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1 <tool id="catchsequence" name="Catch Sequence" version="0.1.0">
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2 <description>Catch sequence for BioloMICS import</description>
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3 <requirements>
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4 <requirement type="package" version="1.0.1">abricate</requirement>
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5 <requirement type="package" version="2.19.0">mlst</requirement>
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6 <!--<requirement type="package" version="6.6.0">emboss</requirement>
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7 <requirement type="package" version="1.3.2">pandas</requirement>-->
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8 </requirements>
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9
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10
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11 <command detect_errors="aggressive"><![CDATA[
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12
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13 #import re
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14 ## Creates symlinks for each input file based on the Galaxy 'element_identifier'
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15 ## Used so that a human-readable name appears in the output table (instead of 'dataset_xyz.dat')
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16 #set $named_input_files = ''
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17 #for $input_file in $input_files
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18 ## Add single quotes around each input file identifier
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19 #set $_input_file = "'{}'".format($input_file.element_identifier)
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20 ln -s '${input_file}' ${_input_file} &&
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21 #set $named_input_files = $named_input_files + ' ' + $_input_file
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22 #end for
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23
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24
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25 perl '$__tool_directory__/catchsequence.pl' $named_input_files > "$output"
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26
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27
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28
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29 ]]></command>
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30 <!-- perl '$__tool_directory__/nucleScore.pl' $_input_file > "$output" -->
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31 <!-- ./nuclescore.sh ${named_input_files} > "$output" -->
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32
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33 <inputs>
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34 <param type="data" name="input_files" format="fasta" multiple="true" label="Genome fasta files"/>
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35 <!-- <param format="fasta" name="input_files" type="data" label="Genome fasta file : " multiple="true" display="checkboxes"/> -->
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36 </inputs>
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37
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38 <outputs>
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39 <data format="tabular" name="output" />
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40 </outputs>
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41
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42 <help>
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43 No documentation
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44 </help>
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45
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46 </tool>
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