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1 <tool id="mirureader" name="mirureader" version="1.0.0">
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2 <description> MIRUReader allows to perform in-silico MIRU-VNTR typing using long reads or assembled genome </description>
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4 <requirements>
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5 <requirement type="package" version="3.2.0">python3-openid</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 <!--<command>cp $input input.fasta; python3 $__tool_directory__/MIRUReader/MIRUReader.py -r input.fasta -p sample 1> $output 2>$logfile</command>-->
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12 <command detect_errors="aggressive"><![CDATA[
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13
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14 #import re
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15 ## Creates symlinks for each input file based on the Galaxy 'element_identifier'
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16 ## Used so that a human-readable name appears in the output table (instead of 'dataset_xyz.dat')
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17
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18 ## Add single quotes around each input file identifier
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19 #set $_input_file = "'{}'".format($input.element_identifier)
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20 #set $_input_file = $_input_file + '.fasta'
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21 ln -s '${input}' ${_input_file} &&
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22
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23 python3 $__tool_directory__/MIRUReader/MIRUReader.py -r $_input_file -p $_input_file > $output
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26
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27
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28 ]]></command>
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29
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30 <!-- for element in `echo $named_input_files`; do python3 MIRUReader.py -r $element -p $element;done > $output
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31 sudo python3 '$__tool_directory__/MIRUReader/MIRUReader.py' '-r' $named_input_files '-p' $named_input_files > $output -->
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32
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33 <inputs>
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34 <!--
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35 <param format="fasta" name="input_files" type="data" label="fasta files :" multiple="true" display="checkboxes"/>
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36 -->
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37 <param format="fasta" name="input" type="data" label="Fasta file"/>
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38 </inputs>
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39
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40 <outputs>
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41 <data format="tabular" name="output" label="MIRUReader output"/>
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42 <!--<data format="txt" name="logfile" label="LogFile"/>-->
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43 </outputs>
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44
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45 <help><![CDATA[
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46 MIRUReader allows to identify 24-locus MIRU-VNTR for Mycobacterium tuberculosis complex (MTBC) directly from long reads generated by Oxford Nanopore Technologies (ONT) and Pacific Biosciences (PacBio). It also work on assembled genome.
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47
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48 GitHub: https://github.com/phglab/MIRUReader.git
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49 ]]>
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50 </help>
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51
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52 <citations>
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53 <citation type="doi">10.1093/bioinformatics/btz771</citation>
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54 </citations>
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55 </tool>
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