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1 <tool id="rename_sequences" name="Rename sequences" version="1.0.0">
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2 <description> Rename sequences using numerical counter, keep required prefix and pair information </description>
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3 <command interpreter="python">
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4 renameSequences2.py $input $paired index.tmp $prefix_length > $output
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5 </command>
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6
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7 <inputs>
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8 <param format="fasta" type="data" name="input" label="Choose your FASTA file" />
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9 <param name="prefix_length" type="integer" size="10" value="0" label="Prefix length" help="Enter the length of prefix to keep in sequences names" />
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10 <param name="paired" type="boolean" truevalue="true" falsevalue="false" checked="False" label="Sequences are paired-end reads in interlaced format" help=""/>
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11 </inputs>
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12
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13
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14 <outputs>
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15 <data format="fasta" name="output" label="Renamed sequences from dataset ${input.hid}" />
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16 </outputs>
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17
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18 <help>
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19 **What is does**
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20
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21 Use this tool to rename your sequences with numerical counter while keeping sequence name prefex as part of the name.
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22 If paired-end reads are used, the last character in sequence name is used to distinguish pairs.
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23
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24 </help>
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25 </tool>
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