Mercurial > repos > galaxyp > filter_by_fasta_ids
comparison filter_by_fasta_ids.xml @ 1:8d15aebf55fd draft
planemo upload commit 88309fbfadbafe82f2d8fb7b96468799f2421e30
author | galaxyp |
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date | Tue, 24 May 2016 13:05:22 -0400 |
parents | |
children | 1bd985f14938 |
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0:463ebeccb854 | 1:8d15aebf55fd |
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1 <tool id="filter_by_fasta_ids" version="1.0" name="Filter by FASTA IDs"> | |
2 <description>Extract sequences from a FASTA file based on a list of IDs</description> | |
3 <command> | |
4 <![CDATA[ | |
5 python $__tool_directory__/filter_by_fasta_ids.py | |
6 $dedup | |
7 '$identifiers' | |
8 '$input' | |
9 '$output' | |
10 ]]> | |
11 </command> | |
12 <inputs> | |
13 <param format="fasta" name="input" type="data" label="FASTA sequences"/> | |
14 <param format="txt" name="identifiers" type="data" label="List of IDs to extract sequences for"/> | |
15 <param name="dedup" type="boolean" truevalue="--dedup" falsevalue="" checked="true" label="Remove duplicate sequences" /> | |
16 </inputs> | |
17 <outputs> | |
18 <data format="fasta" name="output" label="FASTA sequences for ${identifiers.name}"/> | |
19 </outputs> | |
20 <tests> | |
21 <test> | |
22 <param name="input" ftype="fasta" value="input.fasta" /> | |
23 <param name="identifiers" ftype="txt" value="ids.txt" /> | |
24 <output name="output" file="output_dedup.fasta" /> | |
25 </test> | |
26 <test> | |
27 <param name="input" ftype="fasta" value="input.fasta" /> | |
28 <param name="identifiers" ftype="txt" value="ids.txt" /> | |
29 <param name="dedup" value="False" /> | |
30 <output name="output" file="output_not_dedup.fasta" /> | |
31 </test> | |
32 </tests> | |
33 <help> | |
34 <![CDATA[ | |
35 **What it does** | |
36 | |
37 Extract sequences from a FASTA file based on a list of IDs. | |
38 ]]> | |
39 </help> | |
40 </tool> |