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annotate renameSequences.xml @ 29:53dc6aef5441 draft

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author petr-novak
date Thu, 03 Aug 2023 07:32:40 +0000
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1 <tool id="rename_sequences" name="Rename sequences" version="1.0.0.3">
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2 <description>Rename sequences using numerical counter, keep required prefix and pair
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3 information
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4 </description>
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5 <required_files>
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6 <include type="literal" path="renameSequences2.py"/>
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7 </required_files>
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8 <command>
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9 python '$__tool_directory__'/renameSequences2.py $input $paired index.tmp
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10 $prefix_length > $output
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11 </command>
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13 <inputs>
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14 <param format="fasta" type="data" name="input" label="Choose your FASTA file"/>
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15 <param name="prefix_length" type="integer" size="10" value="0"
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16 label="Prefix length"
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17 help="Enter the length of prefix to keep in sequences names"/>
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18 <param name="paired" type="boolean" truevalue="true" falsevalue="false"
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19 checked="False" label="Sequences are paired-end reads in interlaced format"
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20 help=""/>
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21 </inputs>
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24 <outputs>
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25 <data format="fasta" name="output"
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26 label="Renamed sequences from dataset ${input.hid}"/>
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27 </outputs>
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28
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29 <help>
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30 **What is does**
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32 Use this tool to rename your sequences with numerical counter while keeping
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33 sequence name prefex as part of the name.
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34 If paired-end reads are used, the last character in sequence name is used to
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35 distinguish pairs.
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36
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37 </help>
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38 </tool>