view renameSequences.xml @ 9:c2c69c6090f0 draft

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<tool id="rename_sequences" name="Rename sequences" version="1.0.0">
<description> Rename sequences using numerical counter, keep required prefix and pair information </description>
<command interpreter="python">
renameSequences2.py $input $paired index.tmp $prefix_length > $output
</command>

 <inputs>
  <param format="fasta" type="data" name="input" label="Choose your FASTA file" />
  <param name="prefix_length" type="integer" size="10" value="0" label="Prefix length" help="Enter the length of prefix to keep in sequences names" />
  <param name="paired" type="boolean" truevalue="true" falsevalue="false" checked="False" label="Sequences are paired-end reads in interlaced format" help=""/>
 </inputs>


 <outputs>
 	<data format="fasta" name="output" label="Renamed sequences from dataset ${input.hid}" />
 </outputs>

 <help>
**What is does**
 
Use this tool to rename your sequences with numerical counter while keeping sequence name prefex as part of the name. 
If paired-end reads are used, the last character in sequence name is used to distinguish pairs.  
 
</help>
</tool>