annotate macros.xml @ 0:fa3c3a64c993 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
author iuc
date Wed, 24 Nov 2021 21:52:14 +0000
parents
children 2f8d3924bb3b
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fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
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1 <macros>
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
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2 <token name="@TOOL_VERSION@">6.21.7</token>
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
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3 <token name="@VERSION_SUFFIX@">0</token>
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
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4 <token name="@PROFILE@">20.09</token>
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
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5 <xml name="bio_tools">
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
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6 <xrefs>
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
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7 <xref type="bio.tools">megan</xref>
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
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8 </xrefs>
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
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9 </xml>
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
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10 <xml name="requirements">
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
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11 <requirements>
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
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12 <requirement type="package" version="@TOOL_VERSION@">megan</requirement>
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
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13 </requirements>
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
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14 </xml>
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
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15 <macro name="input_type_cond">
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
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16 <conditional name="input_type_cond">
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
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17 <param name="input_type" type="select" label="Choose the category of the reads files to be analyzed">
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
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18 <option value="single" selected="true">Single dataset</option>
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
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19 <option value="pair">Dataset pair</option>
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
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20 <option value="paired">List of dataset pairs</option>
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
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21 </param>
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
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22 <when value="single">
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
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23 <param name="read1" type="data" format="fasta,fasta.gz,fastqsanger.gz,fastqsanger" label="Forward read file" help="This read file should be the one used by Blast to generate the Blast file below"/>
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
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24 <param name="blast1" type="data" format="daa,blastxml,sam,tabular,txt" label="Output file of Blast on input forward read file"/>
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
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25 </when>
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
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26 <when value="pair">
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
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27 <param name="read1" type="data" format="fasta,fasta.gz,fastqsanger.gz,fastqsanger" label="Forward read file" help="This read file should be the one used by Blast to generate the Blast file below"/>
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
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28 <param name="read2" type="data" format="fasta,fasta.gz,fastqsanger.gz,fastqsanger" label="Reverse read file" help="This read file should be the one used by Blast to generate the Blast file below"/>
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
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29 <param argument="--pairedSuffixLength" type="integer" value="0" label="Length of name suffix used to distinguish read names" help="Use 0 if read and mate have the same name"/>
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
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30 <param name="blast1" type="data" format="daa,blastxml,sam,tabular,txt" label="Output file of Blast on input forward read file"/>
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
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31 <param name="blast2" type="data" format="daa,blastxml,sam,tabular,txt" label="Output file of Blast on input reverse read file"/>
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
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32 </when>
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
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33 <when value="paired">
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
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34 <param name="reads_collection" type="data_collection" format="fasta,fasta.gz,fastqsanger,fastqsanger.gz" collection_type="paired" label="Collection of paired read files"/>
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
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35 <param argument="--pairedSuffixLength" type="integer" value="0" label="Length of name suffix used to distinguish read names" help="Use 0 if read and mate have the same name"/>
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
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36 <param name="blast1" type="data" format="daa,blastxml,sam,tabular,txt" label="Blast file for forward read"/>
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
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37 <param name="blast2" type="data" format="daa,blastxml,sam,tabular,txt" label="Blast file for reverse read"/>
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
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38 </when>
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
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39 </conditional>
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
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40 </macro>
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
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41 <macro name="blast_mode_options">
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
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42 <option value="Unknown" selected="true">Unknown</option>
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
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43 <option value="BlastN">BlastN</option>
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
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44 <option value="BlastP">BlastP</option>
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
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45 <option value="BlastX">BlastX</option>
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
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46 <option value="Classifier">Classifier</option>
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
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47 </macro>
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
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48 <macro name="common_blast_params">
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
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49 <param argument="--minScore" type="float" value="50.0" label="Minimum score"/>
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
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50 <param argument="--maxExpected" type="float" value="0.01" label="Maximum expected"/>
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
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51 <param argument="--minPercentIdentity" type="float" value="0.0" min="0.0" max="100.0" label="Minimum percent identity"/>
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
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52 <param argument="--topPercent" type="float" value="10.0" min="0.0" max="100.0" label="Top percent"/>
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
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53 </macro>
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
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54 <xml name="sanitize_query" token_validinitial="string.printable">
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
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55 <sanitizer>
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
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56 <valid initial="@VALIDINITIAL@">
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
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57 <remove value="&apos;" />
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
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58 <add value="|" />
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
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59 </valid>
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
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60 <mapping initial="none">
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
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61 <add source="&apos;" target="&apos;&quot;&apos;&quot;&apos;" />
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
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62 </mapping>
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
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63 </sanitizer>
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
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64 </xml>
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
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65 <xml name="citations">
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
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66 <citations>
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
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67 <citation type="doi">10.1101/gr.5969107</citation>
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
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68 </citations>
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
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69 </xml>
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
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70 </macros>
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
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71