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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 assembled genomes (FASTA format)</description>
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3
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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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11
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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
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21
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22 ln -s '${input}' "${_input_file}" &&
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23 cp "$_input_file" input.fasta &&
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24 python3 $__tool_directory__/MIRUReader/MIRUReader.py -r input.fasta -p $_input_file > $output
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25
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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
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31 <!-- #set $var = ${_input_file//[^[:alnum:]]/}
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32 #set var = ${f//:()/}
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33 #set $_input_file = $_input_file + '.fasta'
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34 $_input_file="${_input_file// /_}" && -->
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35
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36 <!-- for element in `echo $named_input_files`; do python3 MIRUReader.py -r $element -p $element;done > $output
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37 sudo python3 '$__tool_directory__/MIRUReader/MIRUReader.py' '-r' $named_input_files '-p' $named_input_files > $output -->
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38
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39 <inputs>
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40 <!--
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41 <param format="fasta" name="input_files" type="data" label="fasta files :" multiple="true" display="checkboxes"/>
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42 -->
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43 <param format="fasta" name="input" type="data" label="FASTA file"/>
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44 </inputs>
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45
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46 <outputs>
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47 <data format="tabular" name="output" label="MIRUReader output"/>
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48 <!--<data format="txt" name="logfile" label="LogFile"/>-->
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49 </outputs>
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50
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51 <help><![CDATA[
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52 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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53
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54 GitHub: https://github.com/phglab/MIRUReader.git
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55 ]]>
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56 </help>
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57
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58 <citations>
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59 <citation type="doi">10.1093/bioinformatics/btz771</citation>
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60 </citations>
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61 </tool>
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