Mercurial > repos > bgruening > graphclust_cmfinder

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planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CMFinder commit f447414150c19865e904d3914a68e2479fadddce
author bgruening
date Thu, 15 Dec 2016 18:19:27 -0500
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407180a7f27e planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CMFinder commit f447414150c19865e904d3914a68e2479fadddce
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1 <tool id="cmFinder" name="CMFinder_v0" version="0.1.0" >
407180a7f27e planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CMFinder commit f447414150c19865e904d3914a68e2479fadddce
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2 <requirements>
407180a7f27e planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CMFinder commit f447414150c19865e904d3914a68e2479fadddce
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3 <requirement type="package" version="0.1">graphclust-wrappers</requirement>
407180a7f27e planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CMFinder commit f447414150c19865e904d3914a68e2479fadddce
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4 <requirement type="package" version='0.2'>cmfinder</requirement>
407180a7f27e planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CMFinder commit f447414150c19865e904d3914a68e2479fadddce
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5 <requirement type="package" version='2.2.10'>viennarna</requirement>
407180a7f27e planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CMFinder commit f447414150c19865e904d3914a68e2479fadddce
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6 </requirements>
407180a7f27e planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CMFinder commit f447414150c19865e904d3914a68e2479fadddce
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7 <stdio>
407180a7f27e planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CMFinder commit f447414150c19865e904d3914a68e2479fadddce
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8 <exit_code range="1:" />
407180a7f27e planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CMFinder commit f447414150c19865e904d3914a68e2479fadddce
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9 </stdio>
407180a7f27e planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CMFinder commit f447414150c19865e904d3914a68e2479fadddce
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10 <command>
407180a7f27e planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CMFinder commit f447414150c19865e904d3914a68e2479fadddce
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11 <![CDATA[
407180a7f27e planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CMFinder commit f447414150c19865e904d3914a68e2479fadddce
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12
407180a7f27e planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CMFinder commit f447414150c19865e904d3914a68e2479fadddce
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13 python '$__tool_directory__/cmFinder.py' '$model_tree_stk' '$cmfinder_fa' ''
407180a7f27e planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CMFinder commit f447414150c19865e904d3914a68e2479fadddce
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14 $gap_threshold_opts.gap_threshold_opts_selector
407180a7f27e planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CMFinder commit f447414150c19865e904d3914a68e2479fadddce
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15 #if str($gap_threshold_opts.gap_threshold_opts_selector) == '--g':
407180a7f27e planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CMFinder commit f447414150c19865e904d3914a68e2479fadddce
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16 $gap_threshold_opts.gap
407180a7f27e planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CMFinder commit f447414150c19865e904d3914a68e2479fadddce
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17 #end if
407180a7f27e planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CMFinder commit f447414150c19865e904d3914a68e2479fadddce
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18
407180a7f27e planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CMFinder commit f447414150c19865e904d3914a68e2479fadddce
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19 ]]>
407180a7f27e planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CMFinder commit f447414150c19865e904d3914a68e2479fadddce
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20 </command>
407180a7f27e planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CMFinder commit f447414150c19865e904d3914a68e2479fadddce
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21 <inputs>
407180a7f27e planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CMFinder commit f447414150c19865e904d3914a68e2479fadddce
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22 <param name="model_tree_stk" type="data" format="stockholm" label="model_tree_stk" help="" />
407180a7f27e planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CMFinder commit f447414150c19865e904d3914a68e2479fadddce
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23 <param name="cmfinder_fa" type="data" format="text" label="cmfinder_fa" help="" />
407180a7f27e planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CMFinder commit f447414150c19865e904d3914a68e2479fadddce
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24 <conditional name="gap_threshold_opts">
407180a7f27e planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CMFinder commit f447414150c19865e904d3914a68e2479fadddce
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25 <param name="gap_threshold_opts_selector" type="select" label="Use gap threshold" help="">
407180a7f27e planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CMFinder commit f447414150c19865e904d3914a68e2479fadddce
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26 <option value="--g" selected="true">Yes (--g)</option>
407180a7f27e planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CMFinder commit f447414150c19865e904d3914a68e2479fadddce
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27 <option value="">No</option>
407180a7f27e planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CMFinder commit f447414150c19865e904d3914a68e2479fadddce
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28 </param>
407180a7f27e planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CMFinder commit f447414150c19865e904d3914a68e2479fadddce
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29 <when value="--g">
407180a7f27e planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CMFinder commit f447414150c19865e904d3914a68e2479fadddce
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30 <param name="gap" type="float" value="1.0" size="5"
407180a7f27e planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CMFinder commit f447414150c19865e904d3914a68e2479fadddce
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31 label="Define the gap threshold to determine the conserved column (--g)" help=""/>
407180a7f27e planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CMFinder commit f447414150c19865e904d3914a68e2479fadddce
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32 </when>
407180a7f27e planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CMFinder commit f447414150c19865e904d3914a68e2479fadddce
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33 <when value=""/>
407180a7f27e planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CMFinder commit f447414150c19865e904d3914a68e2479fadddce
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34 </conditional>
407180a7f27e planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CMFinder commit f447414150c19865e904d3914a68e2479fadddce
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35 </inputs>
407180a7f27e planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CMFinder commit f447414150c19865e904d3914a68e2479fadddce
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36 <outputs>
407180a7f27e planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CMFinder commit f447414150c19865e904d3914a68e2479fadddce
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37 <data name="model_cmfinder_stk" format="stockholm" label="model_cmfinder_stk" from_work_dir="model.cmfinder.stk"/>
407180a7f27e planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CMFinder commit f447414150c19865e904d3914a68e2479fadddce
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38 </outputs>
407180a7f27e planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CMFinder commit f447414150c19865e904d3914a68e2479fadddce
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39 <tests>
407180a7f27e planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CMFinder commit f447414150c19865e904d3914a68e2479fadddce
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40 <test>
407180a7f27e planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CMFinder commit f447414150c19865e904d3914a68e2479fadddce
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41 <param name="model_tree_stk" value="in.model.tree.stk"/>
407180a7f27e planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CMFinder commit f447414150c19865e904d3914a68e2479fadddce
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42 <param name="cmfinder_fa" value="cmfinder.fa"/>
407180a7f27e planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CMFinder commit f447414150c19865e904d3914a68e2479fadddce
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43 <param name="gap_threshold_opts.gap_threshold_opts_selector" value="--g"/>
407180a7f27e planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CMFinder commit f447414150c19865e904d3914a68e2479fadddce
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44 <param name="gap_threshold_opts.gap" value="1.0"/>
407180a7f27e planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CMFinder commit f447414150c19865e904d3914a68e2479fadddce
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45 <output name="model_cmfinder_stk" file="model.cmfinder.stk"/>
407180a7f27e planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CMFinder commit f447414150c19865e904d3914a68e2479fadddce
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46 </test>
407180a7f27e planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CMFinder commit f447414150c19865e904d3914a68e2479fadddce
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47 </tests>
407180a7f27e planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CMFinder commit f447414150c19865e904d3914a68e2479fadddce
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48 <help>
407180a7f27e planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CMFinder commit f447414150c19865e904d3914a68e2479fadddce
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49 <![CDATA[
407180a7f27e planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CMFinder commit f447414150c19865e904d3914a68e2479fadddce
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50 **What it does**
407180a7f27e planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CMFinder commit f447414150c19865e904d3914a68e2479fadddce
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51
407180a7f27e planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CMFinder commit f447414150c19865e904d3914a68e2479fadddce
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52 At first it converts CLUSTAL format files to STOCKHOLM format. Then using *CMFinder* determines consensus
407180a7f27e planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CMFinder commit f447414150c19865e904d3914a68e2479fadddce
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53 motives for sequences.
407180a7f27e planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CMFinder commit f447414150c19865e904d3914a68e2479fadddce
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54 ]]>
407180a7f27e planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CMFinder commit f447414150c19865e904d3914a68e2479fadddce
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55 </help>
407180a7f27e planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CMFinder commit f447414150c19865e904d3914a68e2479fadddce
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56 <citations>
407180a7f27e planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CMFinder commit f447414150c19865e904d3914a68e2479fadddce
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57 <citation type="bibtex">@inproceedings{costa2010fast,
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58 title={Fast neighborhood subgraph pairwise distance kernel},
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59 author={Costa, Fabrizio and De Grave, Kurt},
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60 booktitle={Proceedings of the 26th International Conference on Machine Learning},
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61 pages={255--262},
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62 year={2010},
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63 organization={Omnipress}
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64 }
407180a7f27e planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CMFinder commit f447414150c19865e904d3914a68e2479fadddce
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65 </citation>
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66 <citation type="doi">10.1093/bioinformatics/btk008</citation>
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67 <citation type="doi">10.1186/1748-7188-6-26</citation>
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68 </citations>
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69 </tool>