Mercurial > repos > rnateam > graphclust_cmfinder

annotate cmFinder.xml @ 2:6ec84eaefe33 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CMFinder commit f971832d2b34a182314e5201ea6895dd207c5923
author rnateam
date Mon, 13 Mar 2017 17:54:10 -0400
parents e6db14916a65
children 8269a9caef07
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
2
6ec84eaefe33 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CMFinder commit f971832d2b34a182314e5201ea6895dd207c5923
rnateam
parents: 1
diff changeset
1 <tool id="cmFinder" name="cmfinder" version="0.1.0" >
6ec84eaefe33 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CMFinder commit f971832d2b34a182314e5201ea6895dd207c5923
rnateam
parents: 1
diff changeset
2 <requirements>
6ec84eaefe33 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CMFinder commit f971832d2b34a182314e5201ea6895dd207c5923
rnateam
parents: 1
diff changeset
3 <requirement type="package" version="0.1.10">graphclust-wrappers</requirement>
6ec84eaefe33 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CMFinder commit f971832d2b34a182314e5201ea6895dd207c5923
rnateam
parents: 1
diff changeset
4 <requirement type="package" version='0.2'>cmfinder</requirement>
6ec84eaefe33 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CMFinder commit f971832d2b34a182314e5201ea6895dd207c5923
rnateam
parents: 1
diff changeset
5 <requirement type="package" version='2.2.10'>viennarna</requirement>
6ec84eaefe33 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CMFinder commit f971832d2b34a182314e5201ea6895dd207c5923
rnateam
parents: 1
diff changeset
6 </requirements>
6ec84eaefe33 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CMFinder commit f971832d2b34a182314e5201ea6895dd207c5923
rnateam
parents: 1
diff changeset
7 <stdio>
6ec84eaefe33 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CMFinder commit f971832d2b34a182314e5201ea6895dd207c5923
rnateam
parents: 1
diff changeset
8 <exit_code range="1:" />
6ec84eaefe33 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CMFinder commit f971832d2b34a182314e5201ea6895dd207c5923
rnateam
parents: 1
diff changeset
9 </stdio>
6ec84eaefe33 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CMFinder commit f971832d2b34a182314e5201ea6895dd207c5923
rnateam
parents: 1
diff changeset
10 <command>
6ec84eaefe33 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CMFinder commit f971832d2b34a182314e5201ea6895dd207c5923
rnateam
parents: 1
diff changeset
11 <![CDATA[
0
b151301a2d25 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CMFinder commit 21aaee40723b5341b4236edeb0e72995c2054053
rnateam
parents:
diff changeset
12
2
6ec84eaefe33 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CMFinder commit f971832d2b34a182314e5201ea6895dd207c5923
rnateam
parents: 1
diff changeset
13 python '$__tool_directory__/cmFinder.py'
6ec84eaefe33 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CMFinder commit f971832d2b34a182314e5201ea6895dd207c5923
rnateam
parents: 1
diff changeset
14 '$model_tree_stk'
6ec84eaefe33 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CMFinder commit f971832d2b34a182314e5201ea6895dd207c5923
rnateam
parents: 1
diff changeset
15 '$cmfinder_fa'
6ec84eaefe33 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CMFinder commit f971832d2b34a182314e5201ea6895dd207c5923
rnateam
parents: 1
diff changeset
16 ''
6ec84eaefe33 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CMFinder commit f971832d2b34a182314e5201ea6895dd207c5923
rnateam
parents: 1
diff changeset
17 $gap_threshold_opts.gap_threshold_opts_selector
6ec84eaefe33 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CMFinder commit f971832d2b34a182314e5201ea6895dd207c5923
rnateam
parents: 1
diff changeset
18 #if str($gap_threshold_opts.gap_threshold_opts_selector) == '--g':
6ec84eaefe33 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CMFinder commit f971832d2b34a182314e5201ea6895dd207c5923
rnateam
parents: 1
diff changeset
19 $gap_threshold_opts.gap
6ec84eaefe33 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CMFinder commit f971832d2b34a182314e5201ea6895dd207c5923
rnateam
parents: 1
diff changeset
20 #end if
6ec84eaefe33 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CMFinder commit f971832d2b34a182314e5201ea6895dd207c5923
rnateam
parents: 1
diff changeset
21 ]]>
6ec84eaefe33 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CMFinder commit f971832d2b34a182314e5201ea6895dd207c5923
rnateam
parents: 1
diff changeset
22 </command>
6ec84eaefe33 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CMFinder commit f971832d2b34a182314e5201ea6895dd207c5923
rnateam
parents: 1
diff changeset
23 <inputs>
6ec84eaefe33 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CMFinder commit f971832d2b34a182314e5201ea6895dd207c5923
rnateam
parents: 1
diff changeset
24 <param name="model_tree_stk" type="data" format="stockholm" label="model_tree_stk" help="" />
6ec84eaefe33 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CMFinder commit f971832d2b34a182314e5201ea6895dd207c5923
rnateam
parents: 1
diff changeset
25 <param name="cmfinder_fa" type="data" format="text" label="cmfinder_fa" help="" />
6ec84eaefe33 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CMFinder commit f971832d2b34a182314e5201ea6895dd207c5923
rnateam
parents: 1
diff changeset
26 <conditional name="gap_threshold_opts">
6ec84eaefe33 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CMFinder commit f971832d2b34a182314e5201ea6895dd207c5923
rnateam
parents: 1
diff changeset
27 <param name="gap_threshold_opts_selector" type="select" label="Use gap threshold" help="">
6ec84eaefe33 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CMFinder commit f971832d2b34a182314e5201ea6895dd207c5923
rnateam
parents: 1
diff changeset
28 <option value="--g" selected="true">Yes (--g)</option>
6ec84eaefe33 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CMFinder commit f971832d2b34a182314e5201ea6895dd207c5923
rnateam
parents: 1
diff changeset
29 <option value="">No</option>
6ec84eaefe33 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CMFinder commit f971832d2b34a182314e5201ea6895dd207c5923
rnateam
parents: 1
diff changeset
30 </param>
6ec84eaefe33 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CMFinder commit f971832d2b34a182314e5201ea6895dd207c5923
rnateam
parents: 1
diff changeset
31 <when value="--g">
6ec84eaefe33 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CMFinder commit f971832d2b34a182314e5201ea6895dd207c5923
rnateam
parents: 1
diff changeset
32 <param name="gap" type="float" value="1.0" size="5"
0
b151301a2d25 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CMFinder commit 21aaee40723b5341b4236edeb0e72995c2054053
rnateam
parents:
diff changeset
33 label="Define the gap threshold to determine the conserved column (--g)" help=""/>
2
6ec84eaefe33 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CMFinder commit f971832d2b34a182314e5201ea6895dd207c5923
rnateam
parents: 1
diff changeset
34 </when>
6ec84eaefe33 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CMFinder commit f971832d2b34a182314e5201ea6895dd207c5923
rnateam
parents: 1
diff changeset
35 <when value=""/>
6ec84eaefe33 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CMFinder commit f971832d2b34a182314e5201ea6895dd207c5923
rnateam
parents: 1
diff changeset
36 </conditional>
6ec84eaefe33 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CMFinder commit f971832d2b34a182314e5201ea6895dd207c5923
rnateam
parents: 1
diff changeset
37 </inputs>
6ec84eaefe33 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CMFinder commit f971832d2b34a182314e5201ea6895dd207c5923
rnateam
parents: 1
diff changeset
38 <outputs>
6ec84eaefe33 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CMFinder commit f971832d2b34a182314e5201ea6895dd207c5923
rnateam
parents: 1
diff changeset
39 <data name="model_cmfinder_stk" format="stockholm" label="model_cmfinder_stk" from_work_dir="model.cmfinder.stk"/>
6ec84eaefe33 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CMFinder commit f971832d2b34a182314e5201ea6895dd207c5923
rnateam
parents: 1
diff changeset
40 </outputs>
6ec84eaefe33 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CMFinder commit f971832d2b34a182314e5201ea6895dd207c5923
rnateam
parents: 1
diff changeset
41 <tests>
6ec84eaefe33 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CMFinder commit f971832d2b34a182314e5201ea6895dd207c5923
rnateam
parents: 1
diff changeset
42 <test>
6ec84eaefe33 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CMFinder commit f971832d2b34a182314e5201ea6895dd207c5923
rnateam
parents: 1
diff changeset
43 <param name="model_tree_stk" value="in.model.tree.stk"/>
6ec84eaefe33 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CMFinder commit f971832d2b34a182314e5201ea6895dd207c5923
rnateam
parents: 1
diff changeset
44 <param name="cmfinder_fa" value="cmfinder.fa"/>
6ec84eaefe33 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CMFinder commit f971832d2b34a182314e5201ea6895dd207c5923
rnateam
parents: 1
diff changeset
45 <param name="gap_threshold_opts.gap_threshold_opts_selector" value="--g"/>
6ec84eaefe33 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CMFinder commit f971832d2b34a182314e5201ea6895dd207c5923
rnateam
parents: 1
diff changeset
46 <param name="gap_threshold_opts.gap" value="1.0"/>
6ec84eaefe33 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CMFinder commit f971832d2b34a182314e5201ea6895dd207c5923
rnateam
parents: 1
diff changeset
47 <output name="model_cmfinder_stk" file="model.cmfinder.stk"/>
6ec84eaefe33 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CMFinder commit f971832d2b34a182314e5201ea6895dd207c5923
rnateam
parents: 1
diff changeset
48 </test>
6ec84eaefe33 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CMFinder commit f971832d2b34a182314e5201ea6895dd207c5923
rnateam
parents: 1
diff changeset
49 </tests>
6ec84eaefe33 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CMFinder commit f971832d2b34a182314e5201ea6895dd207c5923
rnateam
parents: 1
diff changeset
50 <help>
6ec84eaefe33 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CMFinder commit f971832d2b34a182314e5201ea6895dd207c5923
rnateam
parents: 1
diff changeset
51 <![CDATA[
0
b151301a2d25 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CMFinder commit 21aaee40723b5341b4236edeb0e72995c2054053
rnateam
parents:
diff changeset
52 **What it does**
b151301a2d25 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CMFinder commit 21aaee40723b5341b4236edeb0e72995c2054053
rnateam
parents:
diff changeset
53
b151301a2d25 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CMFinder commit 21aaee40723b5341b4236edeb0e72995c2054053
rnateam
parents:
diff changeset
54 At first it converts CLUSTAL format files to STOCKHOLM format. Then using *CMFinder* determines consensus
b151301a2d25 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CMFinder commit 21aaee40723b5341b4236edeb0e72995c2054053
rnateam
parents:
diff changeset
55 motives for sequences.
b151301a2d25 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CMFinder commit 21aaee40723b5341b4236edeb0e72995c2054053
rnateam
parents:
diff changeset
56 ]]>
2
6ec84eaefe33 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CMFinder commit f971832d2b34a182314e5201ea6895dd207c5923
rnateam
parents: 1
diff changeset
57 </help>
6ec84eaefe33 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CMFinder commit f971832d2b34a182314e5201ea6895dd207c5923
rnateam
parents: 1
diff changeset
58 <citations>
0
b151301a2d25 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CMFinder commit 21aaee40723b5341b4236edeb0e72995c2054053
rnateam
parents:
diff changeset
59 <citation type="bibtex">@inproceedings{costa2010fast,
b151301a2d25 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CMFinder commit 21aaee40723b5341b4236edeb0e72995c2054053
rnateam
parents:
diff changeset
60 title={Fast neighborhood subgraph pairwise distance kernel},
b151301a2d25 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CMFinder commit 21aaee40723b5341b4236edeb0e72995c2054053
rnateam
parents:
diff changeset
61 author={Costa, Fabrizio and De Grave, Kurt},
b151301a2d25 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CMFinder commit 21aaee40723b5341b4236edeb0e72995c2054053
rnateam
parents:
diff changeset
62 booktitle={Proceedings of the 26th International Conference on Machine Learning},
b151301a2d25 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CMFinder commit 21aaee40723b5341b4236edeb0e72995c2054053
rnateam
parents:
diff changeset
63 pages={255--262},
b151301a2d25 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CMFinder commit 21aaee40723b5341b4236edeb0e72995c2054053
rnateam
parents:
diff changeset
64 year={2010},
b151301a2d25 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CMFinder commit 21aaee40723b5341b4236edeb0e72995c2054053
rnateam
parents:
diff changeset
65 organization={Omnipress}
b151301a2d25 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CMFinder commit 21aaee40723b5341b4236edeb0e72995c2054053
rnateam
parents:
diff changeset
66 }
b151301a2d25 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CMFinder commit 21aaee40723b5341b4236edeb0e72995c2054053
rnateam
parents:
diff changeset
67 </citation>
b151301a2d25 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CMFinder commit 21aaee40723b5341b4236edeb0e72995c2054053
rnateam
parents:
diff changeset
68 <citation type="doi">10.1093/bioinformatics/btk008</citation>
b151301a2d25 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CMFinder commit 21aaee40723b5341b4236edeb0e72995c2054053
rnateam
parents:
diff changeset
69 <citation type="doi">10.1186/1748-7188-6-26</citation>
b151301a2d25 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CMFinder commit 21aaee40723b5341b4236edeb0e72995c2054053
rnateam
parents:
diff changeset
70 </citations>
b151301a2d25 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CMFinder commit 21aaee40723b5341b4236edeb0e72995c2054053
rnateam
parents:
diff changeset
71 </tool>