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1 <tool id="PGAP" name="PGAP" version="1.0">
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2 <description>Pan-Genome Analysis Pipeline </description>
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3 <requirements>
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10
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4 <requirement type="package" version="2.2.26">blast-legacy</requirement>
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5 <requirement type="package" version="7.480">mafft</requirement>
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6 <requirement type="package" version="14.137">mcl</requirement>
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7 <requirement type="package" version="3.697">phylip</requirement>
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8 <requirement type="package" version="1.7.2">perl-bioperl</requirement>
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10
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9 </requirements>
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10 <command detect_errors="aggressive"><![CDATA[
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11 #import re
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12
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13 ## Creates symlinks for each input file based on the Galaxy 'element_identifier'
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14 ## Used so that a human-readable name appears in the output table (instead of 'dataset_xyz.dat')
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15 #set $named_input_files = ''
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16 #for $input_file in $input_files
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17 ## Add single quotes around each input file identifier
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18 #set $_input_file = "'{}'".format($input_file.element_identifier)
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19 ln -s '${input_file}' ${_input_file} &&
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20 #set $named_input_files = $named_input_files + ',' + $_input_file
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21 #end for
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22
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23 perl ${__tool_directory__}/PGAP_wrapper2.pl -g $input_files -p $proteins -l $named_input_files -o $output >>$logfile 2>&1
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24 ]]></command>
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25
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26
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27
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28 <inputs>
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29 <param format="fasta" name="input_files" type="data" multiple="true" label="Coding genes FASTA files"/>
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30 <param format="fasta" name="proteins" type="data" multiple="true" label="Protein FASTA files"/>
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31 </inputs>
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32
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33 <outputs>
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34 <data format="txt" name="output" label="Pangenome presence absence matrix"/>
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35 <data format="txt" name="logfile" label="Logfile"/>
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36 </outputs>
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37
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38 </tool>
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