Mercurial > repos > rnateam > graphclust_prepocessing_for_mlocarna

annotate preMlocarna.xml @ 3:58a152ea0510 draft

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planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/PrepareForMlocarna commit 5a545fc913b3a07e1452e67f66b2ca593660abdf
author rnateam
date Mon, 27 Feb 2017 12:03:42 -0500
parents aac80391edba
children 516747054585
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58a152ea0510 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/PrepareForMlocarna commit 5a545fc913b3a07e1452e67f66b2ca593660abdf
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1 <tool id="preMloc" name="pgma_graphclust" version="0.1.0" >
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8ad3e79255c1 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/PrepareForMlocarna commit 21aaee40723b5341b4236edeb0e72995c2054053
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2 <requirements>
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58a152ea0510 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/PrepareForMlocarna commit 5a545fc913b3a07e1452e67f66b2ca593660abdf
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3 <requirement type="package" version="0.1.9">graphclust-wrappers</requirement>
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8ad3e79255c1 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/PrepareForMlocarna commit 21aaee40723b5341b4236edeb0e72995c2054053
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4 <requirement type="package" version='0.1'>pgma-simple</requirement>
8ad3e79255c1 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/PrepareForMlocarna commit 21aaee40723b5341b4236edeb0e72995c2054053
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5 </requirements>
8ad3e79255c1 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/PrepareForMlocarna commit 21aaee40723b5341b4236edeb0e72995c2054053
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6 <stdio>
8ad3e79255c1 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/PrepareForMlocarna commit 21aaee40723b5341b4236edeb0e72995c2054053
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7 <exit_code range="1:" />
8ad3e79255c1 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/PrepareForMlocarna commit 21aaee40723b5341b4236edeb0e72995c2054053
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8 </stdio>
8ad3e79255c1 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/PrepareForMlocarna commit 21aaee40723b5341b4236edeb0e72995c2054053
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9 <command>
8ad3e79255c1 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/PrepareForMlocarna commit 21aaee40723b5341b4236edeb0e72995c2054053
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10 <![CDATA[
8ad3e79255c1 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/PrepareForMlocarna commit 21aaee40723b5341b4236edeb0e72995c2054053
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11
8ad3e79255c1 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/PrepareForMlocarna commit 21aaee40723b5341b4236edeb0e72995c2054053
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12 'newpreMlocarna.pl' $CI '$fast_cluster' '$fasta_data' '$fast_cluster_sim' '$data_map' $knn ''
8ad3e79255c1 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/PrepareForMlocarna commit 21aaee40723b5341b4236edeb0e72995c2054053
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13
8ad3e79255c1 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/PrepareForMlocarna commit 21aaee40723b5341b4236edeb0e72995c2054053
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14 ]]>
8ad3e79255c1 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/PrepareForMlocarna commit 21aaee40723b5341b4236edeb0e72995c2054053
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15 </command>
8ad3e79255c1 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/PrepareForMlocarna commit 21aaee40723b5341b4236edeb0e72995c2054053
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16 <inputs>
8ad3e79255c1 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/PrepareForMlocarna commit 21aaee40723b5341b4236edeb0e72995c2054053
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17 <param type="data" name="fast_cluster" label="fast_cluster" format="txt" help="stokholm format" />
8ad3e79255c1 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/PrepareForMlocarna commit 21aaee40723b5341b4236edeb0e72995c2054053
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18 <param type="data" name="fasta_data" label="fasta_data" format="fasta" help="fasta format" />
8ad3e79255c1 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/PrepareForMlocarna commit 21aaee40723b5341b4236edeb0e72995c2054053
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19 <param type="data" name="fast_cluster_sim" label="fast_cluster_sim" format="txt" help="similarity sclores" />
8ad3e79255c1 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/PrepareForMlocarna commit 21aaee40723b5341b4236edeb0e72995c2054053
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20 <param type="data" name="data_map" label="data_map" format="txt" help="data map" />
8ad3e79255c1 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/PrepareForMlocarna commit 21aaee40723b5341b4236edeb0e72995c2054053
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21 <param name="CI" type="integer" value="1" size="5" label="Number of current iteration "/>
8ad3e79255c1 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/PrepareForMlocarna commit 21aaee40723b5341b4236edeb0e72995c2054053
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22 <param name="knn" type="integer" value="20" size="5" label="Number of nearest neighbors" help="must be the same as for previous step"/>
8ad3e79255c1 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/PrepareForMlocarna commit 21aaee40723b5341b4236edeb0e72995c2054053
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23 </inputs>
8ad3e79255c1 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/PrepareForMlocarna commit 21aaee40723b5341b4236edeb0e72995c2054053
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24 <outputs>
8ad3e79255c1 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/PrepareForMlocarna commit 21aaee40723b5341b4236edeb0e72995c2054053
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25 <collection name="centers" type="list" label="centers">
8ad3e79255c1 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/PrepareForMlocarna commit 21aaee40723b5341b4236edeb0e72995c2054053
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26 <discover_datasets pattern="(?P&lt;name&gt;^[0-9]*\.[0-9]*\.center.fa$)" ext="txt" directory="CLUSTER" />
8ad3e79255c1 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/PrepareForMlocarna commit 21aaee40723b5341b4236edeb0e72995c2054053
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27 </collection>
8ad3e79255c1 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/PrepareForMlocarna commit 21aaee40723b5341b4236edeb0e72995c2054053
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28 <collection name="trees" type="list" label="trees">
8ad3e79255c1 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/PrepareForMlocarna commit 21aaee40723b5341b4236edeb0e72995c2054053
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29 <discover_datasets pattern="(?P&lt;name&gt;^[0-9]*\.[0-9]*\.tree$)" ext="txt" directory="CLUSTER" />
8ad3e79255c1 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/PrepareForMlocarna commit 21aaee40723b5341b4236edeb0e72995c2054053
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30 </collection>
8ad3e79255c1 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/PrepareForMlocarna commit 21aaee40723b5341b4236edeb0e72995c2054053
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31 <collection name="cmFa" type="list" label="cmfinder_fa" >
8ad3e79255c1 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/PrepareForMlocarna commit 21aaee40723b5341b4236edeb0e72995c2054053
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32 <discover_datasets pattern="(?P&lt;name&gt;^[0-9]*\.[0-9]*\.cmfinder.fa$)" ext="txt" directory="CLUSTER" />
8ad3e79255c1 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/PrepareForMlocarna commit 21aaee40723b5341b4236edeb0e72995c2054053
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33 </collection>
8ad3e79255c1 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/PrepareForMlocarna commit 21aaee40723b5341b4236edeb0e72995c2054053
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34 <collection name="model_tree_fa" type="list" label="model_tree_fa" >
8ad3e79255c1 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/PrepareForMlocarna commit 21aaee40723b5341b4236edeb0e72995c2054053
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35 <discover_datasets pattern="(?P&lt;name&gt;^[0-9]*\.[0-9]*\.model.tree.fa$)" ext="txt" directory="CLUSTER" />
8ad3e79255c1 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/PrepareForMlocarna commit 21aaee40723b5341b4236edeb0e72995c2054053
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36 </collection>
8ad3e79255c1 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/PrepareForMlocarna commit 21aaee40723b5341b4236edeb0e72995c2054053
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37 <collection name="tree_matrix" type="list" label="tree_matrix" >
8ad3e79255c1 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/PrepareForMlocarna commit 21aaee40723b5341b4236edeb0e72995c2054053
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38 <discover_datasets pattern="(?P&lt;name&gt;^[0-9]*\.[0-9]*\.matrix.tree$)" ext="txt" directory="CLUSTER" />
8ad3e79255c1 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/PrepareForMlocarna commit 21aaee40723b5341b4236edeb0e72995c2054053
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39 </collection>
8ad3e79255c1 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/PrepareForMlocarna commit 21aaee40723b5341b4236edeb0e72995c2054053
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40 </outputs>
8ad3e79255c1 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/PrepareForMlocarna commit 21aaee40723b5341b4236edeb0e72995c2054053
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41 <tests>
8ad3e79255c1 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/PrepareForMlocarna commit 21aaee40723b5341b4236edeb0e72995c2054053
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42 <test>
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43 <param name="fast_cluster" value="data.svector.1.fast_cluster"/>
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44 <param name="fasta_data" value="data.fasta"/>
8ad3e79255c1 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/PrepareForMlocarna commit 21aaee40723b5341b4236edeb0e72995c2054053
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45 <param name="fast_cluster_sim" value="data.svector.1.fast_cluster_sim"/>
8ad3e79255c1 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/PrepareForMlocarna commit 21aaee40723b5341b4236edeb0e72995c2054053
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46 <param name="data_map" value="data.map"/>
8ad3e79255c1 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/PrepareForMlocarna commit 21aaee40723b5341b4236edeb0e72995c2054053
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47 <param name="knn" value="20"/>
8ad3e79255c1 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/PrepareForMlocarna commit 21aaee40723b5341b4236edeb0e72995c2054053
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48 <param name="CI" value="1"/>
8ad3e79255c1 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/PrepareForMlocarna commit 21aaee40723b5341b4236edeb0e72995c2054053
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49 <output_collection name="centers">
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50 <element name="1.1.center.fa" file="CLUSTER/1.1.center.fa"/>
8ad3e79255c1 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/PrepareForMlocarna commit 21aaee40723b5341b4236edeb0e72995c2054053
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51 <element name="1.1.center.fa" file="CLUSTER/1.2.center.fa"/>
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52 </output_collection>
8ad3e79255c1 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/PrepareForMlocarna commit 21aaee40723b5341b4236edeb0e72995c2054053
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53 <output_collection name="trees" >
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54 <element name="1.1.tree" file="CLUSTER/1.1.tree"/>
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55 <element name="1.2.tree" file="CLUSTER/1.2.tree"/>
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56 </output_collection>
8ad3e79255c1 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/PrepareForMlocarna commit 21aaee40723b5341b4236edeb0e72995c2054053
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57 <output_collection name="cmFa">
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58 <element name="1.1.cmfinder.fa" file="CLUSTER/1.1.cmfinder.fa"/>
8ad3e79255c1 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/PrepareForMlocarna commit 21aaee40723b5341b4236edeb0e72995c2054053
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59 <element name="1.2.cmfinder.fa" file="CLUSTER/1.2.cmfinder.fa"/>
8ad3e79255c1 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/PrepareForMlocarna commit 21aaee40723b5341b4236edeb0e72995c2054053
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60 </output_collection>
8ad3e79255c1 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/PrepareForMlocarna commit 21aaee40723b5341b4236edeb0e72995c2054053
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61 <output_collection name="tree_matrix">
8ad3e79255c1 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/PrepareForMlocarna commit 21aaee40723b5341b4236edeb0e72995c2054053
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62 <element name="1.1.matrix.tree" file="CLUSTER/1.1.matrix.tree"/>
8ad3e79255c1 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/PrepareForMlocarna commit 21aaee40723b5341b4236edeb0e72995c2054053
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63 <element name="1.2.matrix.tree" file="CLUSTER/1.2.matrix.tree"/>
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64 </output_collection>
8ad3e79255c1 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/PrepareForMlocarna commit 21aaee40723b5341b4236edeb0e72995c2054053
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65 </test>
8ad3e79255c1 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/PrepareForMlocarna commit 21aaee40723b5341b4236edeb0e72995c2054053
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66 </tests>
8ad3e79255c1 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/PrepareForMlocarna commit 21aaee40723b5341b4236edeb0e72995c2054053
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67 <help>
8ad3e79255c1 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/PrepareForMlocarna commit 21aaee40723b5341b4236edeb0e72995c2054053
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68 <![CDATA[
8ad3e79255c1 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/PrepareForMlocarna commit 21aaee40723b5341b4236edeb0e72995c2054053
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69
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70 **What it does**
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71
8ad3e79255c1 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/PrepareForMlocarna commit 21aaee40723b5341b4236edeb0e72995c2054053
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72 This tool prepares files for locarna step.
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73
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74 .. class:: warningmark
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75
8ad3e79255c1 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/PrepareForMlocarna commit 21aaee40723b5341b4236edeb0e72995c2054053
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76 The number of nearest neighbors must be the same as in the previous step (NSPDK step)
8ad3e79255c1 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/PrepareForMlocarna commit 21aaee40723b5341b4236edeb0e72995c2054053
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77
8ad3e79255c1 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/PrepareForMlocarna commit 21aaee40723b5341b4236edeb0e72995c2054053
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78 ]]>
8ad3e79255c1 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/PrepareForMlocarna commit 21aaee40723b5341b4236edeb0e72995c2054053
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79 </help>
8ad3e79255c1 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/PrepareForMlocarna commit 21aaee40723b5341b4236edeb0e72995c2054053
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80 <citations>
8ad3e79255c1 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/PrepareForMlocarna commit 21aaee40723b5341b4236edeb0e72995c2054053
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81 </citations>
8ad3e79255c1 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/PrepareForMlocarna commit 21aaee40723b5341b4236edeb0e72995c2054053
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82 </tool>