|
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>
|
