateam
parents:
diff changeset
55 <expand macro="citations" />
fccb17c9e7ef planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/cmv commit 3bc676ca60e837f8aca261d0b7860128b3474a5c
rnateam
parents:
diff changeset
56 </tool>