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1 <tool id="removechar" name="removeChar tool" version="1.0.0">
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2 <description>allows to remove positions (or columns) from a multi-Fasta alignment file in function of a given character</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 </requirements>-->
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7
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8 <command detect_errors="aggressive"><![CDATA[
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9
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10 #import re
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11 ## Creates symlinks for each input file based on the Galaxy 'element_identifier'
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12 ## Used so that a human-readable name appears in the output table (instead of 'dataset_xyz.dat')
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13 ## Add single quotes around each input file identifier
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14 #set $_input_file = "'{}'".format($input.element_identifier)
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15 ln -s '${input}' ${_input_file} &&
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16
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17
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18 perl '$__tool_directory__/removeChar.pl' $_input_file $char > "$output"
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19
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20
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21
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22 ]]></command>
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23 <!-- perl '$__tool_directory__/nucleScore.pl' $_input_file > "$output" -->
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24 <!-- ./nuclescore.sh ${named_input_files} > "$output" -->
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25
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26 <inputs>
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27 <param format="fasta" name="input" type="data" label="Multi-FASTA file: "/>
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1
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28 <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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29 </inputs>
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30
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31 <outputs>
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32 <data format="fasta" name="output" />
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33 </outputs>
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34
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35 <help><![CDATA[
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36 removeChar.pl is a Perl script allowing to remove positions (or columns) of an aligned multi-Fasta file in function of a given character (eg. N).
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37 The resulting multi-Fasta file corresponds to the same input multiFasta alignment file without the queried character.
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38
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39 This script belongs to the getSequenceInfo supplementary tools.
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40
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41 - GitHub: https://github.com/karubiotools/getSequenceInfo/tree/master/supplementary_tools
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42 ]]>
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43 </help>
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44
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45 </tool>
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