Mercurial > repos > iuc > megan_blast2rma

annotate blast2rma.xml @ 0:fa3c3a64c993 draft

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"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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0
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"
iuc
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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"
iuc
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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"
iuc
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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"
iuc
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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"
iuc
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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"
iuc
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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($input_type_cond.input_type) == 'paired':
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
iuc
parents:
diff changeset
86 --in '${blast1_identifier}' '${blast2_identifier}'
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
iuc
parents:
diff changeset
87 --reads '${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:
diff changeset
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"
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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"
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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"
iuc
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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"
iuc
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99 --blastMode '${blastMode}'
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
iuc
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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
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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"
iuc
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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"
iuc
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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
parents:
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115 --lcaCoveragePercent $advanced_options.lcaCoveragePercent
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
iuc
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116 --readAssignmentMode '$advanced_options.readAssignmentMode'
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
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117 #if str($advanced_options.con_file_cond.conFile) == 'yes':
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
iuc
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118 --conFile '$advanced_options.con_file_cond.conFile'
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
iuc
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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"
iuc
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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"
iuc
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diff changeset
123 ]]></command>
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
iuc
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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"
iuc
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129 <section name="advanced_options" title="Advanced options" expanded="false">
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
iuc
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130 <param argument="--longReads" type="boolean" truevalue="--longReads" falsevalue="" checked="false" label="Parse and analyse input reads as long reads?"/>
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"/>
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
iuc
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132 <param argument="--classify" type="boolean" truevalue="--classify" falsevalue="" checked="true" label="Run classification algorithm?"/>
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
iuc
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diff changeset
133 <expand macro="common_blast_params"/>
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
iuc
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134 <param argument="--minSupportPercent" type="float" value="0.05" min="0.0" max="100.0" label="Minimum support as percent of assigned reads" help="0 value ignores"/>
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
iuc
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diff changeset
135 <param argument="--minSupport" type="integer" value="0" label="Minimum support" help="0 value ignores"/>
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
iuc
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diff changeset
136 <param argument="--minPercentReadCover" type="float" value="0.0" min="0.0" max="100.0" label="Minimum percent of read length to be covered by alignments"/>
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
iuc
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diff changeset
137 <param argument="--minPercentReferenceCover" type="float" value="0.0" min="0.0" max="100.0" label="Minimum percent of reference length to be covered by alignments"/>
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
iuc
parents:
diff changeset
138 <param argument="--minReadLength" type="integer" value="0" label="Minimum read length"/>
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
iuc
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diff changeset
139 <param argument="--lcaAlgorithm" type="select" label="Select the LCA algorithm to use for taxonomic assignment">
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
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140 <option value="naive" selected="true">naive</option>
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
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141 <option value="weighted">weighted</option>
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
iuc
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142 <option value="longReads">longReads</option>
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
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diff changeset
143 </param>
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
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144 <param argument="--lcaCoveragePercent" type="float" value="100.0" min="0.0" max="100.0" label="Percent for the LCA to cover"/>
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
iuc
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145 <param argument="--readAssignmentMode" type="select" label="Select the read assignment mode">
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
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146 <option value="alignedBases" selected="true">alignedBases</option>
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
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147 <option value="readCount">readCount</option>
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
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diff changeset
148 </param>
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
iuc
parents:
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149 <conditional name="con_file_cond">
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
iuc
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150 <param argument="--conFile" type="select" label="Process a file of contaminant taxa" help="One id or name per line">
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
iuc
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151 <option value="no" selected="true">No</option>
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
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152 <option value="yes">Yes</option>
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
iuc
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diff changeset
153 </param>
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
iuc
parents:
diff changeset
154 <when value="no"/>
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
iuc
parents:
diff changeset
155 <when value="yes">
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
iuc
parents:
diff changeset
156 <param argument="conFile" type="data" format="txt" label="File of contaminant taxa"/>
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
iuc
parents:
diff changeset
157 </when>
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
iuc
parents:
diff changeset
158 </conditional>
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
iuc
parents:
diff changeset
159 </section>
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
iuc
parents:
diff changeset
160 </inputs>
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
iuc
parents:
diff changeset
161 <outputs>
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
iuc
parents:
diff changeset
162 <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
163 </outputs>
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
iuc
parents:
diff changeset
164 <tests>
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
iuc
parents:
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165 <!-- Single dataset input -->
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
iuc
parents:
diff changeset
166 <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
167 <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
168 <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
169 <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
170 <output name="rma6_output" ftype="rma6">
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
iuc
parents:
diff changeset
171 <assert_contents>
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
iuc
parents:
diff changeset
172 <has_size value="19596"/>
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
iuc
parents:
diff changeset
173 </assert_contents>
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
iuc
parents:
diff changeset
174 </output>
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
iuc
parents:
diff changeset
175 </test>
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
iuc
parents:
diff changeset
176 <!-- Single dataset input, contaminants file -->
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
iuc
parents:
diff changeset
177 <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
178 <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
179 <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
180 <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
181 <param name="conFile" value="yes"/>
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
iuc
parents:
diff changeset
182 <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
183 <output name="rma6_output" ftype="rma6">
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
iuc
parents:
diff changeset
184 <assert_contents>
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
iuc
parents:
diff changeset
185 <has_size value="19596"/>
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
iuc
parents:
diff changeset
186 </assert_contents>
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
iuc
parents:
diff changeset
187 </output>
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
iuc
parents:
diff changeset
188 </test>
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
iuc
parents:
diff changeset
189 <!-- Dataset pair input -->
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
iuc
parents:
diff changeset
190 <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
191 <param name="input_type" value="pair"/>
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
iuc
parents:
diff changeset
192 <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
193 <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"
iuc
parents:
diff changeset
194 <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
195 <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"
iuc
parents:
diff changeset
196 <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
197 <output name="rma6_output" ftype="rma6">
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
iuc
parents:
diff changeset
198 <assert_contents>
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
iuc
parents:
diff changeset
199 <has_size value="39887"/>
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
iuc
parents:
diff changeset
200 </assert_contents>
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
iuc
parents:
diff changeset
201 </output>
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
iuc
parents:
diff changeset
202 </test>
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
iuc
parents:
diff changeset
203 <!-- List of dataset pairs input -->
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
iuc
parents:
diff changeset
204 <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
205 <param name="input_type" value="paired"/>
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
iuc
parents:
diff changeset
206 <param name="reads_collection">
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
iuc
parents:
diff changeset
207 <collection type="paired">
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
iuc
parents:
diff changeset
208 <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"
iuc
parents:
diff changeset
209 <element name="reverse" value="13-1941-6_S4_L001_R2_600000.fastq.gz"/>
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
iuc
parents:
diff changeset
210 </collection>
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
iuc
parents:
diff changeset
211 </param>
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
iuc
parents:
diff changeset
212 <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
213 <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"
iuc
parents:
diff changeset
214 <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
215 <output name="rma6_output" ftype="rma6">
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
iuc
parents:
diff changeset
216 <assert_contents>
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
iuc
parents:
diff changeset
217 <has_size value="39806"/>
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
iuc
parents:
diff changeset
218 </assert_contents>
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
iuc
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diff changeset
219 </output>
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
iuc
parents:
diff changeset
220 </test>
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
iuc
parents:
diff changeset
221 </tests>
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
iuc
parents:
diff changeset
222 <help>
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
iuc
parents:
diff changeset
223 **What it does**
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
iuc
parents:
diff changeset
224
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
iuc
parents:
diff changeset
225 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"
iuc
parents:
diff changeset
226 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"
iuc
parents:
diff changeset
227 associated Blast file for this tool.
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
iuc
parents:
diff changeset
228
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
iuc
parents:
diff changeset
229 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"
iuc
parents:
diff changeset
230 The Galaxy MALT Analyzer tool. When these formats are used, this tool will apply the SAM, BlastText and BlastTab format options
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
iuc
parents:
diff changeset
231 required by MEGAN.
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
iuc
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diff changeset
232
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
iuc
parents:
diff changeset
233 * **Direct Access Archive (DAA)** - a proprietary file format developed by PowerISO Computing for disk image files
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
iuc
parents:
diff changeset
234 * **BlastXML** - XML output from Blast
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
iuc
parents:
diff changeset
235 * **Sequence Alignment/Map (SAM)** - a tab-delimited text format consisting of a header section, which is optional, and an alignment section
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
iuc
parents:
diff changeset
236 * **Tabular** - information presented in the form of a table with rows and columns
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
iuc
parents:
diff changeset
237 * **Text** - plain text format
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
iuc
parents:
diff changeset
238
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
iuc
parents:
diff changeset
239 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"
iuc
parents:
diff changeset
240 requires less disk space for files.
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
iuc
parents:
diff changeset
241 </help>
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
iuc
parents:
diff changeset
242 <citations>
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
iuc
parents:
diff changeset
243 <citation type="doi">https://doi.org/10.1101/050559</citation>
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
iuc
parents:
diff changeset
244 </citations>
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
iuc
parents:
diff changeset
245 </tool>
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
iuc
parents:
diff changeset
246