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1 <tool id="countdifferences" name="countDifferences tool" version="1.0.0">
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2 <description>allows to compare sequences from a multi-Fasta alignment file by calculating differences (in bp) and percentage identity</description>
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3
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4 <requirements>
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5 <requirement type="package" version="1.7.2">perl-bioperl</requirement>
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6 <!--<requirement type="package" version="3.27">perl-string-approx</requirement>-->
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7 </requirements>
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8
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9 <command detect_errors="aggressive"><![CDATA[
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10
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11 #import re
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12 ## Creates symlinks for each input file based on the Galaxy 'element_identifier'
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13 ## Used so that a human-readable name appears in the output table (instead of 'dataset_xyz.dat')
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14 ## Add single quotes around each input file identifier
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15 #set $_input_file = "'{}'".format($input.element_identifier)
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16 ln -s '${input}' ${_input_file} &&
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17
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18
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19 perl '$__tool_directory__/countDifferences.pl' $_input_file $output1 $output2
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20
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21
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22
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23 ]]></command>
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24 <!-- perl '$__tool_directory__/nucleScore.pl' $_input_file > "$output" -->
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25 <!-- ./nuclescore.sh ${named_input_files} > "$output" -->
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26
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27 <inputs>
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28 <param format="fasta" name="input" type="data" label="Multi-FASTA file: "/>
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29 <!--<param name="char" type="text" area="false" value="N" label="Character to be removed from Multi-FASTA file:" help="Users can directly write the character to be removed without quotes" />-->
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30 </inputs>
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31
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32 <outputs>
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33 <data format="tabular" name="output1" label="bp_differences.tsv "/>
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34 <data format="tabular" name="output2" label="percentage_identity.tsv "/>
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35 </outputs>
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36
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37 <help><![CDATA[
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38 countDifferences.pl is a Perl script allowing to calculate differences (changes in bp) and sequences percentage identity from an aligned multi-Fasta file.
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39
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40 Two resulting tables are produced:
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41 (i) a table containing a matrix with bp differences for each sequence;
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42 (ii) a table containing a matrix with percentage identity for each sequence
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43
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44 This script belongs to the getSequenceInfo supplementary tools.
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45
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46 - GitHub: https://github.com/karubiotools/getSequenceInfo/tree/master/supplementary_tools
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47 ]]>
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48 </help>
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49
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50 </tool>
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