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comparison cmFinder.xml @ 4:75c7279ef6f1 draft

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planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CMFinder commit f971832d2b34a182314e5201ea6895dd207c5923
author rnateam
date Mon, 13 Mar 2017 18:01:26 -0400
parents 271d673b9aef
children 511da75c73be
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3:271d673b9aef 4:75c7279ef6f1
1 <tool id="cmFinder" name="cmfinder" version="0.1.0" > 1 <tool id="cmFinder" name="cmfinder" version="0.1.0" >
2 <requirements> 2 <requirements>
3 <requirement type="package" version="0.1.9">graphclust-wrappers</requirement> 3 <requirement type="package" version="0.1.10">graphclust-wrappers</requirement>
4 <requirement type="package" version='0.2'>cmfinder</requirement> 4 <requirement type="package" version='0.2'>cmfinder</requirement>
5 <requirement type="package" version='2.2.10'>viennarna</requirement> 5 <requirement type="package" version='2.2.10'>viennarna</requirement>
6 </requirements> 6 </requirements>
7 <stdio> 7 <stdio>
8 <exit_code range="1:" /> 8 <exit_code range="1:" />
9 </stdio> 9 </stdio>
10 <command> 10 <command>
11 <![CDATA[ 11 <![CDATA[
12 12
13 python '$__tool_directory__/cmFinder.py' '$model_tree_stk' '$cmfinder_fa' '' 13 python '$__tool_directory__/cmFinder.py'
14 $gap_threshold_opts.gap_threshold_opts_selector 14 '$model_tree_stk'
15 #if str($gap_threshold_opts.gap_threshold_opts_selector) == '--g': 15 '$cmfinder_fa'
16 $gap_threshold_opts.gap 16 ''
17 #end if 17 $gap_threshold_opts.gap_threshold_opts_selector
18 18 #if str($gap_threshold_opts.gap_threshold_opts_selector) == '--g':
19 ]]> 19 $gap_threshold_opts.gap
20 </command> 20 #end if
21 <inputs> 21 ]]>
22 <param name="model_tree_stk" type="data" format="stockholm" label="model_tree_stk" help="" /> 22 </command>
23 <param name="cmfinder_fa" type="data" format="text" label="cmfinder_fa" help="" /> 23 <inputs>
24 <conditional name="gap_threshold_opts"> 24 <param name="model_tree_stk" type="data" format="stockholm" label="model_tree_stk" help="" />
25 <param name="gap_threshold_opts_selector" type="select" label="Use gap threshold" help=""> 25 <param name="cmfinder_fa" type="data" format="text" label="cmfinder_fa" help="" />
26 <option value="--g" selected="true">Yes (--g)</option> 26 <conditional name="gap_threshold_opts">
27 <option value="">No</option> 27 <param name="gap_threshold_opts_selector" type="select" label="Use gap threshold" help="">
28 </param> 28 <option value="--g" selected="true">Yes (--g)</option>
29 <when value="--g"> 29 <option value="">No</option>
30 <param name="gap" type="float" value="1.0" size="5" 30 </param>
31 <when value="--g">
32 <param name="gap" type="float" value="1.0" size="5"
31 label="Define the gap threshold to determine the conserved column (--g)" help=""/> 33 label="Define the gap threshold to determine the conserved column (--g)" help=""/>
32 </when> 34 </when>
33 <when value=""/> 35 <when value=""/>
34 </conditional> 36 </conditional>
35 </inputs> 37 </inputs>
36 <outputs> 38 <outputs>
37 <data name="model_cmfinder_stk" format="stockholm" label="model_cmfinder_stk" from_work_dir="model.cmfinder.stk"/> 39 <data name="model_cmfinder_stk" format="stockholm" label="model_cmfinder_stk" from_work_dir="model.cmfinder.stk"/>
38 </outputs> 40 </outputs>
39 <tests> 41 <tests>
40 <test> 42 <test>
41 <param name="model_tree_stk" value="in.model.tree.stk"/> 43 <param name="model_tree_stk" value="in.model.tree.stk"/>
42 <param name="cmfinder_fa" value="cmfinder.fa"/> 44 <param name="cmfinder_fa" value="cmfinder.fa"/>
43 <param name="gap_threshold_opts.gap_threshold_opts_selector" value="--g"/> 45 <param name="gap_threshold_opts.gap_threshold_opts_selector" value="--g"/>
44 <param name="gap_threshold_opts.gap" value="1.0"/> 46 <param name="gap_threshold_opts.gap" value="1.0"/>
45 <output name="model_cmfinder_stk" file="model.cmfinder.stk"/> 47 <output name="model_cmfinder_stk" file="model.cmfinder.stk"/>
46 </test> 48 </test>
47 </tests> 49 </tests>
48 <help> 50 <help>
49 <![CDATA[ 51 <![CDATA[
50 **What it does** 52 **What it does**
51 53
52 At first it converts CLUSTAL format files to STOCKHOLM format. Then using *CMFinder* determines consensus 54 At first it converts CLUSTAL format files to STOCKHOLM format. Then using *CMFinder* determines consensus
53 motives for sequences. 55 motives for sequences.
54 ]]> 56 ]]>
55 </help> 57 </help>
56 <citations> 58 <citations>
57 <citation type="bibtex">@inproceedings{costa2010fast, 59 <citation type="bibtex">@inproceedings{costa2010fast,
58 title={Fast neighborhood subgraph pairwise distance kernel}, 60 title={Fast neighborhood subgraph pairwise distance kernel},
59 author={Costa, Fabrizio and De Grave, Kurt}, 61 author={Costa, Fabrizio and De Grave, Kurt},
60 booktitle={Proceedings of the 26th International Conference on Machine Learning}, 62 booktitle={Proceedings of the 26th International Conference on Machine Learning},
61 pages={255--262}, 63 pages={255--262},