view renameSequences.xml @ 3:e320ef2d105a 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 length of prefix to keep in sequences names" />
  <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"/>
 </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 sequences are used, last character in sequence name is used to distinguish pairs.  
 
</help>
</tool>