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comparison renameSequences.xml @ 22:58807b35777a draft

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planemo upload commit 20bdf879b52796d3fb251a20807191ff02084d3c-dirty
author petr-novak
date Wed, 02 Aug 2023 11:31:12 +0000
parents c2c69c6090f0
children cab41d23e2a3
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21:f4ed6a65a2ff 22:58807b35777a
1 <tool id="rename_sequences" name="Rename sequences" version="1.0.0"> 1 <tool id="rename_sequences" name="Rename sequences" version="1.0.0.3">
2 <description> Rename sequences using numerical counter, keep required prefix and pair information </description> 2 <description>Rename sequences using numerical counter, keep required prefix and pair
3 <command interpreter="python"> 3 information
4 renameSequences2.py $input $paired index.tmp $prefix_length > $output 4 </description>
5 </command> 5 <required_files>
6 <include type="literal" path="renameSequences2.py"/>
7 </required_files>
8 <command>
9 python '$__tool_directory__'/renameSequences2.py $input $paired index.tmp
10 $prefix_length > $output
11 </command>
6 12
7 <inputs> 13 <inputs>
8 <param format="fasta" type="data" name="input" label="Choose your FASTA file" /> 14 <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 the length of prefix to keep in sequences names" /> 15 <param name="prefix_length" type="integer" size="10" value="0"
10 <param name="paired" type="boolean" truevalue="true" falsevalue="false" checked="False" label="Sequences are paired-end reads in interlaced format" help=""/> 16 label="Prefix length"
11 </inputs> 17 help="Enter the length of prefix to keep in sequences names"/>
18 <param name="paired" type="boolean" truevalue="true" falsevalue="false"
19 checked="False" label="Sequences are paired-end reads in interlaced format"
20 help=""/>
21 </inputs>
12 22
13 23
14 <outputs> 24 <outputs>
15 <data format="fasta" name="output" label="Renamed sequences from dataset ${input.hid}" /> 25 <data format="fasta" name="output"
16 </outputs> 26 label="Renamed sequences from dataset ${input.hid}"/>
27 </outputs>
17 28
18 <help> 29 <help>
19 **What is does** 30 **What is does**
20 31
21 Use this tool to rename your sequences with numerical counter while keeping sequence name prefex as part of the name. 32 Use this tool to rename your sequences with numerical counter while keeping
22 If paired-end reads are used, the last character in sequence name is used to distinguish pairs. 33 sequence name prefex as part of the name.
23 34 If paired-end reads are used, the last character in sequence name is used to
24 </help> 35 distinguish pairs.
36
37 </help>
25 </tool> 38 </tool>