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1 <tool id="mirutool" name="mirureader" version="6.6.0">
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2 <description> MIRUReader.... </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 name 1> $output 2>$logfile</command>
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11 <!--
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12 <command interpreter="bash" 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 #set $named_input_files = ''
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18 #for $input_file in $input_files
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19 ## Add single quotes around each input file identifier
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20 #set $_input_file = "'{}'".format($input_file.element_identifier)
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21 ln -s '${input_file}' ${_input_file} &&
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22 #set $named_input_files = $named_input_files + ' ' + $_input_file
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23 #end for
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24
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25 #for $element in $named_input_files
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26 sudo python3 '$__tool_directory__/MIRUReader/MIRUReader.py' '-r' $element '-p' $element > $output
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27 #end for
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28
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29
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30
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31 ]]></command>
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32 -->
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33
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34 <!-- for element in `echo $named_input_files`; do python3 MIRUReader.py -r $element -p $element;done > $output
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35 sudo python3 '$__tool_directory__/MIRUReader/MIRUReader.py' '-r' $named_input_files '-p' $named_input_files > $output -->
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36
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37 <inputs>
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38 <!--
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39 <param format="fasta" name="input_files" type="data" label="fasta files :" multiple="true" display="checkboxes"/>
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40 -->
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41 <param format="fasta" name="input" type="data" label="Fasta file"/>
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42 </inputs>
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43
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44 <outputs>
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45 <data format="tabular" name="output" label="MIRUreader output"/>
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46 <data format="txt" name="logfile" label="Logfile"/>
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47 </outputs>
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48
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49 <help>
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50 -Git:https://github.com/phglab/MIRUReader.git
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51 </help>
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52
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53 <citations>
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54 <citation type="doi">10.1093/bioinformatics/btz771</citation>
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55 </citations>
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56 </tool>
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