Mercurial > repos > petr-novak > re_utils
annotate renameSequences.xml @ 30:cab41d23e2a3 draft
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author | petr-novak |
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date | Thu, 03 Aug 2023 08:40:38 +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 <requirements> |
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6 <requirement type="package" version="3">python</requirement> |
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7 </requirements> |
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8 <required_files> |
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9 <include type="literal" path="renameSequences2.py"/> |
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10 </required_files> |
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11 <command> |
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12 python '$__tool_directory__'/renameSequences2.py $input $paired index.tmp |
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13 $prefix_length > $output |
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14 </command> |
3 | 15 |
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16 <inputs> |
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17 <param format="fasta" type="data" name="input" label="Choose your FASTA file"/> |
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18 <param name="prefix_length" type="integer" size="10" value="0" |
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19 label="Prefix length" |
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20 help="Enter the length of prefix to keep in sequences names"/> |
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21 <param name="paired" type="boolean" truevalue="true" falsevalue="false" |
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22 checked="False" label="Sequences are paired-end reads in interlaced format" |
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23 help=""/> |
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24 </inputs> |
3 | 25 |
26 | |
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27 <outputs> |
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28 <data format="fasta" name="output" |
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29 label="Renamed sequences from dataset ${input.hid}"/> |
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30 </outputs> |
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31 |
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32 <help> |
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33 **What is does** |
3 | 34 |
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35 Use this tool to rename your sequences with numerical counter while keeping |
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36 sequence name prefex as part of the name. |
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37 If paired-end reads are used, the last character in sequence name is used to |
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38 distinguish pairs. |
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39 |
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40 </help> |
3 | 41 </tool> |