Mercurial > repos > rnateam > graphclust_cmfinder

annotate cmFinder.xml @ 5:982001a1869b draft

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planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CMFinder commit 6767a5ffb02052c844e9d862c79912f998f39d8e
author rnateam
date Mon, 20 Nov 2017 04:58:49 -0500
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982001a1869b planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CMFinder commit 6767a5ffb02052c844e9d862c79912f998f39d8e
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1 <tool id="cmFinder" name="cmfinder" version="0.3" >
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2 <requirements>
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3 <requirement type="package" version="0.5.2">graphclust-wrappers</requirement>
2
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4 <requirement type="package" version='0.2'>cmfinder</requirement>
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5 <requirement type="package" version='2.2.10'>viennarna</requirement>
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6 </requirements>
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7 <stdio>
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8 <exit_code range="1:" />
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9 </stdio>
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10 <command>
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11 <![CDATA[
0
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12
2
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13 python '$__tool_directory__/cmFinder.py'
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14 '$model_tree_stk'
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15 '$cmfinder_fa'
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16 ''
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17 $gap_threshold_opts.gap_threshold_opts_selector
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18 #if str($gap_threshold_opts.gap_threshold_opts_selector) == '--g':
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19 $gap_threshold_opts.gap
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20 #end if
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21 ]]>
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22 </command>
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23 <inputs>
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24 <param name="model_tree_stk" type="data" format="stockholm" label="model_tree_stk" help="" />
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25 <param name="cmfinder_fa" type="data" format="text" label="cmfinder_fa" help="" />
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26 <conditional name="gap_threshold_opts">
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27 <param name="gap_threshold_opts_selector" type="select" label="Use gap threshold" help="">
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28 <option value="--g" selected="true">Yes (--g)</option>
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29 <option value="">No</option>
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30 </param>
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31 <when value="--g">
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32 <param name="gap" type="float" value="1.0" size="5"
0
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33 label="Define the gap threshold to determine the conserved column (--g)" help=""/>
2
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34 </when>
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35 <when value=""/>
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36 </conditional>
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37 </inputs>
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38 <outputs>
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39 <data name="model_cmfinder_stk" format="stockholm" label="model_cmfinder_stk" from_work_dir="model.cmfinder.stk"/>
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40 </outputs>
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41 <tests>
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42 <test>
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43 <param name="model_tree_stk" value="in.model.tree.stk"/>
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44 <param name="cmfinder_fa" value="cmfinder.fa"/>
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45 <param name="gap_threshold_opts.gap_threshold_opts_selector" value="--g"/>
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46 <param name="gap_threshold_opts.gap" value="1.0"/>
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47 <output name="model_cmfinder_stk" file="model.cmfinder.stk"/>
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48 </test>
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49 </tests>
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50 <help>
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51 <![CDATA[
0
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52 **What it does**
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53
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54 At first it converts CLUSTAL format files to STOCKHOLM format. Then using *CMFinder* determines consensus
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55 motives for sequences.
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56 ]]>
2
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57 </help>
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58 <citations>
0
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59 <citation type="bibtex">@inproceedings{costa2010fast,
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60 title={Fast neighborhood subgraph pairwise distance kernel},
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61 author={Costa, Fabrizio and De Grave, Kurt},
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62 booktitle={Proceedings of the 26th International Conference on Machine Learning},
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63 pages={255--262},
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64 year={2010},
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65 organization={Omnipress}
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66 }
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67 </citation>
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68 <citation type="doi">10.1093/bioinformatics/btk008</citation>
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69 <citation type="doi">10.1186/1748-7188-6-26</citation>
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70 </citations>
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71 </tool>