Mercurial > repos > rnateam > graphclust_cmfinder
annotate cmFinder.xml @ 8:5a1dcc77b0ce draft default tip
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/CMFinder commit 4406735e44aba20859c252be39f4e99df28c7a92
author | rnateam |
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date | Sat, 27 Oct 2018 13:22:16 -0400 |
parents | 68bfc8df36f8 |
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8
5a1dcc77b0ce
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/CMFinder commit 4406735e44aba20859c252be39f4e99df28c7a92
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1 <tool id="cmFinder" name="cmfinder" version="0.4" > |
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planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CMFinder commit f971832d2b34a182314e5201ea6895dd207c5923
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2 <requirements> |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/CMFinder commit 4406735e44aba20859c252be39f4e99df28c7a92
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3 <requirement type="package" version="0.6.0">graphclust-wrappers</requirement> |
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planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CMFinder commit f971832d2b34a182314e5201ea6895dd207c5923
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4 <requirement type="package" version='0.2'>cmfinder</requirement> |
75c7279ef6f1
planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CMFinder commit f971832d2b34a182314e5201ea6895dd207c5923
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5 <requirement type="package" version='2.2.10'>viennarna</requirement> |
75c7279ef6f1
planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CMFinder commit f971832d2b34a182314e5201ea6895dd207c5923
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6 </requirements> |
75c7279ef6f1
planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CMFinder commit f971832d2b34a182314e5201ea6895dd207c5923
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7 <stdio> |
75c7279ef6f1
planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CMFinder commit f971832d2b34a182314e5201ea6895dd207c5923
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8 <exit_code range="1:" /> |
75c7279ef6f1
planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CMFinder commit f971832d2b34a182314e5201ea6895dd207c5923
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9 </stdio> |
75c7279ef6f1
planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CMFinder commit f971832d2b34a182314e5201ea6895dd207c5923
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10 <command> |
75c7279ef6f1
planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CMFinder commit f971832d2b34a182314e5201ea6895dd207c5923
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11 <![CDATA[ |
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planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CMFinder commit 21aaee40723b5341b4236edeb0e72995c2054053
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12 |
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planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CMFinder commit f971832d2b34a182314e5201ea6895dd207c5923
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13 python '$__tool_directory__/cmFinder.py' |
75c7279ef6f1
planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CMFinder commit f971832d2b34a182314e5201ea6895dd207c5923
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14 '$model_tree_stk' |
75c7279ef6f1
planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CMFinder commit f971832d2b34a182314e5201ea6895dd207c5923
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15 '$cmfinder_fa' |
75c7279ef6f1
planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CMFinder commit f971832d2b34a182314e5201ea6895dd207c5923
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16 '' |
75c7279ef6f1
planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CMFinder commit f971832d2b34a182314e5201ea6895dd207c5923
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17 $gap_threshold_opts.gap_threshold_opts_selector |
75c7279ef6f1
planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CMFinder commit f971832d2b34a182314e5201ea6895dd207c5923
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18 #if str($gap_threshold_opts.gap_threshold_opts_selector) == '--g': |
75c7279ef6f1
planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CMFinder commit f971832d2b34a182314e5201ea6895dd207c5923
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19 $gap_threshold_opts.gap |
75c7279ef6f1
planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CMFinder commit f971832d2b34a182314e5201ea6895dd207c5923
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20 #end if |
75c7279ef6f1
planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CMFinder commit f971832d2b34a182314e5201ea6895dd207c5923
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21 ]]> |
75c7279ef6f1
planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CMFinder commit f971832d2b34a182314e5201ea6895dd207c5923
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22 </command> |
75c7279ef6f1
planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CMFinder commit f971832d2b34a182314e5201ea6895dd207c5923
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23 <inputs> |
75c7279ef6f1
planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CMFinder commit f971832d2b34a182314e5201ea6895dd207c5923
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24 <param name="model_tree_stk" type="data" format="stockholm" label="model_tree_stk" help="" /> |
75c7279ef6f1
planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CMFinder commit f971832d2b34a182314e5201ea6895dd207c5923
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25 <param name="cmfinder_fa" type="data" format="text" label="cmfinder_fa" help="" /> |
75c7279ef6f1
planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CMFinder commit f971832d2b34a182314e5201ea6895dd207c5923
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26 <conditional name="gap_threshold_opts"> |
75c7279ef6f1
planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CMFinder commit f971832d2b34a182314e5201ea6895dd207c5923
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27 <param name="gap_threshold_opts_selector" type="select" label="Use gap threshold" help=""> |
75c7279ef6f1
planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CMFinder commit f971832d2b34a182314e5201ea6895dd207c5923
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28 <option value="--g" selected="true">Yes (--g)</option> |
75c7279ef6f1
planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CMFinder commit f971832d2b34a182314e5201ea6895dd207c5923
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29 <option value="">No</option> |
75c7279ef6f1
planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CMFinder commit f971832d2b34a182314e5201ea6895dd207c5923
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30 </param> |
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planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CMFinder commit f971832d2b34a182314e5201ea6895dd207c5923
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31 <when value="--g"> |
75c7279ef6f1
planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CMFinder commit f971832d2b34a182314e5201ea6895dd207c5923
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32 <param name="gap" type="float" value="1.0" size="5" |
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planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CMFinder commit 21aaee40723b5341b4236edeb0e72995c2054053
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33 label="Define the gap threshold to determine the conserved column (--g)" help=""/> |
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planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CMFinder commit f971832d2b34a182314e5201ea6895dd207c5923
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34 </when> |
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planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CMFinder commit f971832d2b34a182314e5201ea6895dd207c5923
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35 <when value=""/> |
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planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CMFinder commit f971832d2b34a182314e5201ea6895dd207c5923
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36 </conditional> |
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planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CMFinder commit f971832d2b34a182314e5201ea6895dd207c5923
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37 </inputs> |
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planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CMFinder commit f971832d2b34a182314e5201ea6895dd207c5923
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38 <outputs> |
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planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CMFinder commit f971832d2b34a182314e5201ea6895dd207c5923
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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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planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CMFinder commit f971832d2b34a182314e5201ea6895dd207c5923
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40 </outputs> |
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planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CMFinder commit f971832d2b34a182314e5201ea6895dd207c5923
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41 <tests> |
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planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CMFinder commit f971832d2b34a182314e5201ea6895dd207c5923
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42 <test> |
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planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CMFinder commit f971832d2b34a182314e5201ea6895dd207c5923
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43 <param name="model_tree_stk" value="in.model.tree.stk"/> |
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planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CMFinder commit f971832d2b34a182314e5201ea6895dd207c5923
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44 <param name="cmfinder_fa" value="cmfinder.fa"/> |
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planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CMFinder commit f971832d2b34a182314e5201ea6895dd207c5923
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45 <param name="gap_threshold_opts.gap_threshold_opts_selector" value="--g"/> |
75c7279ef6f1
planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CMFinder commit f971832d2b34a182314e5201ea6895dd207c5923
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46 <param name="gap_threshold_opts.gap" value="1.0"/> |
75c7279ef6f1
planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CMFinder commit f971832d2b34a182314e5201ea6895dd207c5923
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47 <output name="model_cmfinder_stk" file="model.cmfinder.stk"/> |
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planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CMFinder commit f971832d2b34a182314e5201ea6895dd207c5923
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48 </test> |
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planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CMFinder commit f971832d2b34a182314e5201ea6895dd207c5923
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49 </tests> |
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planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CMFinder commit f971832d2b34a182314e5201ea6895dd207c5923
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50 <help> |
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planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CMFinder commit f971832d2b34a182314e5201ea6895dd207c5923
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51 <![CDATA[ |
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52 **What it does** |
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planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CMFinder commit 21aaee40723b5341b4236edeb0e72995c2054053
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53 |
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planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CMFinder commit 21aaee40723b5341b4236edeb0e72995c2054053
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54 At first it converts CLUSTAL format files to STOCKHOLM format. Then using *CMFinder* determines consensus |
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planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CMFinder commit 21aaee40723b5341b4236edeb0e72995c2054053
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55 motives for sequences. |
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planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CMFinder commit 21aaee40723b5341b4236edeb0e72995c2054053
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56 ]]> |
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57 </help> |
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58 <citations> |
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59 <citation type="doi">10.1093/bioinformatics/btk008</citation> |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/CMFinder commit 4406735e44aba20859c252be39f4e99df28c7a92
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60 <citation type="doi">10.5281/zenodo.597695</citation> |
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61 </citations> |
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62 </tool> |