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comparison cmFinder.xml @ 0:78772eedd780 draft

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planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CMFinder commit 21aaee40723b5341b4236edeb0e72995c2054053
author rnateam
date Fri, 16 Dec 2016 07:34:34 -0500
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1 <tool id="cmFinder" name="CMFinder_v0" version="0.1.0" >
2 <requirements>
3 <requirement type="package" version="0.1">graphclust-wrappers</requirement>
4 <requirement type="package" version='0.2'>cmfinder</requirement>
5 <requirement type="package" version='2.2.10'>viennarna</requirement>
6 </requirements>
7 <stdio>
8 <exit_code range="1:" />
9 </stdio>
10 <command>
11 <![CDATA[
12
13 python '$__tool_directory__/cmFinder.py' '$model_tree_stk' '$cmfinder_fa' ''
14 $gap_threshold_opts.gap_threshold_opts_selector
15 #if str($gap_threshold_opts.gap_threshold_opts_selector) == '--g':
16 $gap_threshold_opts.gap
17 #end if
18
19 ]]>
20 </command>
21 <inputs>
22 <param name="model_tree_stk" type="data" format="stockholm" label="model_tree_stk" help="" />
23 <param name="cmfinder_fa" type="data" format="text" label="cmfinder_fa" help="" />
24 <conditional name="gap_threshold_opts">
25 <param name="gap_threshold_opts_selector" type="select" label="Use gap threshold" help="">
26 <option value="--g" selected="true">Yes (--g)</option>
27 <option value="">No</option>
28 </param>
29 <when value="--g">
30 <param name="gap" type="float" value="1.0" size="5"
31 label="Define the gap threshold to determine the conserved column (--g)" help=""/>
32 </when>
33 <when value=""/>
34 </conditional>
35 </inputs>
36 <outputs>
37 <data name="model_cmfinder_stk" format="stockholm" label="model_cmfinder_stk" from_work_dir="model.cmfinder.stk"/>
38 </outputs>
39 <tests>
40 <test>
41 <param name="model_tree_stk" value="in.model.tree.stk"/>
42 <param name="cmfinder_fa" value="cmfinder.fa"/>
43 <param name="gap_threshold_opts.gap_threshold_opts_selector" value="--g"/>
44 <param name="gap_threshold_opts.gap" value="1.0"/>
45 <output name="model_cmfinder_stk" file="model.cmfinder.stk"/>
46 </test>
47 </tests>
48 <help>
49 <![CDATA[
50 **What it does**
51
52 At first it converts CLUSTAL format files to STOCKHOLM format. Then using *CMFinder* determines consensus
53 motives for sequences.
54 ]]>
55 </help>
56 <citations>
57 <citation type="bibtex">@inproceedings{costa2010fast,
58 title={Fast neighborhood subgraph pairwise distance kernel},
59 author={Costa, Fabrizio and De Grave, Kurt},
60 booktitle={Proceedings of the 26th International Conference on Machine Learning},
61 pages={255--262},
62 year={2010},
63 organization={Omnipress}
64 }
65 </citation>
66 <citation type="doi">10.1093/bioinformatics/btk008</citation>
67 <citation type="doi">10.1186/1748-7188-6-26</citation>
68 </citations>
69 </tool>