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