Mercurial > repos > galaxyp > filter_by_fasta_ids
diff filter_by_fasta_ids.xml @ 1:8d15aebf55fd draft
planemo upload commit 88309fbfadbafe82f2d8fb7b96468799f2421e30
author | galaxyp |
---|---|
date | Tue, 24 May 2016 13:05:22 -0400 |
parents | |
children | 1bd985f14938 |
line wrap: on
line diff
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/filter_by_fasta_ids.xml Tue May 24 13:05:22 2016 -0400 @@ -0,0 +1,40 @@ +<tool id="filter_by_fasta_ids" version="1.0" name="Filter by FASTA IDs"> + <description>Extract sequences from a FASTA file based on a list of IDs</description> + <command> +<![CDATA[ + python $__tool_directory__/filter_by_fasta_ids.py + $dedup + '$identifiers' + '$input' + '$output' +]]> + </command> + <inputs> + <param format="fasta" name="input" type="data" label="FASTA sequences"/> + <param format="txt" name="identifiers" type="data" label="List of IDs to extract sequences for"/> + <param name="dedup" type="boolean" truevalue="--dedup" falsevalue="" checked="true" label="Remove duplicate sequences" /> + </inputs> + <outputs> + <data format="fasta" name="output" label="FASTA sequences for ${identifiers.name}"/> + </outputs> + <tests> + <test> + <param name="input" ftype="fasta" value="input.fasta" /> + <param name="identifiers" ftype="txt" value="ids.txt" /> + <output name="output" file="output_dedup.fasta" /> + </test> + <test> + <param name="input" ftype="fasta" value="input.fasta" /> + <param name="identifiers" ftype="txt" value="ids.txt" /> + <param name="dedup" value="False" /> + <output name="output" file="output_not_dedup.fasta" /> + </test> + </tests> + <help> +<![CDATA[ +**What it does** + +Extract sequences from a FASTA file based on a list of IDs. +]]> + </help> +</tool>