Mercurial > repos > iuc > megan_blast2rma

annotate blast2rma.xml @ 1:2f8d3924bb3b draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit c5facb54a0de925b30cb86f05989e9254d22b89d"
author iuc
date Fri, 03 Dec 2021 23:09:53 +0000
parents fa3c3a64c993
children 5be253dd3e08
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fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
iuc
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1 <tool id="megan_blast2rma" name="MEGAN: Generate RMA files" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
iuc
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2 <description>from BLAST output</description>
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
iuc
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3 <macros>
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
iuc
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4 <import>macros.xml</import>
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
iuc
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5 </macros>
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
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6 <expand macro="bio_tools"/>
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
iuc
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7 <expand macro="requirements"/>
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
iuc
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8 <command detect_errors="exit_code"><![CDATA[
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
iuc
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9 #import re
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
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10
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
iuc
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11 #if str($input_type_cond.input_type) in ['single', 'pair']:
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
iuc
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12 #set read1 = $input_type_cond.read1
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
iuc
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13 #set blast1 = $input_type_cond.blast1
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
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14 #else:
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
iuc
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15 ## Processing paired reads are tricky if we're
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
iuc
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16 ## downstream from MALT. MALT doesn’t have a
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
iuc
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17 ## paired-read mode, so it won’t attempt to analyze
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
iuc
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18 ## reads in pairs. To do paired read processing,
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
iuc
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19 ## set MALT to generate SAM files and then import the
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
iuc
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20 ## SAM files into MEGAN, specifying paired read mode
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
iuc
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21 ## there. If you have multiple SAM files for the same
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
iuc
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22 ## sample, then import them all at the same time to
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
iuc
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23 ## create one unified rma6 file.
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
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24
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
iuc
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25 #set read1 = $input_type_cond.reads_collection['forward']
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
iuc
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26 #set blast1 = $input_type_cond.blast1
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
iuc
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27 #end if
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
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28
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
iuc
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29 #if $read1.is_of_type('fasta', 'fasta.gz'):
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
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30 #set read_ext = '.fasta'
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
iuc
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31 #else:
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
iuc
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32 #set read_ext = '.fastq'
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
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33 #end if
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
iuc
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34 #if $read1.ext.endswith('.gz'):
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
iuc
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35 #set read_ext = $read_ext + '.gz'
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
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36 #end if
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
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37
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
iuc
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38 #if $blast1.is_of_type('daa'):
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
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39 #set blast_format = 'DAA'
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
iuc
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40 #else if $blast1.is_of_type('txt'):
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
iuc
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41 #set blast_format = 'BlastText'
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
iuc
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42 #else if $blast1.is_of_type('blastxml'):
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
iuc
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43 #set blast_format = 'BlastXML'
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
iuc
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44 #else if $blast1.is_of_type('tabular'):
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
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45 #set blast_format = 'BlastTab'
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
iuc
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46 #else if $blast1.is_of_type('sam'):
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
iuc
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47 #set blast_format = 'SAM'
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
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48 #end if
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
iuc
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49 #set blast_ext = '.' + $blast_format
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
iuc
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50 #if $blast1.ext.endswith('.gz'):
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
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51 #set blast_ext = $blast_ext + '.gz'
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
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52 #end if
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
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53
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
iuc
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54 #set read1_identifier = 'read1' + $read_ext
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
iuc
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55 ln -s '${read1}' '${read1_identifier}' &&
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
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56
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
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57 #set blast1_identifier = 'blast1' + $blast_ext
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
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58 ln -s '${blast1}' '${blast1_identifier}' &&
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
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59
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
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60 #if str($input_type_cond.input_type) in ['pair', 'paired']:
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
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61 #if str($input_type_cond.input_type) == 'pair':
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
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62 #set read2 = $input_type_cond.read2
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
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63 #set blast2 = $input_type_cond.blast2
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
iuc
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64 #else if str($input_type_cond.input_type) == 'paired':
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
iuc
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65 #set read2 = $input_type_cond.reads_collection['reverse']
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
iuc
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66 #set blast2 = $input_type_cond.blast2
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
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67 #end if
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
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68 #set read2_identifier = 'read2' + $read_ext
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
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69 ln -s '${read2}' '${read2_identifier}' &&
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
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70 #set blast2_identifier = 'blast2' + $blast_ext
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
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71 ln -s '${blast2}' '${blast2_identifier}' &&
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
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72 #end if
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
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73
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
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74 blast2rma
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
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75 #if str($input_type_cond.input_type) == 'single':
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
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76 --in '${blast1_identifier}'
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
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77 --reads '${read1_identifier}'
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
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78 --out '${rma6_output}'
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
iuc
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79 #else if str($input_type_cond.input_type) == 'pair':
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
iuc
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80 --in '${blast1_identifier}' '${blast2_identifier}'
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
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81 --reads '${read1_identifier}' '${read2_identifier}'
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
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82 --paired
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
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83 --pairedSuffixLength $input_type_cond.pairedSuffixLength
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
iuc
parents:
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84 --out '${rma6_output}'
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
iuc
parents:
diff changeset
85 #else if str($input_type_cond.input_type) == 'paired':
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
iuc
parents:
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86 --in '${blast1_identifier}' '${blast2_identifier}'
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
iuc
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87 --reads '${read1_identifier}' '${read2_identifier}'
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
iuc
parents:
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88 --paired
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
iuc
parents:
diff changeset
89 --pairedSuffixLength $input_type_cond.pairedSuffixLength
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
iuc
parents:
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90 ## Strangely, megan requires an output
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
iuc
parents:
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91 ## directory when processing paired reads
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
iuc
parents:
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92 ## even though it produces a single file.
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
iuc
parents:
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93 ## We'll accommodate thie by prepending ./
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
iuc
parents:
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94 ## to a temporary output file and then move
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
iuc
parents:
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95 ## it later.
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
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96 --out './tmp.rma6'
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
iuc
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97 #end if
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
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98 --format '${blast_format}'
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
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99 --blastMode '${blastMode}'
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
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100 --threads \${GALAXY_SLOTS:-8}
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
iuc
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101 --useCompression false
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
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102 $advanced_options.longReads
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
iuc
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103 --maxMatchesPerRead '$advanced_options.maxMatchesPerRead'
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
iuc
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104 $advanced_options.classify
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
iuc
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105 --minScore $advanced_options.minScore
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
iuc
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106 --maxExpected $advanced_options.maxExpected
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
iuc
parents:
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107 --minPercentIdentity $advanced_options.minPercentIdentity
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
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108 --topPercent $advanced_options.topPercent
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
iuc
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109 --minSupportPercent $advanced_options.minSupportPercent
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
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110 --minSupport $advanced_options.minSupport
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
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111 --minPercentReadCover $advanced_options.minPercentReadCover
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
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112 --minPercentReferenceCover $advanced_options.minPercentReferenceCover
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
iuc
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113 --minReadLength $advanced_options.minReadLength
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
iuc
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114 --lcaAlgorithm '$advanced_options.lcaAlgorithm'
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
iuc
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115 --lcaCoveragePercent $advanced_options.lcaCoveragePercent
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
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116 --readAssignmentMode '$advanced_options.readAssignmentMode'
1
2f8d3924bb3b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit c5facb54a0de925b30cb86f05989e9254d22b89d"
iuc
parents: 0
diff changeset
117 #if $advanced_options.conFile:
2f8d3924bb3b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit c5facb54a0de925b30cb86f05989e9254d22b89d"
iuc
parents: 0
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118 --conFile '$advanced_options.conFile'
0
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
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119 #end if
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
iuc
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120 #if str($input_type_cond.input_type) == 'paired':
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
iuc
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121 && mv './tmp.rma6' '$rma6_output'
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
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diff changeset
122 #end if
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
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123 ]]></command>
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
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124 <inputs>
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
iuc
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125 <expand macro="input_type_cond"/>
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
iuc
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126 <param argument="--blastMode" type="select" label="Blast mode">
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
iuc
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127 <expand macro="blast_mode_options"/>
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
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128 </param>
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
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129 <section name="advanced_options" title="Advanced options" expanded="false">
1
2f8d3924bb3b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit c5facb54a0de925b30cb86f05989e9254d22b89d"
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parents: 0
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130 <expand macro="long_reads_param"/>
0
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
iuc
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131 <param argument="--maxMatchesPerRead" type="integer" value="100" label="Maximum matches per read"/>
1
2f8d3924bb3b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit c5facb54a0de925b30cb86f05989e9254d22b89d"
iuc
parents: 0
diff changeset
132 <expand macro="classify_param"/>
2f8d3924bb3b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit c5facb54a0de925b30cb86f05989e9254d22b89d"
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parents: 0
diff changeset
133 <expand macro="blast_params"/>
2f8d3924bb3b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit c5facb54a0de925b30cb86f05989e9254d22b89d"
iuc
parents: 0
diff changeset
134 <expand macro="min_max_params"/>
2f8d3924bb3b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit c5facb54a0de925b30cb86f05989e9254d22b89d"
iuc
parents: 0
diff changeset
135 <expand macro="lca_params"/>
2f8d3924bb3b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit c5facb54a0de925b30cb86f05989e9254d22b89d"
iuc
parents: 0
diff changeset
136 <expand macro="read_assignment_mode_param"/>
2f8d3924bb3b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit c5facb54a0de925b30cb86f05989e9254d22b89d"
iuc
parents: 0
diff changeset
137 <expand macro="con_file_param"/>
0
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
iuc
parents:
diff changeset
138 </section>
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
iuc
parents:
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139 </inputs>
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
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140 <outputs>
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
iuc
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141 <data name="rma6_output" format="rma6"/>
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
iuc
parents:
diff changeset
142 </outputs>
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
iuc
parents:
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143 <tests>
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
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parents:
diff changeset
144 <!-- Single dataset input -->
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
iuc
parents:
diff changeset
145 <test expect_num_outputs="1">
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
iuc
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diff changeset
146 <param name="read1" value="13-1941-6_S4_L001_R1_600000.fastq.gz" ftype="fastqsanger.gz"/>
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
iuc
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147 <param name="blast1" value="blast_R1.txt" ftype="txt"/>
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
iuc
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148 <param name="blastMode" value="BlastN"/>
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
iuc
parents:
diff changeset
149 <output name="rma6_output" ftype="rma6">
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
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150 <assert_contents>
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
iuc
parents:
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151 <has_size value="19596"/>
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
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152 </assert_contents>
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
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153 </output>
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
iuc
parents:
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154 </test>
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
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155 <!-- Single dataset input, contaminants file -->
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
iuc
parents:
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156 <test expect_num_outputs="1">
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
iuc
parents:
diff changeset
157 <param name="read1" value="13-1941-6_S4_L001_R1_600000.fastq.gz" ftype="fastqsanger.gz"/>
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
iuc
parents:
diff changeset
158 <param name="blast1" value="blast_R1.txt" ftype="txt"/>
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
iuc
parents:
diff changeset
159 <param name="blastMode" value="BlastN"/>
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
iuc
parents:
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160 <param name="conFile" value="contaminants.txt" ftype="txt"/>
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
iuc
parents:
diff changeset
161 <output name="rma6_output" ftype="rma6">
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
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parents:
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162 <assert_contents>
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
iuc
parents:
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163 <has_size value="19596"/>
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
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parents:
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164 </assert_contents>
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
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165 </output>
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
iuc
parents:
diff changeset
166 </test>
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
iuc
parents:
diff changeset
167 <!-- Dataset pair input -->
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
iuc
parents:
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168 <test expect_num_outputs="1">
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169 <param name="input_type" value="pair"/>
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170 <param name="read1" value="13-1941-6_S4_L001_R1_600000.fastq.gz" ftype="fastqsanger.gz"/>
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171 <param name="read2" value="13-1941-6_S4_L001_R2_600000.fastq.gz" ftype="fastqsanger.gz"/>
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
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172 <param name="blast1" value="blast_R1.txt" ftype="txt"/>
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173 <param name="blast2" value="blast_R2.txt" ftype="txt"/>
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
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174 <param name="blastMode" value="BlastN"/>
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175 <output name="rma6_output" ftype="rma6">
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176 <assert_contents>
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177 <has_size value="39887"/>
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178 </assert_contents>
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179 </output>
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180 </test>
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181 <!-- List of dataset pairs input -->
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182 <test expect_num_outputs="1">
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183 <param name="input_type" value="paired"/>
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184 <param name="reads_collection">
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185 <collection type="paired">
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186 <element name="forward" value="13-1941-6_S4_L001_R1_600000.fastq.gz"/>
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
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187 <element name="reverse" value="13-1941-6_S4_L001_R2_600000.fastq.gz"/>
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188 </collection>
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189 </param>
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190 <param name="blast1" value="blast_R1.txt" ftype="txt"/>
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
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191 <param name="blast2" value="blast_R2.txt" ftype="txt"/>
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192 <param name="blastMode" value="BlastN"/>
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193 <output name="rma6_output" ftype="rma6">
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194 <assert_contents>
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195 <has_size value="39806"/>
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196 </assert_contents>
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197 </output>
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198 </test>
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199 </tests>
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200 <help>
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201 **What it does**
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202
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203 Computes MEGAN RMA files from BLAST (or similar) files. Inputs consist of reads in fasta or fasqsanger format (gzip compressin
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
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204 is supported) and associated Blast files. Each read file should have been used previously as the Blast input to produce the
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
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205 associated Blast file for this tool.
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206
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207 This wrapper supports the following formats for the input Blast file. The SAM, Tabular and Text formats can be produced by
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
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208 The Galaxy MALT Analyzer tool. When these formats are used, this tool will apply the SAM, BlastText and BlastTab format options
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209 required by MEGAN.
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210
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211 * **Direct Access Archive (DAA)** - a proprietary file format developed by PowerISO Computing for disk image files
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212 * **BlastXML** - XML output from Blast
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213 * **Sequence Alignment/Map (SAM)** - a tab-delimited text format consisting of a header section, which is optional, and an alignment section
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214 * **Tabular** - information presented in the form of a table with rows and columns
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215 * **Text** - plain text format
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216
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217 This tool outputs a RealMedia Audio (RMA) file. MEGAN uses an update of the original RMA file format known as RMA6. This update
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
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218 requires less disk space for files.
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219 </help>
1
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220 <expand macro="citations"/>
0
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221 </tool>
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222